CA1311428C

CA1311428C - Deoxyribonucleoside phosphoramidites in which an aliphatic amino group is attached to the sugar ring and their use for the preparation of oligonucleotides containing aliphatic amino groups, fluorescent dyes, and other detectable moieties

Info

Publication number: CA1311428C
Application number: CA000540324A
Authority: CA
Inventors: Steven Fung; Lloyd M. Smith; Robert J. Kaiser, Jr.
Original assignee: California Institute of Technology CalTech
Current assignee: California Institute of Technology CalTech
Priority date: 1986-06-24
Filing date: 1987-06-23
Publication date: 1992-12-15
Anticipated expiration: 2009-12-15
Also published as: US4849513A; DE3750080D1; EP0270651B1; EP0270651A4; JPH07300494A; EP0270651A1; WO1988000201A1; JPH01501149A; DE3750080T2

Abstract

ABSTRACT OF THE DISCLOSURE

The invention consists of compounds and methods for the synthesis of oligonucleotides which contain one or more free aliphatic amino groups attached to the sugar moieties of the nucleoside subunits. The synthetic method is versatile, permitting amino groups to be selectively placed at any position on oligonuc-leotides of any composition or length which is attain-able by current DNA synthetic methods. Fluorescent dyes or other detectable moieties may be covalently attached to the amino groups to yield the corresponding modified oligonucleotide.

Description

:~ 3 1 ~ 8 BACKGROUND OF THE INVENTION

An oligonucleotide is a short polymer consisting of a linear sequence of four nucleotides in a defined order. The nucleotide subunits are joined by phospho-diester linkages joining the 3'-hydroxyl moiety oE
one nucleotide to the 5'-hydroxyl moiety of the next nucleotide. An example of an oligonucleotide is S'>
ApCpGpTpApTpGpGpC<3'. The letters A, C, G, and T
refer to the nature of the purine or pyrimidine base coupled at the l'-position of deoxyribose: A, adenine;
C, cytosine; G, guanine; and T, thymine. "p" represents the phosphodiester bond. The chemical s-tructure of a section of an oligonucleotide is shown in Figure 1.
-o--P=O
o H I 5 r ~ H H A' H ~,~ H
O H

o __ ~ H H /
H ~/ H
O H
-O--P=O

H2C~,O~rse ~H
O H

Figure 1 Structure of part of a DNA chain.
This figure is taken from the text book Biochemistry~
by Lubert Stryer, First Edition 1975~ W. H. Freeman & Co., page 558.

13~2~

Synthetic oligonucleotides are powerful tools in modern molecular biology and recombinant DNA work.
There are numerous applications for these molecules, including a) as probes for the isolation of specific genes based on the protein sequence of the gene product, b) to direct the ln vitro mutagenesis of a desired gene, c) as primers for DNA synthesis on a sin~le-stranded template, d) as steps in the total synthesis of genes, and many more, reviewed in Wm. R. Bahl et al, Prog. Nucl. Acid Res. Mol. Biol. 21, 101, (1978).
A very considerable amount of effort has therefore been devoted to the development of efEicient chemical methods for the synthesis of such oligonucleotides.
A brief review of these methods as they have developed to the present is found in Crockett, G. C., Aldrichimica Acta 16(3), 47-55 (1983), and "Oligonucleotide Syn-thesis: A Practical Approach", ed. Gait, M.J., IRL
Press, Oxford, England (1984). The best methodology currently available utilizes the phosphoramidite deri-vatives of the nucleosides in combination with a solid phase synthetic procedure, Matteucci, M.D. and Caru-thers, M~H~ ~ Am Chem. Soc. 103, 3185, (1981);
and Beaucage, S.L., and Caruthers, M~Ho ~ Tet. Lett.
22(20), 1858-1862 (1981). In this chemistry, the 3'-nucleoside of the sequence to be synthesized is attached to a solid suppor~ via a base-labile linker arm. Subsequent nucleosides are attached sequentially to the previous nucleoside to generate a linear polymer of defined sequence extending off of the solid support.

~ 3~ ~28 The general structure of a deoxyribonucleoside phos-phoramidite is shown in Figure 2:

DMTr--OH2Ck~H

O H

/ \
R' O NR'2 Bn = nucleoside base DMTr = di-p-anisylphenylmethyl (also known as dimethoxytrityl) Rl = a hydrocarbyl radical containing up to lU carbons NR2 = a secondary group Figure 2 ~= .j ~3~1~L28 and the chemical steps used in each cycle of oligo-nucleotide synthesis are shown in Figure 3:

D b1 T~
Olldl~ ~nd C~p 81 D~trl~yl~
D M T 1 0 ~ ~ ~~

CHP O
M T ~ O~,~

cO~OI~ s~, ~ Ico~pl~
¦ D~rllyl~ DMT~O~
DMT~O p N~ HO~I CH10 ~ 'd~

P--N~_ C) / CH,C! O
CH,O
/ OSldl~ ~nd C~p OMT~O~
~ p~ ,~
CB~ Reactior. cyclo 8"81,~: A~C~G o~ T c /~O ~y ~) : D~ d S~ppo~ ~
Solid phase oligodeoxyribonucleotide synthesis by ~he phosphite-triester method.

E'igure 3 (This figure is taken from "Oligonucleotide Synthesis:
a Practical Approach", ed. Gait, M. J., IRL Press (1984), p. 37) ~3~2~

Oligonucleotldes o length up to 40 bases may be made on a routine basis in this manner, and molecules as long as 106 bases have been made. Machines that employ this chemistry are now commercially available.
There are many reasons to want a method for cova-lently attaching other chemical species to synthetic oligonucleotides. Fluorescent dyes attached to the oligonucleotides permit one to eliminate radioisotopes from the research, diagnostic, and clinical procedures in which they are used, and improve shelf-life and availability. The development of appropriate -techniques and instrumentation for the detection and use of fluores-cent-labeled oligonucleotides allows the automation of other currently laborious laboratory and clinical techniques. The attachment of DNA cleavage chernicals such as those disclosed by Schultz et al, J. Am._Chem.
Soc. 1~4, 6861 (1982); and Hertzberg, R.P., and Dervan, P.B., J. Am. Chem. Soc. 104, 313 (1982) permits the construction of synthetic restriction enzymes, whose specificity is directed by the oligonucleotide sequence.
There are several reports in the literature o-E
the derivitization of DNA. A modified nucleoside triphosphate has been developed wherein a biotin group is conjugated to an aliphatic amino group at the 5-position of uracil, Langer et al., Proc. Nat. Acad. Sci. U.S.A.
78, 6633-6637 (1981). This nucleotide derlvative is effectively incorporated into double stranded DNA
in a process referred to as "nick translation." Once in DNA it may be bound by anti-biotin antibody which can then be used for detection by fluorescence or enzymatic methods~ The DNA which has had biotin-con-jugated nucleosides incorporated therein by the method of Langer et al is fragmented into smaller single and double stranded pieces which are heterogeneous with respect to the sequence of nucleoside subunits and variable in molecular weight. Draper and Gold, 2~

Biochemistry 19, 1774-1781 (1980), reported the intro-duction oE aliphatic amino groups by a bisulfite ca-talyzed transamination reaction, and their subsequent reaction with a fluorescent tag. In Draper and Gold the amino group is attached directly to a pyrimidine base. The amino group so positioned inhibits hydrogen bonding and for this reason, these materials are not useful in hybridization and the like. Also, this method does not permit amino groups to be inserted selectively at a desired position. Chu et al, Nucleic Acids Res. 11(18), 6513-6529 (1983), have reported a method for attaching an amine to the terminal 5'-phos-phate of oligonucleotides or nucleic acids. This method involves a number of sequential reaction and purification steps which are laborious to perform and difficult to scale up. It also is restricted to the introduction of a single amino group at the 5'-terminus of the oligonucleotide. Takeda and Ikeda, _u ~ , 101-104 (1984) have reported the synthesis and use of phosphotriester derivatives of putrescinyl thymidine for the preparation of amino-derivatized oligonucleotides. These materials differ from those reported herein in that the amino CQntaining moiety is attached to the base moiety and not to the sugar moiety of the oligonucleotides, and also in that the DNA synthetic chemistry used was phosphotriester and not phosphoramidite.
The present invention presents a general method for the introduction of one or more free alipha~ic amino groups into synthetic oligonucleotides. These groups may be selectively inserted at any desired position in the oligonucleotide. They are readily ~3~ 2~

and specifically reacted with a variety of amino re-active functionalities, and thereby permit the covalent attachment of a wide variety of chemical species in a position specific manner. This is illustrated by the preparation of a number of fluorescent oligonuc-leotide derivatives. The materials prepared in this fashion are effective in DNA hybridization methods, as illustrated by their use as primers in DNA sequence analysis, and also by a study of their melting behaviour in DNA duplex formation.
According to the present invention, aliphatic amino groups are introduced into an oligonucleotide by first synthesizing a 3'-0-phosphoramidite derivative of a nucleoside analogue containing a protected ali-phatic amino group attached to the sugar moiety of the nucleoside. This phosphoramidite is then reacted with the oligonucleotide being synthesized on a solid support. If the amino protecting group is base-labile, the process of oligonucleotide cleavage from the solid phase and deprotection of the base moieties and ali-phatic amino group yields the amino-derivatized oli-gonucleotide. If the amino protecting group is acid-labile, it may be removed by treatment with anhydrous or aqueous acid prior to cleavage of the oligonucleotide from the support and deprotection of the base moieties, or it may be retained during cleavage and deprotection to simplify and improve the chromatographic purification of the oligonucleotide, and then removed subsequently by treatment with aqueous acid, yielding the amino-deri-vatized oligonucleotide in either case.
More specifically, the present invention concerns modified deoxynucleoside phosphoramidites in which an aliphatic amino group, which has been protected as specified herein, is attached to the sugar moiety 1311~28 of the nucleoside. The chemical structure of a typical nucleoside is shown in Figure 4.

4' H\~/ H
R' R" Figure 4 It is characterized by a heterocyclic pyrimidine or purlne base tB) linked by a carbon-nitrogen bond to the furanose (sugar) ring of ribose (R = R' = R'' = OH) or deoxyribose (R ~ R' = OH; R'' - H). The numbering of the sugar carbon atoms is 1' to 5' as indicated in the figure; thus, the base is connected to C-l' of the sugar. An alipha-tic amino group may be attached in principle to any of the five ring car~
bons. It also comprises the respective phosphoramidite derivatives which are synthesized by reacting an appro-priate phosphine with the free 3'-hydroxyl group of the suitably protected amino nucleosides.

~ 3 ~ 2 P~

SUMMARY OF THE INVENTION

srlefly~ our invention includes novel protected amino nucleosides having the formula:
B

R5~

Figure 5 R4 R2 wherein B is a common nucleoside purine or pyrimidine base, such as adenine, guanine, thymine, cytosine, uracil, or hypoxanthine, or their protected derivatives, especially those currently used in DNA chemical syn-thesis, namely N6~Benzoyladenine, N2-isobutyrylguanine, N4- benzoylcytosine, N6-di-n-butylformamidinyladenine, N6-(N-methyl-2-pyrrolidineamidinyl)-adenine, N6-succinyladenine, N6-phthaloyladenine, N6-dimethylaceta-midinyladenine, or N2-di-n-butylformamidinylguanine;
or an uncommon purine or pyrimidine base, such as purine, isocytosine, or xanthine (3,7-dihydro-lH-purine-2,6-dione), or their protected derivatives; or a substituted purine or pyrimidine base. Such substituents include, but are not limited to cyano, halo, haloalkyl, carboxy, formyl, hydroxy, alkoxy, aryl, azido, mercapto, nitro, carboxy esters, and carboxamides. Such bases include, but are not limited to, 6 chloropurine, 6-chloro-2~
fluoropurine, 2,6-diaminopurine, 2-fluoro-N6-hydroxy-adenine, 2,6-dihydroxyaminopurine, 8-bromoadenine, 2-chloroadenine, 8-azidoadenine, 8-mercaptoadenine, 8-aminoadenine, 6-thioguanine, 2,6-dichloropurine, N,N-dimethyl-6-aminopurine, N6-benzyladenine, 1,3-di-~ 3~2~

methylxanthine, 2-amino-6,8-dihydroxypurine, 6-methoxy-purine, 6-mercaptopurine, 6-(2-hydroxyethyl)-amino-purine, N6-(2-isopentyl)-adenine, N6-furfuryladenine (kinetin), 5-bromomethyluracil, 5-dibromomethyluracil, 5-hydroxy- methyluracil, 5-formyluracil, 5-fluorouracil, 5-bromoura- cil, 6-methyl-2-thiouracil, 5-hydroxymethyl-6-methyluracil, 5-hydroxyuracil (isobarbituric acid), 5-methoxyuracil, 5-methylcytosine, 5-trifluoromethyluracil, 5-nitrouracil, 5-aminouracil, 2-thiocytosine, 2-amino-4, 6-dihydroxypyrimdine, 4-amino-2,6-dihydroxypyrimidine, 2-amino-4-hydroxy-6- methylpyrimidine, or 4-amino-6-hy-droxy-2-mercaptopyrimidine, or their protected derivatives.
B may also be a nucleoside base analog; such analogs are molecules that mimic the normal purine or pyrimidine bases in that their structures (the kinds of atoms and their arrangement) are similar to the normal bases, but may either possess additional or lack certain of the functional properties of the normal bases; such base analogues include, but are not limited to, imidazole and its 2-,4-, and/or 5-subs-tituted derivatives (substituents are as defined above), indole and i.ts 2-,3-,4-,5-,6-, and/or 7-substituted derivatives, benzimidazole and its 2-,4-,5-,6-, and/or 7-substituted derivatives, indazole and its 3-,~-,5-,5-, and/or 7-substituted derivatives, pyrazole and its 3-,4-, and/or 5-substituted derivatives, triazole and its 4- and/or 5-substituted derivatives, tetrazole and its 5-substituted derivatives, benzotriazole and its 4-,5-,6-, and/or 7-substituted derivatives, 8-azaa-denine and its substituted derivatives, 8-azaguanine and its substituted derivatives, 6-azathymine and its substituted derivatives, 6-azauracil and its subs-tituted derivatives, 5-azacytosine and its substituted derivatives, 8-azahypoxanthine and its substituted derivatives, pyrazolopyrimidine and its substituted derivatives, 3-deazauracil, orotic acid (2,6-dioxo-1, :~3~2~

2,3,6-tetrahydro- 4-pyrimidine carboxylic acid), barbi-turic acid, uric acid, ethenoadenine, and allopurinol (4-hydroxy-pyrazolo ~3,4-d]pyrimidine), or their pro-tect.ed derivatives.
B can also be a "C-nucleosidel', in which the normal C-N bond between the base and C-l' of the sugar is replaced by a C-C bond; such bases include, but are not limited to, uracil (in the C-nucleoside pseudo-uridine), l-methyluracil, 1,3-dimethyluracil, 5(4)-carbo-methoxy-1,2,3- triazole, 5(4)-carboxamido-1,2,3-tria-æole, 3(5)-carboxy- methylpyrazole, 3(5)-carbomethoxy-pyrazole, 5-carboethoxy-1- methylpyrazole, maleimide (in the C-nucleoside showdomycin), and 3(4)-carboxa-mido-4(3)-hydroxypyrazole (in the C-nucleoside pyra-zomycin), or their protected derivatives.
In Figure 5, Rl, R2, R3, R4 and Rs (sometimes collectively referred to as Rn) are defined as follows:
R3 = H, R4 = OH, and Rl, R2 and Rs are either H, OR, or NHR', wherein R and R' are appropriate protecting groups; R is generally a lower alkyl or aryl ether, such as methyl, t-butyl, benzyl, o-nitrobenzyl, p-nitro-benzyl, o-nitrophenyl, or triphenylmethyl, or a lower alkyl or aryl ester, such as acetyl, benzoyl, or p-nitro-benzoyl, or an alkyl acetal, such as tetrahydropyranyl, or a silyl ether, such trimethylsilyl or t~butyl-dime-thylsilyl, or a sulfonic acid ester, such as p-tolue-nesulfonyl or methanesulfonyl; R' is any common, stand-ard nitrogen protecting group, such as those commonly used in peptide synthesis (R. Geiger and W. Konig, in "The Peptides: Analysis, Synthesis, Biology", E. Gross and J. Meienhofer, eds., v. 3, Academic Press, New York (1981), pp. 1-99); this includes, but is not limited to, acid-labile protecting groups such as formyl, t-butyloxycarbonyl, N-benzyloxycarbonyl-6-aminohexanoyl, 2-chlorobenzyloxycarbonyl, 4-chloro-benzyloxycarbonyl, 2-4-dichlorobenzyloxycarbonyl, ~3~142~
- 13 - 68299-9~

furfuryloxycarbonyl, t-amyloxycarbonyl, adamantyloxy-carbonyl, 2-phenylpropyl t2)oxycarbonyl, 2-(4-biphenyl)-propyl(2)-oxycarbonyl, triphenylmethyl, p-anisyldiphenylmethyl, dl-p-anisylphenylmethyl, 2-nitrophenylsulfenyl, or diphenylphosphinyl;
base labile protecting groups such as trifluoroacetyl-glycyl, 4-toluene-sulfonylethyl-oxycarbonyl, methylsulfonylethyl-oxycarbonyl, and 2-cyano-t-butyloxycarbonyl; and o-thers, such as chloroacetyl, aceto-acetyl, 2-nitro-benzoyl, dithiasuccinoyl, maleoyl, isonicotinyl, 2-bromoethyloxy-carbonyl, and 2,2,2-tri-chloroethyloxycarbonyl, with the proviso that when Rl or R2 is NHR', the R' is any of the foregoing groups, or trifluoroacetyl or 9-fluoroenylmeth~loxy-carbonyl.
At most one of Rl, R2, and R5 may be NHR', and only R4 may be OH.
The "R" protecting groups referred to hereinabove, when containing carbon atoms, can contain from 1 to about 25 carbon atoms.
Accordingly, the invention herein comprlses novel protected amino nucleoside of the formula described in figure 5 wherein B is selected from the group consisting of a nucleoside base, a nucleoside base analog, or their protected derivatives;
Rl, R2, R3, R4 and R5 are defined as follows: R3 = H, R4 = OH, and Rl, R2 and R5 are either H, OR, or NHR', with the proviso that at most only one of Rl, R2 or R5 must be NHR', wherein R
is a monovalent organic group containing up to 25 carbon atoms, R' is a nitrogen protecting group which is acid labile~ or base labile protecting group selected from the group consisting of trifluoroacetylglycyll 4-toluene-sulfonylethyl-oxycarbonyl, ,. ~

~31~2~

13a 6~299-92 methylsulfonylethyl-oxycarbonyl, 2-cyano-t-butyl oxycarbonyl;
chloracetyl, aceto-acetyl, 2-nitro-benzoyl, dithiasuccinoyl, maleoyl, isonicotinyl, 2-bromoethyloxy-carbonyl, and 2,2,2-trichloroethyloxycarbonyl, with the proviso that when Rl or R2 is NHR', then R' is any of the foregoing groups, or trifluoroacetyl or 9-fluoroenylmethyloxy-carbonyl.

CASES
l) If Rl = NHR', then R2 = H; R5 may be either OR or H; the molecule in this case is termed a protected 2'-amino-2'-deoxyarabinonucleoside.
2) If R2 = NHR', then Rl = H; R5 may either be OR or H; the molecule in this case is termed a protected 2'-amino-2'-deoxyribonucleoside.
3) If R5, = NHR', then either Rl or R2 may be OR, with the other being H, or both may be H; if Rl is OR, the molecule is -termed a protected 5'-amino-arabinonucieoside; if R2 is OR, the molecule is termed a protected 5'-amino-ribonucleoside; iE both R
and R2 are H, the molecule is termed a protected 5'-amino-2'-deoxyribonucleoslde.
The invention further includes novel phosphora-1 3 ~

midites having the formula:

R5t~ ,~0~¦

0 R~

Figure 6 / \
R 7 0 N (P~

wherein B, Rl, R2 and Rs are as defined above, R6 = lower alkyl, preferably lower alkyl such as methyl or isopropyl, or heterocyclic, such as mor-pholino, pyrrolidino, or 2,2,6,6-tetramethylpyrrolidino, R7 = methyl, beta-cyanoethyl ? p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl.
Once again, the "R" groups referred to hereinabove, when containing carbon atoms, can contain from 1 -to about 25 carbon atoms.
It must be noted that the moiety symbolized by "B" in Figure 5 must also be appropriately protected prior to synthesis of the phosphoramidite symbolized by Figure 6, in order to render the phosphoramidite compatible with the DNA chain assembly chemistry.
Such protection is thoroughly discussed in Gait, "Oligo-nucleotide Synthesis: A Practical Approach", and generally involves acylation or amidination of the exocyclic amino groups of "B"; such acyl groups include, but are not limited to, acetyl, benzoyl, isobutyryl, succinyl, phthaloyl, or p-anisoyl; such amidine groups include, but are not limited to dimethylformamidine, di-n-butylformamidine, or dimethylacetamidine; if "B" is substituted with other reactive groups~ such 1 3 ~
~ 15 - 6~2g9-92 as carboxyl, hydroxyl, or mercapto, these are approprlately protected as well.
In another aspect, this invention comprehen~s the synthesis of oligonucleotides on a solid phase support, wherein the oligonucleotide is reacted with the protected amino-derivatized nucleoside phosphoramidite of Figure 6.
In addition, this invention includes -the novel oligonucleotides having inserted therein at least one amino-derivatized nucleoside via phosphoramidite precursor of Figure 6.
The present in~ention still further comprises the aforementioned novel aliphatic amino-derivatized single stranded oligonucleotides conjugated to a detectable moiety which is a chromophore, fluorescent agent, protein, enzyme, radioactive atom such as Il25, or other "tag".
The in~ention further comprises novel protected amino nucleoside phosphoramidites of the formula described in Figure 6 wherein B is selected from the group consisting of a nucleoside base, a nucleoside base analog, or their protected derivatives;
Rl, R2 and R5 are defined as follows: Rl/ R2 and R5 are elther H t OR, or NHR', with the proviso that at most onl.y one of Rl, R2 or R5 must be NHR'; wherein R is a monovalent organic group contain-ing up to 25 carbon atoms, R' is a nitrogen protecting group which is acid labile, or base labile protecting group selected from the group consisting of trifluoroacetylglycyl, 4-toluene-sulfonylethyl-oxycarbonyl, methylsulfonylethyloxycarbonyl, 2-cyano-t-butyl-oxycarbonyl; chloracetyl, acetoacetyl, 2-nitro-benzoyl, dithiasuccinoyl, maleoyl, isonicotinyl, 2-bromoethyloxy-carbonyl, and 2,2,2-trichloroethyloxycarbonyl, with the proviso ,,. y~
.. ~..

~3~L2~
- 15a - 68299-92 that when Rl or R2 is NHR', then R' is any of the foregoing groups, or triEluoroacetyl or 9-~luoroenylmethoxy-carbonyl; R6 is lower alkyl or when (R632 is taken with the N of the P-N bond it forms a heterocyclic group; and R7 is lower alkyl, cyano-lower alkyl, halo-lower alkyl, or nitrophenyl-lower alkyl.
The invention still further comprises an improved method of the synthesis of 5'-amino oligonucleotides which comprises reacting a phosphoramidite compound having the formula described in Figure 6 wherein B is selected from the group consisting of a nucleoside base, a nucleos.ide base analog, or their protected derivatives; Rl, R2 and R5 are deEined as follows: Rl and R2 can be H or OR and R5 is NHR', wherein R is a monovalent organic group containincJ up to 25 carbon a-toms, R' is a nitrogen protecting group which is acid labile, or base labile protecting group selected from the group consisting of trifluoroacetylglycyl, 4-toluene-sulfonylethyl-oxycarbonyl, methylsulfonylethyl-oxycarbonyl, 2-cyano-t-butyl-oxycarbonyl; chloracetyl, aceto-acetyl, 2-nitro-benzoyl, dithiasuccinoyl, maleoyl, isonicotinyl, 2-bromoethyloxy-carbonyl, and 2,2,2-trichloroethyloxycarbonyl;
R6 is lower alkyl or when (R6)~ is taken with the N of the P-N
bond it forms a heterocyclic group; and R7 is lower alkyl, cyano-lower alkyl, halo-lower alkyl, or nitrophenyl-lower alkyl;
in the last coupling step in solid phase oligonucleotide synthesis with an oligonucleotide bound to a solid support.
The invention still further comprises novel protected 5'-amino nucleoside phosphoramidites having the general formula ~5 , ~, ', .

~3~2~

15b 68299-92 l ~1 Fiaure 7 ~ '~

wherein B is selected from the group consi~ting of a nucleoside base, or a nucleoside base analog, or their protected derivatives;
Xl is selected from p-anisyldiphenylmethyl, triphenylmethyl, and protected amino acyl having the formula: Y-NH-(CHR)n-CO wherein Y
is selected from the group consisting of trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-anisyldiphenylmethyl, and triphenylmethyl; n is an integer from l to lO0, R i.s an amino acid side chain or hydrogen when n - l; and R i~ hydrogen when n i.s an integer from 2 to 100; Rl is selected from the group consisting of lower alkyl (in which case m = 2) and heterocyclic which includes the nitrogen of the P-N bond (in which case m = l), and R2 is selected from the group consisting of methyl, beta cyanoethyl, p-ni~rophenethyl, o-chlorophenyl, or p-chlorophenyl.
The invention al~so comprises an improved method of the synthesis of 5'-amino oligonucleotides which comprises reacting a phosphoramidite compound having the formula depicted in Figure 7 wherein B is selected from the group consi.sting of a nucleoside base, or a nucleoside ba.se analogr or their protected derivatives;

"

13~ 2~

15c 68299-92 Xl i.s selected from p-anisyldiphenylmethyl, triphenylmethyl, and protected amino acyl having the formula: Y-NH-(CHR)n-CO
wherein Y is .selected from the group consi.sting of trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-anisyldiphenylmethyl, and triphenylmethyl; R i.s an amino acid sidechain or hydrogen when n=l; and R is hydrogen when n is an integer from 2 to 100; Rl is selected from the group consisting of lo~er alkyl (in which case m=2) and when m=l and Rl is taken in conjunction with the N of the P-N bond it forms a heterocyclic group, and R2 is selected from the group consisting of methyl, beta~cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl; in the last coupling step in solid phase oligonucleotide synthesis with an oligonucleotide bound to a solid support.
The invention still further compri.ses a novel protected 2'-amino-nucleoside phosphoramidites having the general formula f l_XI

~ R ~ Fi~ure 8 wherein B is selected from the group con.sisting of a nucleoside base, or a nucleoside base analog, or their protected derivatives; Xl is selected from trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-ani.syldiphenylmethyl, "~

~31~ ~2~
15d 68299-92 triphenylme-thyl, and protected amino acyl having the formula:
~-NH-(CHR)n-CO wherein Y is selected from the group consisting oE
t:rifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p~
anisyldiphenylmethyl, and triphenylmethyl; R is an amino acid side chain or hydrogen when n=l; and R is hydrogen when n is an integer from 2 to 100; Rl is selected from the group consisting of lower alkyl (in which case m=2) and when m = 1 and Rl is taken in conjunction with the N of the P-N bond it -forms a heterocyclic group, and R2 is selected from the group consisting of methyl, beta-cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl; and X2 is a hydroxyl protecting group selected from triphenylmethyl, p-anisyldiphenylmethyl, di-p-anisylphenylmethyl, and 9-phenyl-xanthenyl.
The inven-tion also comprises an improved method of the synthesis of 2'-amino oligonucleoti.des which comprises reacting a phosphoramidite compound having the formula depicted in Figure 8 wherein ~ i.s ~elected from the group consisting of a nucleoside base, or a nucleoside base analog, or their protected derivatives;
Xl is selected from trifluoroacetyl, 9-fluoroenyl~ethyloxycarbonyl, p-anisyldiphenylmethyl, triphenylmethyl, and protected amino acyl having the formula:
Y-NH-(CHR)n-C0 wherein Y is selected from the group consisting of trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-anisyldiphenylmethyl, and triphenylmethyl; R is an amino acid side chain or hydrogen when n=l; and R is hydrogen when n is an integer from 2 to 100; Rl is selected from the group consisting of lower alkyl (in which case m=2) and when m=l and Rl is taken in conjunction with the N of the P-N bond it forms a heterocyclic , Yi ~3~28 15e 6829g-g2 group, and R2 is selected from the group consisting of methyl, beta-cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl; and X2 i5 a hydroxyl protecting group .selected from triphenylmethyl, p-anisyl-diphenylmethyl, di-p-anisylphenylmethyl, and 9-phenylxanthenyl; in one or more coupling step(s) in solid phase oligonucleotide synthesis with an oligonucleotide bound to a solid support.
The invention still further comprise~s novel protected 2'-amino-nucleoside pho.sphoramidites having the general formula Fi~ure 9 ~ \NI~R~
wherein B is selected from the group consisting of a nucleoside base, or a nucleoside base analog, or their protected derivatives;

Xl is selected from trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-anisyldiphenylmethyl, triphenylmethyl, and protected amino acyl having the formula:
Y-NH-(CHR)n-CO wherein Y is selected from the group consisting of trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-anisyldiphenylmethyl, and triphenylmethyl; R is an amino acid side chain or hydrogen when n=l; and R is hydrogen when n is an integer from 2 to 100; Rl is selected from the group consisting of lower alkyl (in which case m=2) and when m=l and Rl is taken in conjunction with the N of the P-N bond it forms a heterocyclic ~ I' ~31~

15f 6829g-92 group, and R2 is selected from the group con.sisting of methyl, beta-cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl; and X2 i.s a hydroxyl protecting group selected from triphenylmethyl, p-ani.syl- diphenylmethyl, di-p-anisylphenylmethyl, and 9-phenylxanthenyl.
The invention also comprises an improved method of the synthesis of 2'-amino oligonucleotides which comprises reacting a phosphoramidite compound having the formula depicted in Figure 9 wherein B is selected from the group consisting of a nucleoside base, or a nucleoside base analog, or their protected derivatives;
Xl is selected from trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-anisyldiphenylmethyl, triphenylmethyl, and protected amino acyl having the formula:
Y-NH-(CHR)n-CO wherein Y is selected from the group consisting of trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-ani.syldiphenylme-thyl, and triphenylmethyl; R is an amino acid side chain or hydrogen when n=l; and R is hydrogen when n is an in-teger from 2 to 100; Rl is selected from the group consistin~ of lower alkyl ( in which case m=2) and when m=l and Rl is taken in conjunction with the N of the P-N bond it forms a heterocyclic group, and R2 is selected from the group consisting of methyl, beta-cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl; and X2 is a hydroxyl protecting group selected from triphenylmethyl, p-anisyldiphenylmethyl, di-p-anisylphenylmethyl~
and 9-phenylxanthenyl; in one or more coupling step~s) in solid phase oligonucleotide synthesis with an oligonucleotide bound to a solid support.

~l3~2~
15g 68299-92 It is an object of this i.nvention to provide novel protected nucleoside.s.
It i.s yet another object of this invention to provide novel phosphoramidites.
In another important aspect of thi.s inventlon, it is an object to provide novel oligonucleotide.s bound to a solid support which have been reacted with the aforementioned phosphoramidites.
It is still another object of this invention to provide novel tagged oligonucleotides which are readily detectable by standard detec-tion means.
These and other objects and advantages of our invention will be apparent to those skilled in the art from the more elaborate and detailed description whlch follows.

~311 1428 DETAILED DESCRIPTION OF THE INVENTION

The following citations comprise a list of syn-theses of amino nucleoside starting materials used in the preparation of the compounds of Figure 5 here-inabove.

I) Synthesis of 5'-amino-5'-deoxythymidine and 5'-amino-5'-deoxyuridine and appropriate intermediates (embodiment of case 3)o 1. Horwitz, J.P., Tomson, A.J., Urbanski, J.A., and Chua, J., J. Am. Chem._Soc. 27, 3045-3048 (1962).

II) Synthesis of 2'-amino-2'-deoxyuridine and 2'-amino-2'-deoxycytidine and appropriate intermediates (embodiment of case 2):
1. Verheyden, J.P.H., Wagner, D., and Moffatt, J.G., J. Or~. Chem. 36, 250-254 (1971).
2. Imazawa, M., and Eckstein, F., J. Orq. Chem.
44, 2039-2041 (1979).
3. Torrence, P. F., and Witkop, B., in "Nucleic Acid Chemistry", vol. 2, Townsend, L.B., and Tipson, R.S., eds., pp. 977-989, J. Wiley and Sons, New York (1978).
4. Sasaki, T., Minamoto, K., Sugiura, To~ and Niwa, M., J. Org. Chem. 41, 3138-3143 (1976).

III) Synthesis of 2'-amino-2'-deoxyadenosine and 2'-amino-2'-deoxyguanosine and appropriate inter~
mediates (embodiment of case 2):
1. Imazawa, M., and Eckstein, F. J. Or~ Chem.
_ , 2039-20~1 (1979).
2. Hobbs, J.B., and Eckstein, F., J. Org. Chem.
_ , 714-719 (1976).
3. Ranganathan, R., Tetrahedron I,ett. 1~, 1291-1294 (1977).

~3.~1~2~

4. Mengel, R., and Wiedner, H., Chem. Ber.
109, 433-443 (1976).
5. Wol~rom, M.L., and Winkley, M.W., J. Org.
Chem. 32, 1823-1825 (1967).

6. Ikehara, M., Maruyama, T., and Miki, H., Tetrahedron Lett. 49, 4485-4488 (1976).

7. Ikehara, M., and Maruyama, T., Chem. Pharm.
Bull. Japan 26, 240-244 ~1978).

IV) Synthesis of some C-nucleoside analogs of natural nucleosides (relevant to all cases):
1. ~e Las Heras, F.G., Tam, S. Y-K., Klein, R.S., and Fox J.J., J~ Or~. Chem. 41, 84-90 (1976).
2. Trummlitz, G., Repke, D.B., and Moffatt, J.G., J. Org. Chem. 40, 3352-3356 (1975).
3. Chu, C.K., Reichman, U., Watanabe, K.A., and ~ox, J.J., J. Heterocyclic Chem. 14, 1119-1121 (1977).
4. Ogawa, T., Pernet, A.G., and Hanessian, S., Tetrahedron Lett. 37, 3543-3546 (1973).
5. "Nucleosldes, Nucleotides, and Their Biological Applications", J.L. Rideout, D.W. Henry, and L.M.
Beacham III, eds., Academic Press, New York (1983).

V) Synthesis o~ amino sugars and amino nucleosides by glycosylation and transylycosidation reactions (relevant to all cases):
1. Azuma, T., and Ishono, Ko~ Chem. Pharm., Bull. Japan 25, 3347-3353 (1977).
2. Hashizume, T., and Iwamura, H., Tetrahedron Lett. 35, 3095-3102 (1965).
3. Anisuzzaman, A.X.M., and Whistler, R.L., J. Org. Chem. 37, 3187-3189 (1972).
4. Bishop, C.T., and Cooper, F.P., Can. J.
Chem. 41, 2743-2758 (1963).

~311~2~

5. Unger, F.M., Christlan, R., and Walclstatten, P., Tetrahedron Lett. 50, 4383-4384 (1977).
.
6. Unger, F.M., Chrlstian, R., and Waldstatten, P., Tetrahedron Lett. 7, 605-608 (1979).
7. Bobek, M., and Martin, V.~ Tetrahedron Lett.
22, 1919-1922 (1978).

8. Wolfrom, M.L., Shafizadeh, F., Armstrong, R.K., and Shen Han, T.M., J. Am. Chem. Soc. 81, 3716-3719 ( 1959 ) .

9. Wolfrom, M.L., Shafizadeh, F., and Armstrong, R.K., J. Am. Chem. Soc. 80, 4885-4888 (1958).
lO. Wulff, G., Rohle, G., and Kruger, W. t An~ew.
Chem. 82, 455-456 (1970).
11. Schroeder, L.R., and Green, J.W., J. Chem.
Soc. C, 530-531 (1966).
A preferred class of compounds within the scope of Figure 5 is given by the following.
Composition of Matter No. 1: 5'-N-protected derivatives of 5l-amino-5'-deoxythymidine having the generic formula:

~N-H2 HC) H

~31~

wherein X = a standard nitrogen protecting group as defined in the generic description of the invention accompanying Figure 5; preferably, X = triphenyl-methyl (trityl)l or p-anisyldiphenylmethyl ~also re-ferred to as monomethoxytrityl, ~MT).
The formula also encompasses a related class of compounds formed by reacting the compound wherein X = El with an activated appropriately protected amino acid derivative; in this case, X is represented by X = Y-NH-(CHQ)n-CO, wherein Y = a nitrogen protec~ing group, especially those listed as preferable for X
hereinabove, trifluoroacetyl or 9-fluroenyl methoxymethyl oxycarbonyl; and Q = any common amino acid side chain, with n = 1 to about 12; generally n <=6; for n =1, Q includes, but is not limited to, such moieties as H (from the amino acid glycine), methyl (from the amino acid alanine), isopropyl (valine), benzyl (phenyla-lanine), p-hydroxybenzyl (tyrosine), carboxymethyl (aspartic acid), carboxyethyl (glutamic acid), 4-ami-nobutyl (lysine), imida~olyl- methyl (histidine), indolylmethyl (tryptophan), mercaptomethyl (cystine), or hydroxymethyl (serine); for n >1, Q ls generally H: for example, when n = 2, the corresponding amino acid is beta-alanine; when n = 3, 4-aminobutyric acid;
when n - 5, 6-aminohexanoic acid. If Q contains re-active moieties such as OH, SH, C02H, or NH2, these are also appropriately protected with standard groups (see Geiger and Konig, "The Peptides: Analysis, Syn-thesis, Biology", for a thorough description of such groups). In this class of compounds, the protected amino group is spatially removed from the sugar ring of the nucleoside, either to improve its reactivity or to spatially separate the DNA chain from the "tag"
that is to be affixed to the amino group.
The formula also encompasses a class of compounds 13~ ~2~

related to this latter class by having more than one amino acid linked in linear fashion (termed a peptide) attached to the compound wherein X = H; in this case, X is represented by X = Y-[NH-(CHQi)n-CO]m, wherein Y and n are as defined hereinabove, the various Qi are as defined for o hereinabove, with i = 1 to the maximum value of m, and m = 1 to about 100; m - 1 represents the class defined in the paragraph above.
EXAMPLES
The synthesis of the 5'-O-p-toluenesulfonylthy-midine, 5'-azido-5'-deoxythmidine, and 5'-amino-5'-deoxy-thymidine starting materials are given in:
Horwitz, J.P., Tomson, A.J., Urbanski, J.A., and Chua, J., J. Org. Chem. 27, 3045-3048 (1962).

~3~2~

Example 1 5'-N-p-anisyldiphenylme~hyl-5'-amino-5'-deoxythymidine having the .~ormula:

OCH3~ H~c~3 5'-amino-~'-deoxythymidine (2.41 g, 10 mmoles) was coevaporated twice with anhydrous pyridine (25 ml each time) and then suspended in anhydrous pyridine (100 ml). Triethylamine (2.1 ml), N,N-dimethylamino-pyridine (0.80 mg; Aldrich Chemical Company), and p-anisyl- chlorodiphenylmethane (4.68 g, 15.2 mmoles;
Aldrich Chemical Company) were added. The reaction mixture was protected from moisture and light, and the yellow-orange solution stirred overnight at room temperature. The reaction was then cooled in ice, and cold sa-turated aqueous sodium bicarbonate (100 ml) was added to decompose excess tritylating agent.
After thirty minutes, the mixture was transferred to a one liter separatory funnel and was extracted twice with ethyl acetate (200 ml portions). The com-bined ethyl acetate layers were washed twice with water (100 ml portions) and once with saturated aqueous sodium chloride (100 ml), dried over anhydrous magnesium sulfate, filtered, and rotary evaporated to drynes under reduced pressure. The gummy orange-yellow product ~ 3 ~ % ~

was then coe~aporated twice with anhydrous toluene (100 ml portions) to remove residual pyridine. The residue was dissolved in a minimum amount of ethyl acetate and applied to a column (100 cm by 3.0 cm) of neutral alumina (activity grade V, 15~ water by weight; Woelm Pharma GmbH and Company) packed in he-xanes. The column was first eluted with ethyl ace-tate:hexanes (1:1 v/v) until almost all of the bright yellow material had been eluted from the column, and then with pure ethyl acetate. The fractions contalning product were pooled and rotary evaporated to dryness.
The nearly colorless gummy residue was dissolved in a small volume of ethyl acetate and precipitated into hexanes (400 ml) at room temperature. The product was filtered and dried in a vacuum dessicator to give 4.53 g (~.8 mmoles, 88%) of a white powder, not crys-tallized. TLC analysis of the purified product on silica gel LQ6DF plates (Pierce Chemical Company) developed in acetonitrile:water (9:1 v/v) showed one spot by short wave UV detection, Rf 0.87, that gave an orange-yellow color characteristic of the p-anisyl-diphenylmethyl cation after spraying the plate with perchloric acid:ethanol solution (3:2 v/v). The struct-ure of the product was further confirmed by lH NMR
spectroscopy in perdeuterated dimethyl sulfoxide (Merck Isotopes).
- Similarly, the following compounds are prepared:
1) 5'-N-p-anisyldiphenylmethyl-5'-amino-2',5'-dideoxy-N6-benzoyladenosine from 5'-amino-2',5'-dideoxy-N6-benzoyl-adenosine.
2) 5'-N-p-anisyldiphenylmethyl-5'-amino-2',5'-dideoxy-N2-isobutyrylguanosine from 5'-amino-2l,5'-dideoxy-N2-isobutyrylguanosine.
3) 5'-N-p-anisyldiphenylmethyl-5'-amino~2',5l-dideoxy-N4-benzoylcytidine from 5'-amino 2',5'-dideoxy-N4-benzoylcytidine.

~311~2~

4) 5'-N-p-anisyldiphenylmethyl-5'-amino-2',5'-dideoxy-uridine from 5'-amino-2',5'-dideoxyuridine.
5) 5'-N-p-anisyldiphenylmethyl-5'-amino-2',5'-dideoxy-inosine from 5'-amino-2',5'-dideoxyinosine.
6) 5'-N-(p-anisyldiphenylmethyl)-5'-amino-2'-tetra-hydropyranyl-5'-deoxyuridine from 5'-amino-2'-tetra-hydropyranyl-5l-deoxyuridine.
7) 5'-N-(p-anisyldiphenylmethyl)-5'-amino-2'-tetra-hydropyranyl 5'-deoxyinosine from 5'-amino-2'-tetra-hydropyranyl-5'-deoxyinosine.
8) 5'-N-(p-anisyldiphenylmethyl)-5'-amino-2'-tetra-hydropyranyl-N6-benzoyl-5'-deoxyadenosine from 5'-amino-2'-~etrahydropyranyl-N6-benzoyl-5'-deoxyadenosine.
9) 5'-N-(p-anisyldiphenylmethyl)-5'-amino-2'-tetra-hydropyranyl-N4-benzoyl-5'-deoxycytosine from 5'-amino-2'-tetrahydropyranyl-N4-benzoyl-5'-deoxycytosine.

10) 5'-N-~p-anisyldiphenylmethyl)-5'-amino-2'-tetra-hydropyranyl-N2-isobutyryl-5'-deoxyguanosine from 5'-amino-2'-tetrahydropyranyl-N2-isobutyryl-5'-deoxy-guanosine.

11) 5'-N-triphenylmethyl-5'-amino-2',5'-dideoxy-N6-benzoyladenosine from 5'-amino-2',5'-dideoxy-N~-benzoyl-adenosine.

12) 5'-N-triphenylmethyl-5'-amino-2',5'-dideoxy-N2-isobutyrylguanosine from 5'-amino-2',5'-dideoxy-N2-isobutyrylguanosine.

13) 5'-N-triphenylmethyl-5'-amino-2',5'-dideoxy-N4-benzoylcytidine from 5'-amino-2',5'-dideoxy-N4-benzoyl-cytidine.

14) 5'-N-triphenylmethyl-5'-amino-2',5'-dideoxyuridine from 5'-amino-2',5'-dideoxyuridine.

15) 5'-N-triphenylmethyl-5'-amino-2',5'-dideoxyinosine from 5'-amino-2',5'-dideoxyinosine.

16) 5'-N-triphenylmethyl-5'-amino-2'-tetrahydropyranyl-5'-deoxyuridine from 5'-amino-2'-tetrahydropyranyl-5'-deoxyuridine.

~3~3.42~

17) 5'-N-triphenylmethyl-5'-amino-2'-tetrahydropyranyl-5'-deoxyinosine from 5'-amlno-2'-tetrahydropyranyl-5'-deoxylnoslne .18) 5'-N-triphenylmethyl-5'-amino-2'-tetrahydropyranyl-N6-benzoyl-5'-deoxyadenosine from 5'-amino-2'-tetra-hydropyranyl-N6-benzoyl-5'-deoxyadenosine.
l9) 5'-N-triphenylmethyl-5'-amino-2'-tetrahydropyranyl-N4-benzoyl-5'-deoxycytosine from 5'-amino-2'-tetra-hydropyranyl-N4-benzoyl-5'-deoxycytosine.
20) 5'-N-triphenylmethyl-5'-amino-2'-tetrahydropyranyl-N2-isobutyryl-5'-deoxyguanosine from 5'-amino-2'-tetrahydropyranyl-N2-isobutyryl-5'-deoxyguanosine.
Example 2 5'-N-(N-benzyloxycarbonyl-6-aminohexanoyl)-5'-amino-5'-deoxythymidine having the formula:

~N
o ~CH2J5~
~:H;~ HO H
~q .

5'-amino-5'-deoxythymidine (1.21 g, 5.0 mmoles) and N-benzyloxycarbonyl-6-aminohexanoic acid p-nitro-phenyl ester (2.12 g, 5.5 mmoles; see note below) were dissolved in anhydrous DMF (25 ml) and stirred -three days at room temperature. The solution was then rotary evaporated to dryness under reduced pressure to give a yellow solid, which was extensively triturated under several chan~es of dry ethyl ether. The powdery white product was then filtered, washed well with diethyl ether, and dried in a vacuum dessicator to give 2.31 g (4.7 mmoles, 95%).

N _ : N-benzyloxycarbonyl-6-aminohexanoic acid p-nitro-phenyl ester was synthesized by standard techniques from N-benzyloxycarbonyl-6-aminohexanoic acid (Sigma Chemical Company), p-nitrophenol (Aldrich Chemical Company), and N,Nl-dicyclohexylcarbodiimide (Aldrich Chemical Company) in ethyl acetate solution.
Similarly, the following compounds are prepared:
1) 5'-N~(N-benzyloxycarbonyl-6-aminohexanoyl)-5'-amino-2',5'-dideoxy-N6-benzoyladenosine from 5'-amino-2',5'-dideoxy-N5-benzoyl-adenosine.
2) 5'-N-(N-benzyloxycarbonyl-6-aminohexanoyl)-5'-amino-2',5'-dideoxy--N2-isobutyrylguanosine from 5'-amino-2',5'-dideoxy-N2-isobutyrylguanosine.
3) 5'-N-(N-benzyloxycarbonyl-6-aminohexanoyl)-5'-amino-2',5'-dideoxy-N4 benzoylcytidine from 5'-amino-2',5'-dideoxy-N4-ben7oylcytidine.
4) 5'-N-(N-benzyloxycarbonyl-6-aminohexanoyl)-5'-amino-2',5'-dideoxyuridine from 5'-amino-2',5'-dideoxyuridine.
5) 5'-N-(N-benzyloxycarbonyl-6-aminohexanoyl)-5' amino-2',5'-dideoxyinosine from 5'-amino-2',5'-dideoxyinosine.
6) 5'-N-(N-benzyloxycaxbonyl-6-aminohexanoyl)-5'-amino-2'-tetrahydropyranyl-5'-deoxyinosine from 5'-amino~2'-tetrahydropyranyl-5'-deoxyinosine.
7) 5'-N-(N-benzyloxycarbonyl-6-aminohexanoyl)-5'-amino-2 ~

2'-tetrahydropyranyl-N2-isobutyryl-5'-deoxyguanosine from 5'-amino-2'-tetrahydropyranyl-N2 isobutyryl-5'-deoxyguanosine.
8) 5'-N-(N-benzyloxycarbonyl-6-aminohexanoyl)-5'-amino 2',5'-dideoxyuridine from 5'-amino-2',5'-dideoxy-uridine.
Composition of Matter No. 2: 3'-0-phosphoramidites of compounds described in composition of matter No.
1 having the generic formula:
o N

X-N-H

tl p 7 ~(R(o) wherein X = as defined in previous section (composition of matter No. 1), R6 = a lower alkyl, preferably a lower alkyl such as methyl or isopropyl, or a non-aromatic nitrogen-containing heterocycle, such as morpholino, piperidino, pyrrolidino or 2,2~6,6-tetramethylpiperidino, R7 = methyl, beta-cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl.

~31~

EXAMPLES

NOTE: The phosphine starting materials used to syn-thesize the following phosphoramidite compounds were prepared according to literature procedures:
1) McBride, L.J., and Caruthers, M.H., Tetrahedron Lett. 24, 245-248 (1983); and 2) Sinha, N.D.I Biernat, J., McManus, J., and Koster, H., Nucl. Acids Res. 12. 4539-4557 (1984).

Example 3~
5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythymidine-3'-0-beta-cyanoethyl-N,N-diisopropylamino phosphoramidite having the formula:

OCH3 H~N~CH3 o H
NC C H2CH2~ N~C~ H3 ~H3 i3114~g 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythy-midine (0.785 g, 1.5 mmole) was dissolved in dry dich-loromethane (10 ml, dried by distillation from phos-phorous pentoxide and then calcium hydride) containing N,N-diisopropylethylamine (1.3 ml) under a dry argon atmosphere. Chloro-N,N-di- isopropylamino-beta-cyano-ethoxyphosphine (O.70 ml, 3.0 mmole) was added dropwise to the solution from a syringe over about one minute and the reaction stirred at room temperature. TLC
on silica gel 60 F-254 plates developed in ethyl ace-tate: triethylamine (99:1 v/v) indicated that the reaction was complete after thirty minutes. Anhydrous methanol (0.1 ml) was then added to decompose excess phosphitylating agent, and the reaction stirred a few minutes longer. The reaction mixture was then transferred to a separatory funnel with ethyl acetate (50 ml, previously washed with 50 ml of cold 10% (w/v~
aqueous sodium carbonate) and washed twice with cold 10% (w/v) aqueous sodium carbonate (80 ml portiorls) and twice with cold saturated aqueous sodium chloride (80 ml portions). The organic solution was then dried over anhydrous sodium sulfate, filtered, and rotary evaporated under reduced pressure to a clear foam.
The foam was dissolved in dry ethyl acetate (10-15 ml) and this solution was added dropwise to hexane (200 ml) at -78C (dry ice/acetone bath). The pre-cipitated product was filtered, washed well with -78 hexane, and dried in a vacuum dessicator to yield 0.932 g (1.31 mmoles, 87%) of a white powdery solid.
The structure of the product was further confirmed by lH NMR spectroscopy in perdeuterated acetonitrile.
31p NMR spectroscopy in perdeuterated acetonitrile showed two singlets at 147.74 and 147.53 ppm (relative to phosphoric acid in perdeuterated acetonitrile) as expected for the diastereomeric phosphoramidite 13~142~

product, and only traces (<5~) of other phosphorous-con-taining impurities. TLC in the above solvent system on silica gel LQ6DF plates showed two closely migrating spots under short wave UV detection, Rf 0.87 and 0.92, once a~ain due to the diastereomeric product. These spots gave an yellow-orange color characteristic of the p-anisyldiphenylmethyl cation when exposed to perchloric acid:ethanol solution (3:2 v/v).
When the foregoing Example was repeated using chloro-N,N-diisopropylaminome-thoxyphosphine in lieu of chloro-N,N-diisopropylamino-beta-cyanoethoxyphos-phine, 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxy-thymidine- 3'-0-methyl-N,N-diisopropylamino phospho-ramidite was obtained.
Similarly, the following compounds are prepared:
l) 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythy-midine- 3'-0-methyl-N,N-diisopropylamino phosphorami~
dite.
2) 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythy-midine- 3'-0-methyl-N,N-dimethylamino phosphoramidi-te.
3) 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythy-midine- 3'-0-methylmorpholino phosphoramidite.
4) 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythy-midine- 3'-0-beta-cyanoethylmorpholino phosphoramldite.
5) 5'-N p-anisyldiphenylmethyl-5'-amino-5'-deoxythy~
midine- 3'-0-p-nitrophenethyl-N,N-dimethylamino phos-phoramidite.
6) 5'-N-p-anisyldiphenylmethyl-51-amino-5'-deoxythy-midine- 3'-0-betacyanoethyl-N,N-dimethylamino phos-phoramidite.
7) 5'-N-p-anisyldiphenylmethyl 5'-amino-2',5'-dideoxy-uridine-3'-0-beta-cyanoethyl-N,N-diisopropylamino phosphoramidite.
8~ 5'-N-p-anisyldiphenylmethyl 5'-amino-2',5'-dideoxy-inosine-3'-0-methyl-N,N-diisopropylamino phosphorami-dite.

~331 ~2~

9) 5'-N-p-anisyldiphenylmethyl 5'-amino-N6-benzoyl-2',5'-dideoxyadenosine-3'-0-methyl-N,N-dimethylamino phosphoramidite.
10) 5'-N-p-anisyldiphenylmethyl 5'-amino-N4-benzoyl-2',5'-dideoxycytosine-3'-0-methylmorpholino phosphor-amidite.11) 5'-N-p-anisyldiphenylmethyl 5'-amino-N2-isobutyryl-2',5'-dideoxyguanosine-3'-0-beta-cyanoethylmorpholino phosphoramidite.
12) 5'-N-p-anisyldiphenylmethyl 5'-amino-2'-tetrahydro-pyranyl-5'-deoxyuridine-3'-0-p-nitrophenethyl-N,N-dime-thylamino phosphoramidite.
13) 5'-N-p-anisyldiphenylmethyl 5'-amino-2'-tetrahydro-pyranyl-5'-deoxyinosine-3'-0-beta-cyanoethyl-N,N-dime-thyl amino phosphoramidite.
14) 5'-N-p-anisyldiphenylmethyl 5'-amino-2'-tetrahy-dropyrenyl- N6-benzoyl-5'-deoxyadenosine-3'-0-beta-cya-noethyl-NJN- diisopropylamino phosphoramidite.
15) 5'-N-p-anisyldiphenylmethyl 5'-amino-2'-tetrahy-dropyranyl- N4-benzoyl-5'-deoxycytosine-3'-0-methyl-N, N-diisopropylamino phosphoramidite.
16) 5'-N-p-anisyldiphenylmethyl 5'-amino-2'-tetrahy-dropyranyl- N2-isobutyryl-5'-deoxyguanosine-3'-0-methyl-N,N-dimethylamino phosphoramidite.
Composition of Matter No. 3: 2'-N-protected deri~atives of 5'-0-protected 2'-amino-2'-deoxyuridine and 5'-0-protected 2'-N-aminoacyl-2'-amino-2'-deoxyuridine, a preferred class of compounds within the scope of ~31~42~

Figure 5 r having the generic ~ormula:

OlN~I

3~0 NH-X

wherein R = triphenylmethyl (trityl), p-anisyldiphenyl-methyl (monomethoxytrityl, l~MT), di-p~anisylphenylmethyl (dimethoxytrityl, DMT), 9-phenylxanthenyl (pixyl), di-o-anisyl-l-napthylmethyl, p-anisyl-l-napthylphenyl-methyl, or the like;
wherein X = a standard nitrogen protecting group as defined in ~he generic description of the invention accompanying Figure 5; preferably, X = trifluoroacetyl (Tfa), 9-fluorenylmethylo~ycarbonyl (Fmoc), triphenyl-methyl (trityl~, or p-anisyldiphenylmethyl (also re-ferred to as monomethoxytrityl, MMT).
The formula also encompasses a related class of compounds formed by reacting the compound wherein X = H with an activated appropriately protected amino acid derivative; in this case, X is represented by X = Y-NH-(CHQ)n-CO, wherein Y = a standard nitrogen protecting group as defined for X hereinabove, espe-cially those listed as preferable for X hereinabove;

~L3~142~
-32~

and Q = any common amino acid side chain, with n =
1 to about 12, generally n <=6; for n =1, Q includes, but is not limited to, such moieties as H (from ~he amino acid glycine), methyl (from the amino acid ala-nine), isopropyl (valine), benzyl (phenylalanine), p-hydroxybenzyl (tyrosine), carboxymethyl (aspartic acid), carboxyethyl (glutamic acid), 4-aminobutyl (lysine), imidazolyl- methyl (histidine), indolylmethyl (tryptophan), mercaptomethyl (cystine), or hydroxymethyl (serine); for n >1, Q is generally H: for example, when n =2, the corresponding amino acid is beta-alanine;
when n =3, 4-aminobutyric acid; when n =5, 6-aminohe-xanoic acid. If Q CQntainS reactive moieties such as OH, SH, CO2H, or NH2, these are also appropriately protected with standard groups (see Geiger and Konig, "The Peptides: Analysis, Synthesis, Biology", for a thorough description of such groups). In this class of compounds, the protected amino group is spatially removed from the sugar ring of the nucleoside, either to improve its reactivity or to spatially separate the DNA chain from the "tag" that is to be affixed to the amino group.
The formula also encompasses a class of compounds related to this latter class by having more than one amino acid linked in linear fashion (termed a peptide) attached to the compound wherein X = H; in this case, X is represented by X = Y-[NH-(CHQi)n-CO]m, wherein Y and n are as defined hereinabove, the various Qi are as defined for Q hereinabove, with i = 1 to the maximum value of m, and m = 1 to about 100; m = 1 represents the class defined in the paragraph above.

EXAMPLES
The syntheses of the starting compounds 2'-aæido-2'-deoxyuridine, 2'-amino-2'-deoxyuridine, 2'-N-(~-ben-zyloxy- carbonylglycyl)-2'-amino-2'-deoxyuridine, 1 3~2~

2'-N-glycyl-2'-amino- 2'~deoxyuridine, and 2'-trifluoro-acetamido-2'-deoxyuridine are given in:
Verheyden, J.P.H., Wagener, D., and Moffatt, J.G., J. Org. Chem. 36, 250-254 (1971).
Sharma, R.A., Bobek, M., and Bloch, A., J. Med.
Chem. 18, 955-957 (1975).
Imazawa, M., and Eckstein, F., J. Org. Chem.
_ , 2039-2041 (1979).
Generally, the procedures found therein were followed with only minor modifications to the workups, except:
l) 2'-azido-2'-deoxyuridine was purified on a column of neutral alumina in methanol:acetone (l:l v/v) instead of on silica gel;
2) 2'-amino-2'-deoxyuridine was obtained by re-duction of 2'-azido-2'-deoxyuridine with hydrogen in the presence of 5% palladium on carbon catalyst, instead of using triphenylphosphine and ammonia;
3) N-trifluoroacetylation of 2'-amino-2l-deoxy-uridine was carried out using p-nitrophenyl trifluoro-acetate followed by column chromatography on silica gel in chloroform:methanol (6:1 v/v), instead of using S-ethylthioltrifluoroacetate.

~3:1L142~

Example ~
5l-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2l-deoxyuridine having the formula:

~H3 H~`'N

0~3~0~0~
~ ' HO ~ CF

2'-N-trifluoroacetyl-2'-amino-2'-deoxyuridine (1.25 g, 3.8 mmoles) was dissolved in anhydrous pyridine (50 ml), and di-p-anisylphenylmethyl chloride (1.42 g, 4.2 mmoles; American Bionuclear Corporation) was added. The orange solution was then stirred overnight at room temperature in the dark. Water (10 ml) was added, and the mixture stirred an additional hour.
The solvent was removed by rotary evaporation at 40C
to give a resinous product, which was co-evaporated twice with toluene (100 ml portions). The Eoamy product was partitioned between water (50 ml) and ethyl acetate (100 ml), the layers separated, and the organic layer extracted with water (50 ml) and saturated aqueous sodium chloride (50 ml). The ethyl acetate solution was dried over anhydrous sodium sulfate, filtered, and evaporated to a yellow foam. This ~oam was then dissolved in an minimum volume of ethyl acetate:trie-thyl- amine (9:1 v/v), and applied to a column of ~3~1~2~

silica yel (3 cm x 25 cm) poured in the same solvent mixture. The column was eluted with ethyl acetate:trie~
thylamine (9:1 v/v); fractions containing product were pooled and evaporated to a clear glassy solid.
The product was dissolved in a minimum volume of ethyl acetate (about 10 ml) and precipitated into hexane (200 ml) at room temperature. The gelatinous preci-pitate was filtered and dried in a vacuum dessicator to give 2.06 g (3.3 mmoles, 86%) of a white power, not crystallized. TLC analysis of the purified product on silica gel 60 F-254 plates developed in chloroform:
ethanol (9:1 v/v) showed one spot by short wave UV
detection, RE 0.60, that gave a bright orange color characteristic of the di-p-anisylphenylmethyl cation after spraying the plate with perchloric aci~:ethanol solution (3:2 v/v). The structure of the product was further confirmed by lH NMR spectroscopy in per-deuterated dimethyl sulfoxide. Fluorine (19F) NMR
spectroscopy in deuterated chloroform ~Aldrich Chemical Company) showed one singlet at 6.03 ppm (relative to trifluoracetic acid in deuterated chloroform) as expected for the sing]e trifluoroacetyl group.
Similarly, the following compounds are prepared:
1) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino~2'-deoxyinosine.
2) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2' amino-N6-benzoyl-2'-deoxyadenosine.
3) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-N4-benzoyl-2'-deoxycytosine.
4) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-N2-isobutyryl-2'-deoxyguanosine.
5) 5'-0-di-p-anisylphenylmethyl-2'-N-(9-fluorenyl-methyloxycarbonyl)-2'~amino-2'-deoxyinosine.
6) 5'-0-di-p-anisylphenylmethyl-2'-N-(9-fluorenyl-11 311~2~

methyloxycarbonyl)-2'-amino-N6-benzoyl-2'-deoxyade-nosine.
7) 5'-0-di-p-anisylphenylmethyl-2'-N-(9-fluorenyl-methyloxycarbonyl-2'-amino-N4-benzoyl-2'-deoxycytosine.
8) 5'-0-di-p-anisylphenylmethyl-2'-N-(9-fluorenyl-methyloxycarbonyl-2'-amino-N2-isobutyryl-2'-deoxygua-nosine.
9) 5'-0-di-p-anisylphenylmethyl-2'-N-(9-fluorenyl-methyloxycarbonyl)-2'-amino-2'-deoxyuridine.

Example 5 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoroacetyl-glycyl)-2'-amino-2'-deoxyuridine having ~he formula:

~H3 H~3 ~3~~3~
HO NH CGH~NHCCF3 ~3~2~
~37-2'-N-glycyl-2'-amino-2'-deoxyuridine (1.2 g, 4.0 mmole~ and p-nitrophenyl trifluoroacetate (1.2 g, 5.1 mmole; Aldrich Chemical Company) were dissolved in anhydrous DMF (20 ml) and the mixture was stirred overnight at room temperature. The reaction mixture was then rotary evaporated to dryness at 50C, and the gummy yellow residue flash chromatographed (see Still, W.C., Kahn, M., and Mitra, A., J. Org. Chem.
43, 2923-2925 (1978)) on a column of silica gel 60 (2.5 cm x 10 inches) in ethyl ac~tate:methanol (~5:5 v/v). Fractions containing product were evaporated to dryness to give a white foam (1.5 g, 3.7 mmoles, 93%) which was not crystallized, but used directly in the next step.
The above material (1.5 g, 3.7 mmoles) was eva-porated twice with dry pyridine (30 ml portions), and the residue dissolved in dry pyridine (50 ml).
N,N-dimethy- laminopyridine (23 mg, 0.19 mmoles), triethylamine (0.8 ml, 5.2 mmoles), and di-p~anisyl-phenylmethyl chloride (1.54 g, 4.4 mmoles) were added, and the orange mixture stirred overnight at room tempe-rature. Aqueous sodium bicar~onate (5% w/v, 50 ml) was then added, and the mixture stirred fifteen minutes more. The mixture was extracted twice with ethyl acetate (100 ml portions), and the combined ethyl acetate layers washed once with saturated aqueous sodium chloride (50 ml), dried over anhydrous sodium sulfate, filtered, and evaporated to dryness. After two co-evaporations with toluene (100 ml portions) r the foamy yellow product was purified by chromatography on a column (3 cm x 25 cm) of silica gel ~0 using chloroform:methanol: triethylamine (~9:10:1 v/v) as the eluant. Fractions containing product were pooled and evaporated to dryness to give a clear glassy solid. This material was dissolved in a minimum of ethyl acetate (about 10 ml) and precipitated into ~3~2~

hexane (300 ml) at room -temperatuare. The product was filtered and dried in a vacuum dessicator to give 1.62 g (2.3 mmoles, 62%) of a powdery white solid, which could be crystallized from benzene~hexane.
TLC analysis of the purified product on silica gel 60 F-254 plates developed in dichloromethane:methanol (92:8 v/v) showed one spot by short wave UV detection, Rf 0.33, that gave a bright orange color characteristic of the di-p-anisylphenylmethyl cation after spraying the plate with perchloric acid:ethanol solution ~3:2 v/v). The structure of the product was further con-firmed by lH NMR spectroscopy in perdeuterated dimethyl sulfoxide. 19F NMR spectroscopy in deuterated chlo-roform showed one singlet at 5.98 ppm (relative to trifluoroacetic acid in deuterated chloroform) as expected for the single trifluoroacetyl group.
Similarly, the following compounds are prepared:
1) 5'-0-di-p-anisylphenylmethyl-2'-N-(N trifluoro-acetylglycyl)-2'-amino-N2-isobutyryl-2'-deoxyguanosine.
2) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-2'-deoxyinosine.
3) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-N6-benzoyl-2'-deoxyadenosine.
4) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-N~-henzoyl-2'-deoxycytosine.
5) 5'-0-di-p-anisylphenylmethyl~2'-N-(N-9-fluorenyl-methyloxycarbonyl-glycyl)-2'-amino-N2-isobutyryl-2'-deoxyguanosine.
6) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-9-fluorenyl-methyloxycarbonyl-glycyl)-2'-amino-2'-deoxyuridine.
7) 5'~0-di-p-anisylphenylmethyl-2'-N-(N-9-fluorenyl-methyloxycarbonyl-glycyl)-2'-amino-2'-deoxyinosine.
8~ 5'-0-di-p-anisylphenylmethyl-2' N-(N-9-fluorenyl-methyloxycarbonyl-glycyl)-2'-amino-N6-benzoyl-2l-deoxyadenosine.
9) 5'-0-di-p-anisylphenyLmethyl-2'-N-(N-9-fluorenyl-~3~ 42~

me-thyloxycarbonyl-glycyl)-2'-amino-N4-benzoyl-2'-deoxycytosine.
Composition of Matter No. _:
3'-0-phosphoramidites of compounds described in composition of matter No. 3 having the generic formula:

~N~
ROt~

~ H-X
p 7 \N(P~,)æ

wherein R = as defined in the previous section (composition of matter No. 3);
X = as defined in the previous section (composition of matter No. 3);
R6 = a lower alkyl, preferably a lower alkyl such as methyl or isopropyl, or a non-aromatic nitrogen-containing heterocycle, such as morpholino, piperidino, pyrrolidino, or 2,2,6,6-tetramethylpiperidono, R7 = methyl, beta-cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl.

EXAMPLES
NOTE: The procedures described in this section a.re essentially the same as those described in the section ~3~142~
- '1 0 -entitled "Composition of Matter No. 2". The phosphine starting material used to synthesize the following phosphoramidite compounds were prepared according to the literature references given in that section.

5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxyuridine-3'-0-methyl-N,N-diisopropylamino phosphoramidite having the formula:
~H3 a~l'N~

H3Co~ ~2~

O NH (~CF~S
H3~0~ '`N ~H~H3 H3C-H ~ Ctl~
~H3 5'-0-di-p-anlsylphenylmethyl-2'-N trifluoroacetyl~
2'-amino-2'-deoxyuridine (0.95 g, l.S mmoles) was dissolved in dry dichloromethane (10 ml, dried by distillation from phosphorous pentoxide and then calcium hydride) containing N,N-diisopropylethylamine (1.3 ml, 5.0 mmoles). The solution was stirred at room temperature under a dry argon atmosphere, and chloro-N,N-diisopropylaminomethoxyphosphine ~0.45 ml, 2.4 mmoles) was added dropwise from a syringe over about one minute.

~3~ ~2~

TLC on silica gel 60 F-254 plates developed in ethyl acetate:triethylamine ~99:1 v/v) indicated that the reaction was complete after thirty minutes. Anhydrous methanol (0.1 ml) was then added to decompose excess phosphitylating agent, and the reaction stirred a few minutes longer. The reaction mixture was then transferred to a separatory funnel with ethyl acetate ~50 ml, previously washed with 50 ml of cold 10~ (w/v) aqueous sodium carbonate) and washed twice with cold 10% ~w/v) aqueous sodium carbonate (80 ml portions), and twice with cold saturated aqueous sodium chloride (80 ml portions). The organic solution was dried over anhydrous sodium sulfate, filtered, and rotary evaporated under reduced pressure to a clear foam.
The foam was dissolved in dry ethyl acetate (10-15 ml) and this solution was added dropwise to hexane (200 ml) at -78C (dry ice-acetone bath). The pre-cipitated product was filtered, washed well with -78C
hexane, and dried in a vacuum dessicator to yield 1.04 g (1.3 mmoles, 87~ of a white powdery solid.
The structure of the product was confirmed by 1H NMR
spectroscopy in perdeuterated acetonitrile. 31p NMR
spectroscopy in perdeuterated acetonitrile showed two singlets at 152.11 and 150.43 ppm (relative to phosphoric acid in perdeuterated acetonitrile) as expected for the diastereomeric phosphoramidite product, :L 3 ~

and only very slight traces (< 1%) of other phospho-rus-containing impurities. l9F NMR spectroscopy in deuterated chloroform also showed two singlets at 0.42 and 0.38 ppm (relative to trifluoroacetic acid in deuterated chloroform), due to a slight influence of the neighboring chiral phosphorous~ TLC in the above solvent system on silica gel LQ6DF plates showed only one spot under short wave UV detection, Rf 0.96.
This spot gave a bright orange color characteristic of the di-p-anisylphenyl- methyl cation when exposed to perchloric acid:ethanol (3:2 v/v).
Similarly, the following compounds are prepared:
1) 5'-0-di-p-anisylphenylmethyl-2'-~-trifluoroacetyl-2'-amino-2'-deoxyuridine-3'-0-beta-cyanoethyl-N,N-diisopropylamino phosphoramidite.
2) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxyuridine-3'-0-methyl-N,N-dimethylamino phosphoramidite.
3) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxyuridine-3'-0-methyl-morpholino phos-phoramidite.
4) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxyuridine-3'-0-beta-cyanoethyl-morpholino phosphoramidite.
5) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxyuridine-3'-0-p-nitrophenethyl-N,N-dimethylamino phosphoramidite.

2 ~

6) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxyuridine-3'-0-beta-cyanoethyl-N,N-dime-thyl amino phosphoramidite.
7) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxyinosine-3'-0-methyl-N,N-diisopropyl-amino phosphoramidite.
8) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-N6-benzoyl-2'-deoxyadenosine-3'-0-methyl-N,N-dimethylamino phosphoramidite.
9) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-N4-benzoyl-2'-deoxycytosine-3'-0-methyl-mor-pholino phosphoramidite.

10) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-N2-isobutyryl-2'-deoxyguanosine-3'-0-beta-cya-noethyl- morpholino phosphoramidite.
11) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxyinosine-3'-0-betacyanoethyl-N,N-dime-thyl amino phosphoramidite.
]2) 5'-0-di-p-anisylphenylmethyl-2'N-(-9-fluorenyl-methyl- oxycarbonyl)-2'-amino-2'-deoxyuridine-3'-0-be-ta-cyanoethyl- N,N~diisopropylamino phosphoramidite.
13) 5'-0-di-p-anisylphenylmethyl-2'N-(-9-fluorenyl-methyl- oxycarbonyl)-2'-amino-2'-deoxyuridine-3'-0-me-thyl-N,N- diisopropylamino phosphoramidite.
14) 5'-0-di-p-anisylphenylmethyl-2'N-(-9-fluorenyl-methyl- oxycarbonyl)-2'-amino-2'-deoxyuridine-3'-0-me-thyl-N,N- dimethylamino phosphoramidite.

1 3 ~ 8 -4~-15) 5'-0-dl-p-anisylphenylmethyl-2'N-(-9-fluorenyl-methyl- oxycarbonyl)-2'-amino-2'-deoxyuridine-3'-0-me-thyl- morpholino phosphoramidite.
16) 5'-0-di-p-anisylphenylmethyl-2'N-(-9-fluorenyl-methyl- oxycarbonyl)-2'-amino-2'-deoxyuridine-3'-0-be-ta-cyanoethyl- morpholino phosphoramidite.
17) 5'-0-di-p-anisylphenylmethyl-2'N-(-9-fluorenyl-methyl- oxycarbonyl)-2'-amino-2'-deoxyuridine-3'-0-p-ni-trophenethyl- N,N-dimethylamino phosphoramiditeO

18) 5'-0-di-p-anisylphenylmethyl-2'N-(-9-fluorenyl-methyl- oxycarbonyl)-2'-amino-2'-deoxyuridine-3'-0-be-ta-cyanoethyl- N,N-dimethylamino phosphoramidite.

19) 5'-0-di-p-anisylphenylmethyl-2'N-(-9-fluorenyl-methyl- oxycarbonyl)-2'-amino-2'-deoxyinosine-3'-0-me-thyl-N,N- diisopropylamino phosphoramidite.

20) 5'-0-di-p-anisylphenylmethyl-2'N-(-9-fluorenyl-methyl- oxycarbonyl)-2'-amino-N6-benzoyl-2'-deoxyade-nosine-3'-0 methyl-N,N-dimethylamino phosphoramidi-te.

21) 5'-0-di-p-anisylphenylmethyl-2'N-(-9-fluorenylme-thyl- oxycarbonyl)-2'-amino-N~-benzoyl-2'-deoxycyto-sine-3'-0-methyl- morpholino phosphoramidite.

22) 5'-0-di-p-anisylphenylmethyl-2'N-(-9-fluorenyl-methyl- oxycarbonyl)-2'-amino-N2-isobutyryl-2'-deoxy-guanosine-3'- 0-beta-cyanoethyl morpholino phospho-ramidite.

23) 5'-0-di-p-anisylphenylmethyl-2'N-(-9-fluorenyl-methyl- oxycarbonyl)-2'-amino-2'-deoxyinosine-3'-0 be-~3~142~

ta-cyanoethyl- N,N-dimethylamino phosphoramidite.

Example 7 5'-0-di-p-anisylphenylmethyl-2'-N-(N--trifluoroacetylglycyl)-2'-amino-2'-deoxyuridine-3'-0-methyl-NtN-diisopropylamino phosphoramidite having the formula:

~H3 H3C0~0 ~2~

cH2~H
H3C0~ N~C~~l3 e~3 1 13~ H3 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-2'-deoxyuridine (1.07 g, 1.5 mmoles) was dissolved in dry dichloromethane ~10 ml, dried by distillation from phosphorous pentoxide and then calcium hydride) containing N,N-diisopropyl-ethylamine (1.3 ml, 5.0 n~oles). The solution was stirred at room temperature under a dry argon atmos-phere, and chloro-N,N-diisopropylaminomethoxyphosphine ~ 3 1 ~
--46~

(0.45 ml, 2.4 n~oles) was added dropwise from a syringe over about one minute. TLC on silica gel 60 F-254 p]ates developed in ethyl acetate:triethylamine (99:1 v/v) indicated that the reaction was complete after thirty minutes. Anhydrous methanol (0.1 ml) was added to decompose excess phosphitylating agent, and the reaction stirred a few minutes longer. The reaction mixture was then transferred to a separatory funnel with ethyl acetate (50 ml, previously washed with 50 ml of cold 10~ (w/v) aqueous sodium carbonate) and washed twice with cold 10% (w/v) aqueous sodium carbonate (80 ml portions), and twice with cold sa-turated aqueous sodium chloride (80 ml portions)O
The organic solution was dried over anhydrous sodium sulfate, filtered, and rotary evaporated under reduced pressure to a clear foam. The foam was dissolved in dry ethyl acetate (10-15 ml) and this solution was added dropwise to hexane (200 ml) at -78C (dry ice-acetone bath). Tlle precipitated product was fil-tered, washed well with -78C hexane, and dried in a vacuum dessicator to yield 1.23 g (1.4 mmoles, 93~) of a white powdery solid. The structure of the product was confirmed by lH NMR spectroscopy in perdeuterated acetonitrile. 31p NMR spectroscopy in perdeuterated acetonitrile showed two singlets at 151.25 and 148.96 ppm (relative to phosphoric acid in perdeuterated acetonitrile) as expected for the diastereomeric phos-phoramidite product, and only very slight traces (<2~) of other phosphorous containing impurities. 19F NMR
spectroscopy in deuterated chloroform showed one singlet at 0.66 ppm (relative to trifluoroacetic acid in deute-rated chloroform). TLC in the above solvent system on silica gel LQ6DF plates showed only one spot under short wave UV detection, Rf 0 91. This spot gave a bright orange color characteristic of the di-p-ani-13~12~

sylphenylmethyl cation when exposed to perchloric acid:ethanol (3:2 v/~).
Similarly, the following compounds are prepared:
1) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-2'-deoxyuridine-3'-0-beta-cya-noethyl- N,N-diisopropylamino phosphoramidite.
2) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl~-2'-amino-2'-deoxyuridine-3'-0-methyl-N, N-dimethylamino phosphoramidite.
3) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trlfluoro-acetyl- glycyl)-2'-amino-2'-deoxyuridine-3'-0-methyl-mor-pholino phosphoramidite.
4) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-2'-deoxyuridine-3'-0-beta-cya-noethyl- morpholino phosphoramidite.
5) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-2'-deoxyuridine-3'-0-p-nitro-phenethyl-N,N- diméthylamino phosphoramidite.
6) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-2'-deoxyuridine-3'-0-betacya-noethyl-N,N- dimethylamino phosphoramidite.
7) 5'-0-di-p--anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-2'-deoxyinosine-3'-0-methyl-N, N-diiso- propylamino phosphoramidite.
8) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-N6-benzoyl-2'-deoxyadenosi.ne-3'-O- methyl-N,N-dimethylamino phosphoramidite.
9) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-N4-benzoyl-2'-deoxycytosine-3'-O-methyl- morpholino phosphoramidite.
10) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-2'-deoxyinosine-3'-0-beta-cya-noethyl-N,N- dimethylamino phosphoramidite.
11) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- g]ycyl)-2'-amino-N5-benzoyl-2'-deoxyadenosine-3'-0- p-~itrophenethyl-N,N-dimethylamino phosphorami-~31~2~

dite.
12) 5'-0-di-p-anisylphenylmethyl-2'-N (N-trlfluoro-acetyl- glycyl)-2'-amino-N4-benzoyl-2'-deoxycytosine-3'-O-beta- cyanoethyl morpholino phosphoramidite.
13) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-9-fluorenyl-methyloxycarbonyl-glycyl)-2'-amino-2'-deoxyuridine-3'-0-beta-cyanoethyl-r~,N-dimethylamino phosphoramidite.
14) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-9-fluorenyl-methyloxycarbonyl-glycyl)-2'-amino-2'-deoxyinosine-3'-0-beta-cyanoethyl-N,N-dimethylamino phosphoramidite.
15) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-9 fluorenyl-methyloxycarbonyl-glycyl)-2'-amino-N6-benzoyl-2'-deoxy-adenosine 3'-0-p-nitrophenethyl-N,N-dimethylamino phosphoramidite.
16) 5'-0-di-p-anisylphenylmethyl-2'-N-(~I-9-fluorenyl-methyloxycarbonyl-glycyl)-2'-amino-N~-benzoyl-2'-deoxy-cytosine-3'-0-beta-cyanoethyl-morpholino phosphorami-dite.

Uses of the Invention 1) Synthesis of oligodeoxyribonucleotides con-taining a 5'-amino terminus.
The steps involved in the use of protected 5'--arnino-nucleoside phosphoramidites for the synthesis of oligodeoxyribonucleotides containing a 5'-amino terminus are shown in the Figure of Example 8, and are described in the following text.
The protected 5l-amino-nucleoside-3'-0-phosphor-amidites, preferably those in which Bn = thymine, X = MMT, R6 = isopropyl, and R7 - methyl or beta-cya-noethyl, most preferably beta-cyanoethyl, are coupled to the 5'-hydroxyl of a growing oligo- deoxyribonuc-leotide attached to a solid support using standard phosphoramidite DNA synthesis techniques (see Atkinson, ~3~1~2~

T., and Smith, M., in "Oligonucleotide Synthesis:
A Practical Approach," Gait, M.J., pp. 35-82, IRL
Press, Oxford, England (1984) and the references cited therein). ~riefly, this procedure consists of reacting a protecte~ 5'-amino-nucleoside 3l_0- phosphoramidite in anhydrous acetonitrile solution with the support-bound oligonucleotide in the presence of lH-tetrazole under inert atmosphere, washing away excess reactants from product on the support, and then oxidizing the phosphite product to the desired phosphate with a solution of iodine in basic aqueous tetrahydrofuran. Generally, a ten-to-twenty-fold excess of phosphoramidite and a fifty-to-one hundred- fold excess of tetrazole over support-bound oligonucleotide are used; for the syn-thesis using the protected 5'-amino phosphoramidites, a twenty-fold excess of phosphoramidite and a one hundred-fold excess of tetrazole are preferred. Under these conditions, the MMT-protected (Example 3) phos-phoramidite routinely couples in better than 90% yield, generally in better than 95% yield. The coupling can be performed manually utilizing a six minute coupl-ing reaction time and a three minute oxidation reaction time, or on an Applied Biosystems Model 380A automated DNA synthesizer (or similar instrument designed to accomodate the phosphoramidite chemistry) utilizing the accompanying pre-programmed synthesis cycles.
The 5'-amino oligonucleotide is then obtained by cleaving the DNA from the support by treatment for at least four hours with concentrated ammonium hydroxide solution at room temperature, followed by deprotection of the DNA bases in the same solution at 55C for twelve to sixteen hours. When R7 = methyl, a treatment with triethylammonium thiophenoxide in dioxane for one hour at room temperature is also re-quired prior to cleavage of the DNA from the support.

~ 3 ~ 2 ~

When X = MMT, the cleavage and deprotection treat-ments in ammonium hydroxide do not af~ect the base-stable, acid-labile MMT amino-protecting group. Thus, the desired product retains the MMT moiety on the 5'-amino group. This MMT group imparts an increased hydropho-bicity to the desired product DNA, resulting in a marked increase in retention time during RP HPLC on a C18 column. The contaminating failure DNA sequences elute from the column much earlier than the desired oligonucleo- tide, which subsequently elutes in a clean and well-resolved fashion. The MMT protecting group can then be removed by mild acid treatment with acetic acid/water ~80:20 v/v) solution at room tem-perature for twenty to thirty minutes, yielding highly purified free amino oligonucleotide.

~31~428 Synthesis of 3'>Ho-CpApTpGpCpTpGpT-NH2<5' using 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythymi-dine~3'0-methyl-N,N-diisopropylamino phosphoxamidite Reaction Scheme for Example 8 ~ ' ' p' A p'T p'G p'C p T p'G-OH ~ ~ x = ~ T
~ co' ~--~-c~
~C~
~H~

I)IH TETRAzoLE
~ 2~12 ~ H20~ THF~ LUTlDlNE

Cp'Ap'Tp'Gp'C p'T p'Gp'T-NH-X

) C6HsSH/E~ OXANE3 20 C
. 2) NH,~OH, 20 /::
1 ~) NH40H, 55 C
. .

1 X=~A~T

HO-C p A p T p G p C p ~ p ~ p T-NH-MMT
WHERE:
I ~O~xOHoAeJ2o%H~o ~3b SUPPO~T
jn ~ ; pq ~ H~C p A p T p l; p C: p T p G p T -N~3 131~2~

The ollgodeoxyribonucleotide 3'>HO-CpApTpGpCpTpG-OH<5' was synthesized manually on an aminopropyl silica support (containing about 4 micromoles of bound 5'-0-dimethoxytrityl-N~-benzoyl-2'-deoxycytidine) using standard phosphoramidite DNA synthesis techniques (Caruthers, M.H., Beaucage, S.L~, Becker, C., Efcavitch, W., Fisher, E.F., Gallupi, G., Goldman, R., deHaseth, F., Martin, F., Mateucci, M., and Stabinsky, Y., in "Genetic Engineering", Setlow, A., and Hollander, J.K., eds., vol. 4, pp. 1-17, Plenum Press, New York (1982)). The 3'-0-methyl-N,N-diisopropylamino phos-phora- midites of 5'-0-dimethoxytritylthymidine, 5'-0-di-methoxy- trityl-N6-benzoyl-2'-deoxyadenosine, 5'-0-dime-thoxytrityl- N4-benzoyl-2'-deoxycytidine, and 5'-0-dime-thoxytrityl- N2-isobutyryl-2'-deoxyguanosine were synthesized according to published procedures (McBridge, L.J., and Caruthers, M.H., Tetrahedron I.ett~ 24, 245-248 (1983)). Spectroscopic analysis of the yield of dime-thoxytrityl cation after each cycle of the synthesis indicated an overall yield of 88.8% for the heptamer, for a stepwise yield of 97.7%. The support was treated with the MMT-protected phosphoramidite. A twenky-Eold excess of phosphoramidite and a one hundred-fold excess of lH-tetrazole over support-bound oligodeoxyribonucleo~
tide was used, with a six minute coupling reaction time and a three minute oxidation reaction time.
After washing and drying, the support was treated for one hour with triethylammonium thiophenoxide in dioxane, washed well, dried, and treated for four hours at room temperature with concentrated ammoniurn hydroxide in a tightly capped conical centrifuge tube.
The supernatant was then decanted from the support, another aliquot of concentrated ammonium hydroxide added, and the solution heated at 55C for 16 hours in a tightly sealed tube (rubber septum). The DNA-con-taining solutions were then aliquoted into 1.5 ml ~3~2~

Eppendorf tubes, lyophilized, and the resulting pellets dissolved in water. An aliquot of the oligonucleotide solution was then chromatographed on a RP HPLC system consisting of two Altex llOA pumps, a dual chamber gradient mixer, a Rheodyne injector, a Kratos 757 UV-VIS detector, and an Axxiom 710 controller. A
Vydac C18 column (5 micron, 25 cm) was used.
Amino oligonucleotide derived from ~MT-protected 5'-amino-5'-deoxythymidine phosphoramidite was first chromatographed as the dimethoxytritylated adduct, using a linear gradient of 20~ buffer B/80P~ buffer A to 60% buffer B/40~ buffer A over forty minutes (buffers A and s as described above). The product eluted at 39 minutes under these conditions (1 ml/minute flow rate). A preparative run of the ~T product was performed, the product collected and lyophilized, and the pellet treated with acetic acid/water (80:20 v/v) at room temperature for twenty minutes. Following lyophilization and re-dissolution in water, an aliquot was chromatographed using the same conditions as for the Fmoc-derived oligonucleotide. The product eluted at 17.5 minutes. The purified amino oligonucleotide had UV spectrum typical of DN~ (major peak at 260 nm).
The following compounds may be employed in a similar fashion to prepare the correspondin~ 5'-amino oligonucleotides:
1) 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythy-midine- 3'-0-methyl-N,N-diisopropylamino phosphorami-dite.
2) 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythymi-dine- 3'-0-methyl-N,N-dimethylamino phosphoramidite.
3) 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythymi-dine- 3'-0-methyl morpholino phosphoramidite.
4) 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythymi-~3~%~

dine- 3'-0-beta-cyanoethyl morpholino phosphoramidite.
5) 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythymi-dine- 3'-0-p-nitrophenethyl-N,N-dimethylamino phospho-ramidite.
6) 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythymi-dine- 3'-0-betacyanoethyl-N,N-dimethylamino phosphora-midite.

2) Synthesis in aqueous solution of oligodeoxy-ribonucleotides containing a fluorescent moiety on the 5'-terminus.
The presence of a nucleophilic aliphatic amino group on the 5'-end of an oligonucleotide allows for further reaction of the amino DNA with a variety of electrophilic reagents, notably amino reactive fluores-cent dye derivatives. Such dye derivatives include, but are not restricted to, fluorescein isothyiocyanate, tetramethylrhodamine isothiocyanate, eosin isothiocya-nate, erythrosin isothiocyanate, rhodamine X isothio-cyanate, lissamine rhodamine B sulfonyl chloride, Texas Red, Lucifer Yellow, acridine-9-isothiocyanate, pyrene sulfonyl chloride, 7-diethylamino-4-methylcGu-marin isothiocyanate, and 4-fluoro-and 4~chloro-7-nitro-benz-2- oxa-1,3-diaæole and their derivatives, such as succinimidyl 12-(N-methyl-N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)) aminododecanoate. The resultant dye-oligo-nucleotide conjugates may then be used for a variety of diagnostic or detection purposes.
The basic procedure used for attaching dye mole-cules to an amino oligonucleotide is to combine the amino DNA and the dye in an aqueous (or aqueous/organic) solution buffered at pH 9, allow it to stand at room temperature for several hours, and then to purify the product in two stages. Excess unreacted dye is removed from dye-DNA conjugate and unreacted DNA by ~3~1~28 ~55~

gel filtration. After lyophilization, pure dye-DNA
conjugate is obtained using RP HPLC.

Conjugation of fluorescein-5-isothiocyanate with 3'>Ho--CpApTpGpCpTpGpT-NH2<5' Reaction Scheme For Example 9.
.

HO~O~f~O
3' 5' ~J
H~CpApTp~ipCpTpGpT-NH2 ~ ~,C0 N-C=S

pH 9 ~ .

HO~O

~f~co2~
3' 5' HO-~;p Ap Tp Gp C p~ p GpT-NH-,C,-NH

WHERE: p. ~ _ 0~

~3~4~

5'-amino oligonucleotide was synthesized as described in Example 8. The purified amlno oligonucleotide (75 ul of a 1200 ug/ml solutlon in water) is diluted with water (105 ul) and 1 M aqueous sodium bicarbo-nate/sodium carbonate buffer, pH 9 (50 ul). A solution of fluorescein- 5-isothiocyanate (FITC) in DMF (20 ~g/ml, 20 ul) is added, and the yellow solution mixed well and allowed to sit in the dark overnight at room temperature (about 12-16 hours). The reaction m xture was then applied to a column (10 ml) of Sephadex G-25 (Pharmacia Fine Chemicals) packed in water in a 10 ml disposable plastic pipet, and the column was eluted with water. The fast moving yellow band (fluorescent under long wave UV) that eluted with the void volume of the column was collected. Unreacted dye remained nearly immobile at the top of the column. The crude dye-DNA conjugate was then lyophilized, dissolved in water, and subjected to RP HPLC~ A Kratos FS970 LC fluorometer was used in conjunction with the UV
detector in the system described in Example 8 to iden-tify the desired product. A linear gradient of 10%
buffer B/90% buffer A to 30% buffer B/70% buffer A
over thirty minutes was used (buffers A and B are as described in Example 8). A small amount (<10%) of the starting amino oligonucleotide was eluted at 17.5 minutes (1 ml/minute flow rate), followed by a small amount of a fluorescent species at 29 minutes and the desired fluorescent product (the major product) at 33 minutes (UV detection at 260 nm, fluorescent excitation at 240 nm and detection using a S25 nm band pass filter). The purified fluorescent oligo-nucleotide had a UV absorbance maximum at 260 nm (cha-racteristic of DNA) and a visible absorbance maximum at 496 nm (characteristic of fluorescein).
Similar conjugates can be obtained by using Texas ~"~ c~ ncl~

~3~ 2~

Red, tetramethyl rhodamine isothiocyanate, eosin iso-thio- cyanate, erythrosin isothiocyanate, rhodamine X isothiocyanate, lissamine rhodamine B sulfonyl chlo-ride, pyrene sulfonyl chloride, 7-diethylamino-4-methyl-coumarin isothiocyanate, Lucifer Yellow, acridine-9-iso-thiocyanate, 4-fluoro-7- nitrobenz-2-oxa-1,3-diazole, and 4-chloro-7-nitrobenz- 2-oxa-1,3-diazole.

3) Synthesis of oligodeoxyribonucleotides con-taining a fluorescent moiety on the 5'~terminus uti-lizing a solid support.
The two step purification described in Example 9 can be avoided by reacting the fluorescent dye di-rectly with the oligonucleotide containing a free 5'-amino group while it is still covalently linked to the support. In this case, experience has determined that the oligonucleotide must be assembled using the beta-cyanoethyl phosphorous-protected phosphoramidite monomers. This is necessary as the beta-cyanoethyl groups may be removed from the oligonucleotide phosphate triesters to give phosphate diesters under basic, anhydrous conditions, such as 20% ~v/v) tertiary amine in anhydrous pyridine or 0.5 M 1,8-diazabicyclo [5.4.0]
undec-7-ene (DBU) in anhydrous pyridine, at room tempe~
rature. Sueh treatment does not otherwise affect the DNA, nor does it cleave appreciable amounts from the support if strictly anhydrous conditions are ob-served. Generation of diesters is eritieal as the triester-eontaining oligonucleotide having a free amino group is unstable to the basic eonditions needed to effeet rapid reaetion with the dye, and degrades to an as yet uneharaeterized DNA-like speeies no longer having an aceessible amino terminus. Conversion to the dies-ter form retards this degradation.

13~4L2~

It is also necessary to employ an acid-labile protecting group such as p-anisyldiphenylmethyl (MMT) on the 5'-amino-5' deoxythymidine phosphoramidite to introduce the S'-amino terminus into the oligonucleo-tide. This is required as the MMT group is stable to the basic conditions needed to remove the phosphate protecting groups, where it is needed to prevent the basic degrada- tion of the DNA described previously, but can subsequently be removed using mildly acidic conditions under which the DNA remains linked to the support, thus affording a free amino oligonucleotide for reaction with dye.
Dye conjugation to the amino oligonucleotide is carried out using an excess of dye (ten-to-one hundred-fold) in concentrated solution in anhydrous N,N-dimethylformamide/tertiary amine, preferably N,N-diisopropylethylamine t90:10 v/v) or triethylamine ~80:20 v/v). After twelve to twenty-four hours, the excess dye is washed away, the dye-DNA conjugate is cleaved from the support, and the base-protecting groups are removed using concentrated ammonium hydroxide under the standard conditions described in Example 8. The product is then purified by RP HPLC.

13~2~

Example 10 Conjugation of eosin-5-isothiocy~nate and Texas Red with 3'>HO-TpTpTpTpTpTpT-NH2<5' on a solid support Reaction Scheme for Example lQ

~ ,I~T p'Tp'T p'T p'T p'T pT p'~ NHMMT

0-~ ~ CIIU W Ç~t5N

(~ _~TpTpTpTpTpTpTpT NllMM~

11 110% HOAc~ 20 Y. H20 ~ 21 20 ~ E1~5N IN C6H5N

(~O-T p T p T p T p T p T p T pT NH2 ¦ D`fE IN 10 X liF'rl2NE~ IN DMF
~TEXAS RED

H

=~'D
OTpTpTpTpTpTpTpT-NH~H (~OTpTpTpTpTpTpTpT-l'lH

j 2I Nl~OH, 5~ C ¦ ~ ) NH$H ~ 20~C

H~sO (~

~toTpTpTpTpTpT~TpT-NH~H HO-TpTpTpTpTpT~'rpT-NI~

WME~:
~ ~2C~ o SOLID

~3~2~

The oligodeoxyribonucLeotide 3'?~1~-TpTpTpTpTpT-OH<5' was synthesized as described in Example 8 on a controlled pore glass support on a one micromole scale using beta-cyanoethyl-protected phosphoramidites (obtained from American BioNuclear Corporation or synthesized as described in Example 3). Analysis of the yield of dimethoxytrityl cation after each cycle indicated an overall yield of 89.6% for the hexamer, for a stepwise yield of 97.8%. The final addition of 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythymidine-3'-0-beta-cyanoethyl-N,N-diisopropyl-amino phosphoramidite was performed as described in Example 8.
An aliquot of the fully protected, support-bound amino oligonucleotide containing about 0.5 umole of DNA (about 20 mg of support) was then treated with a mixture of a 5% (w/v) solution of N,N~dimethylamino-pyridine (Aldrich Chemical Company) in anhydrous pyri-dine (500 ul) and a 10% (w/v) solution of p-anisyldi-phenylmethyl chloride in anhydrous pyridine (500 ul) for one hour at room temperature. This was done in order to insure that all terminal amino groups were protected, and is probably unnecessary if the dye conjugation is to be performed soon after the oligo-nucleotide synthesis. The support was next washed well with dry pyridine and treated for two hours with 0.5 M DBU in anhydrous pyridine at room temperature.
The support was again washed well with pyridine and then with diethyl ether and air dried. An aliquot (about 4 mg) was taken and cleaved, deprotected, and subjected to RP HPLC as usual as a control.
The dry support-bound MMT-protected amino oligo-nucleotide was detritylated for twenty minutes at room temperature with acetic acid/water (80:20 v/v).
The support was then washed with water and methanol, and treated for two minutes with triethylamine in ~ 3 ~
~61-anhydrous pyridine (20:80 v/v) to generate the free amine from the acetate salt. It was washed with pyri-dine and ether and air and vacuum dried. An aliquot (4 mg) was taken and cleaved, deprotected, and subjected to RP HPLC as usual as a control.
The dye conjugation reactions were carried out in 1.5 ml Eppendorf tubes. Dyes were obtained from Molecular Probes Inc., Junctlon City, Oregon. About 0.1 umole of support-bound amino oligonucleotide (4-5 mg) was treated with either eosin-5-isothiocyanate (3.5 mg, a 50-fold excess) or Texas Red (2.4 mg, a 38-fold excess) in anhydrous DMF containing 10% (v/v) N,N-diisopropylethylamine (50 ul). The reactions were allowed to proceed in the dark for 12 to 16 hours at room temperature. The reaction mixture was then transferred to a small glass-fritted funnel and washed well wlth DMF, methanol, and ether, and air dried.
At this point, the eosin-conjugated support was pink and the Texas Red-conjugated support was purple.
Both supports fluoresced strongly under long wave UV light.
Each dye-DNA conjugate was cleaved from its support as described in Example 8 (four hours at room tempe-rature in concentrated ammonium hydroxide), and sub-jected to base-deprotection conditions (twelve hours at 55C in concentrated ammonium hydroxide). Although unnecessary for a poly-T oligonucleotide, this latter treatment was performed to test the effect of the treatment on the dye moiety and the dye-DNA linkage~
The strongly fluorescent orange (eosin) and pink-red (Texas Red) dye-DNA solutions were then lyophilized, dissolved in water~ and each fluorescent oligonucleo~ide purified by RP HPLC using a linear gradient of 10%
buffer B/90% buffer A to 30% buffer B/70% buffer A
over ten minutes, then 30% buffer B/70% buffer A to 60% buffer B/40~ buffer A over ten minutes (buffers ~3~7 42~

A and s as described in Example 8).
~ PLC analysis of the two dye-oligonucleotide conjugates indicated that, in the case of eosin-5--isothiocyanate, the reaction had proceeded to about 80~ completion, as judged from the disappearance of starting amino oligonucleotide, while in the case of Texas Red, a sulfonyl chloride, the reaction had proceeded to only about 20-30~ completion. In each chromatogram, a peak representing underivatized amino oligonucleotide was observed at 16 minutes. The desired eosin-DNA conjugate eluted from the column at 25 mi-nutes, and the Texas Red-DNA conjugate at 29.5 minutes.
Control HPLC analyses of the starting amino oligonucleo-tide and of each fluorescent oligonucleotide separately synthesized using the solution method described in Example 5 confirmed the above assignments. In addition, while the Texas Red-oligonucleotide appeared unharmed by the deprotection conditions, the eosin-oli~onucleo-tide did appear to have suffered a small amount of degradation. However, in both cases, the overal]
yield of dye-DNA conjugate using the solid phase method was as good or better than that using the solution method, and the workup and purification was much simpler.
The UV-visible spectrum of each purified dye-DNA con-jugate showed two major peaks, as anticipated: for the eosin- oligonucleotide, one at 262 nm (DNA absorb-ance), and one at 524 nm ~dye absorbancel; and for the Te~as Red-oligonucleotide, one at 262 nm (DNA
absorbance), and one at 596 nm (dye absorbance~.
Similar conjugates can be obtained by using fluor-escein isothiocyanate, tetramethyl rhodamine isothio-cyanate, eosin isothiocyanate, erythrosin isothiocya-nate, rhodamine X isothiocyanate, lissamine rhodamine B sulfonyl chloride, pyrene sulfonyl chloride, 7-die-thylamino-4-methylcoumarin isothiocyanate, 4-fluoro-7-ni-~ 3 ~

trobenz-2-oxa-1,3-diazole, 4-chloro-7-nitrobenz-2-oxa-1, 3-diazoler acridine-9- isothiocyanate, and Lucifer Yellow.

4) Synthesis of oligodeoxyribonucleotides con-taining one or more internal aliphatic amino groups.
The trifluoracetyl-protected (Tfa-protected) 2'-amino-2'-deoxyuridine-3'-0-phosphoramidites described in the section entitled "Compositlon of Matter No.
4" can be used to synthesize oligodeoxyribonucleotides containing one or more free amino groups at internal positions in the DNA oligomer. This is possible since the position of the amino group (that is, on the 2'-car--bon atom of the sugar ring) in these compounds is not involved in the formation of the 3',5'-phospho-diester backbone of the DNA chain. As such, these compounds may be coupled to the 5'-hydroxyl of a growing oligo- deoxyribonucleotide attached to a solid support using the standard phosphoramidite DNA synthesis tech-niques described in Example 8. Unlike the protected 5'-amino- 5'-deoxythymidine compounds, whose use forces the termination of the growing DNA chain due to the presence of the amino group on the 5'-terminus~ the 5'-0-di-p- anisylphenylmethyl group present on the 5'-hydroxyl of the Tfa-protected 2'-amino-2'deoxyuridine compounds may be removed in the next cycle of the synthesis allowing for further elongation of the syn-thetic oligonucleotide by the usual procedure. Since a Tfa-protected 21-amino- 2'-deoxyuridine unit can be inserted at any position in the chain, the resultant oligomer can contain any desired number of reactive amino groups.
These compounds can be coupled to a growing DNA
chain using the chemistry outlined in Example 8; how-ever, the presence of a group other than hydrogen at the 2'-position necessitates the use of longer ~6~-coupling times to achieve a coupling efficiency similar to that observed using normal deoxyribonucleotide phosphoramidites. Once again, a ten-to-twenty-fold excess of phosphoramldite and a fifty-to-one hundred-fold excess of lH-tetrazole over support-bound oligonucleo-tide are required; the larger excesses are strongly preferable in this case. Coupling times using these quantitites are generally one to one and one-half hours, as opposed to the six minutes used for normal phosphoramidite couplings. Since the Tfa-protected 2'-amino-2'-deoxyuridine phosphoramidites appear to undergo some degradation during this longer coupling time, two or three shorter couplings (twenty to thirty minutes each) are preferable to one extended coupling.
Under these conditions, the Tfa-protected 2'-amino-2'-deo-xyuridine-3'-0-phosphor- amidites (Examples 6 and 7) routinely couple in better than 80% yield, and generally in better than 85~ yield.
The oligonucleotide product containing one or more internal amino groups is then obtained using the standard cleavage and deprotection conditions outlined in Example 8. Since the Tfa group is base-labile, it is easily removed during the concentrated ammonium hydroxide treatmen-ts, yielding an oligonucleo-tide product containing the desired number of free amino groups. After lyophilization, the product DNA
may be purified either by RP HPLC or by gel electro-phoresis, as described previously. Furthermore, the crude product DNA can be obtained containing a 5'-0-di-p-anisylphenylmethyl group, thus simplifying RP HPLC
purification in a manner analogous to that described for the 5'-N-p-anisyldiphenyl- methyl group.

13~1~2~
~65-Example 11 Synthesis of 3'>HO-CpApTpGpCpU(2'-NH2)pGpT-OH<5' using 5'-0-di-p-anisylphenylmethyl-2~-N-trifluoroacetyl~
2'-amino-2'-deoxyuridine-3'-0-methyl-N,N-diisopropyl-amino phosphoramidite, and of 3'~HO-CpApTpGpCpU(2'-NHCOCH2-NH2) pGpT-OH<5' using 5'-O-di-p-anisylphenylmethyl-2'-N-(N- trifluoracetylglycyl)-2'-amino-2'-deoxyuridine-3'-0-methyl-N,N-diisopropylamino phosphoramidite 131~2,~

Reactlon Scheme for Example 1~

3' 5' 0~ jA j- ~G~'C-~ccr~ ____ ~to~ ~ c iH ~ETR~ILE~ It~l TE~R~ZOLE
21 2 M2O'TMF~2~-LUTIDIN 2) l2~H2o~TMF~2~ -uTlDiNE
S) 2 2jj-LUT~OINE 3) AC202~DMAP~ TrgF~
4) H' . t , 4) H

O-C p'~ p'T p'G p'C p'U-QH ~~O-C p A p T p G p C p U OH
(~ F~CCONH F3CCONHCH2CONH

3 , 5 o-Cp Ap Tp Gp C p Up'Gp'T-OOMT
~0 C p'~ p~T p'G p C p lJ~ipT ODMr (~ FSCCONHCH2CON2, ;2 11 C6M~5H/Et N/~tlOX~NE~ Z0'C

21 NH~tOH ~ 20~C
~I Nil~tOM~ 55 C

HOCpApTpGpCpUpGpT-ODMr HO-CpApTPGpcpupGpTolMT
P~H2 H2NcH?coNH
~10 ~. HOAc ~ 20 % H20 llo-Cp~pTPGpcpupGproH HO-CpApTPGpcpupGpT-~l~tEl~ SU~ORT; i~; P~

~31~L42~

The oligodeoxyribonucleotide 3'~HO-CpApTpGpC-OH<5' was synthesized manually on an aminopropyl silica support as described in Example 8. The support was then split into two equal portions. One portion was used in a coupling with 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxyuridine (DMT-TfaNHdU) phosphoramidite, and the other in a coupling with 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoroacetyl-glycyl)-2'-amino-2'-deoxyuridine (DMT-TfaGlyNHdU) phosphoramidite. In each case, two sequential couplings of thirty minutes each were performed prior to the oxidation reaction, with the support being washed well with anhydrous acetonitrile between couplings.
In each coupling, a twenty-fold excess of phosphoramite and a one-hundred-fold ~xcess oE lH-tetrazole were used. Under these conditions, both the DMT-TfaNHdU
phosphoramidite and the D~T-TfaGlyNHdU phosphoramidite coupled in 83-85% yield (as judged by the yield of dimethyoxytrityl cation after this cycle). After a three minute oxidation reaction and a three minute capping reaction, the last two nucleotide phosphora-midites were coupled to the amino uridine-containing oligonucleotide. In each case, the first of these two couplings proceeded in better than 98% yield;
the final di-p-anisylphenylmethyl group was retained on the 5'-end of each oligonucleotide in order to simplify RP HPLC purification.
After washing and drying, each aliquot of the support-bound oligonucleotide was treated under the standard cleavage and deprotection conditions described in Example 8, lyophilized, and dissolved in water.
An aliquot of each solution was then subjected to RP HPLC analysis using the system described in Example 8. A linear gradient of 20% buffer B/80% buffer A

~L31~2~

to 60~ buffer s/40% buffer A (buffers A and B as des-cribed in Example 8) over forty minutes was used to purify each tritylated adduct. soth the U(2'-NH2)-containing oligonucleotide and the U(2'-NHCOCH2NH2)-containing oligonucleotide eluted at 39 minutes under these conditions (1 ml/minute flow rate). A preparative purification was performed for each oligonucleotide, the product collected and lyophilized, and the pellet treated with acetic acid/water (80:20 v/v) for thirty minutes at room temperature to remove the 5'-di-p-ani-syl- phenylmethyl group. Following lyophilization and re-dissolution in water, an ali~uot of each solution was chromatographed using a linear gradient of 10~
buffer B/90% buffer A to 30% buffer B/70% buffer A
over thirty minutes. Under these conditions (1 ml/minute flow rate), the U(2'-NH2)-containing octamer eluted cleanly at 18 minutes (UV detection at 260 nm), while the U(2'-NHCOCH2NH2)-containing octamer eluted slightly less cleanly at 19 minutes. No peak eluting at 18 minutes was seen in this latter chromatogram, indicating that little if any of the glycine moiety had been hydrolyzed from the DNA by any chemical treatment during the synthesis. Both purified 2'-amino oligo-nucleotides had UV spectra typical of DNA (major peak at 260 nm).
The following compounds may be employed in a similar fashion to prepare the corresponding 2' amino oligonucleotides:
1) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2l-deoxyuridine-3'-0-beta-cyanoethyl-N,N-diisopropylamino phosphoramidite.
2) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxyinosine-3'-0-methyl-N,N~diisopropyl-amino phosphoramidite.
3) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-N6-benzoyl-2'-deoxyadenosine-3'-0-methyl-N,N-diisopropylamino phosphoramidite.
4) 5'-0-di-p-anisylphenylmethyl-2l-N~-trifluoroacetyl-2'-amino-2'-N4-benzoyl-2'-deoxycytosine-3'-0-methyl-N,N-diisopropylamino phosphoramidite.
5) 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-N2-isobutyryl-2'-deoxyguanosine-3'-0-methyl-N,N-diisopropylamino phosphoramidite.
6) 5'-0-di-p-anisylphenylmethyl-2'-N-(9-fluorenylme-thyl oxycarbonyl)-2'-amino-2'-deoxyuridine-3'-0-methyl-N,N- diisopropylamino phosphoramidite.
7) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2l-amino-2'-deoxyuridine-3'-0- beta-cya-noethyl- N,N-diisopropylamino phosphoramidite.
8) 5'-0-di-p-anisylphenylmethyl-2l-N-(N-trifluoro-acetyl- glycyl)-2l-amino-2'-deoxyuridine-3l-0-methyl-N, N-dimethylamino phosphoramidite.
9) 5l-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-2'-deoxyuridine-3'-0-methyl--mor-pholino phosphoramidite.
10) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-2'-deoxyuridine-3'-0-beta-cya-noethyl- morpholino phosphoramidite.
11) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-2'-deoxyuridine-3'-0-p-nitro-phenethyl- N,N-dimethylamino phosphoramidite.
12) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-2'-deoxyuridine-3'-0-beta-cya-noethyl- N,N-dimethylamino phosphoramidite.
13) 5l-0-di-p-anisylphenylmethyl-2l-N-(N-trifluoro-acetyl- glycyl)-2'-amino-2l-deoxyinosine-3'-0-methyl-N, N-diisopropyl- amino phosphoramidite.
14) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-N6-benzoyl-2'-deoxyadenosine-3'-0-methyl-N,N-diisopropylamino phosphoramidite.
15) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl) 2l-amino-N4-benzoyl-2l-deoxycytosine-~31~2~

3'-0- methyl-N,N-diisopropylamino phosphoramidite.
16) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetyl- glycyl)-2'-amino-N2-isobutyryl-2'-deoxygua-nosine-3'-0- methyl-N,N-diisopropylamino phosphorami-dite.
17) 5'-0-di-p-anisylphenylmethyl-2'-N-(N-9-fluorenyl-methyloxycarbonyl-glycyl)-2'-amino-2'-deoxyuridine-3'-0-methyl-N,N-diisopropylamino phosphoramidite.

5) Synthesis in aqueous solution of oligodeoxy-ribonucleotides containing one or more fluorescent moieties at internal 2'-positions.
As has been described in Section 2, the presence of an aliphatic amino group in an oligonucleotide allows for further reaction of the DNA with a variety of reagents. In the case of fluorescent dyes, enhanced detection sensitivity may be achieved by conjugating more than one dye molecule to an oligonucleotide, thus increasing the amount of fluorescence per oligomer.
The ability to incorporate any desired number of amino groups into an oligonucleotide via the 2'-amino-2'-deoxyuridinQ phosphoramidites can be utilized to achieve this enhancement.
The basic procedure for conjugating a fluorescent dye to a 2'-amino oligonucleotide is the same as that described in Example 9.

71- ~31~2~

Example 12 Conjugation of fluorescein-5-isothiocyanate with 3'~HO-CpApTpGpCpU~2'-NH2~pGpT-OH<5' and 3'>HO-CpApTpGpCpU(2'-NHCOCH2NH2)pGpT-OH<5' i 13~2~

Reaction Scheme for Example 12 A ) HO-C p A p T p G p C P U pG prOH ~ HO~O
~co2~
NCS
pH 9 HOCp Ap Tp Gp C p UpGpTOH

C- S

~C02H

O~OH

HO-C p A p T p G p C p UpGprOH ~ HO~

¢~C02H

pH 9 ! NCS

~10-Cp Ap Tp Gp C P UpGpT-OH
~NCH2CO~H
~-S
NH

~ C02H

o~f ~OH

Wl ~ER p~

2 ~

The 2'-amino oligonucleotides were synthesized as described in Example 11. Each of the purified amino oligonucleotides (75 ul of a 600-1000 ug/ml solution in water) was diluted with water (105 ul) and 1 M aqueous sodium bicarbonate/sodium carbonate buffer, pH 9 (50 ul) ln 1.5 ml Eppendor~ tubes. A
solution of fluorescein-5-isothiocyanate (FITC) in DMF ~20 mg/ml, 20 ul) was added, and the yellow solution mixed well and allowed to stand at room temperature overnight in the dark (about 12-16 hours). Each re-action mixture was then applied to a separate column (10 ml) of Sephadex G-25 packed in water in a 10 ml disposable plastic pipet, and the column was eluted with water. The fast moving yellow band (fluorescent under long wave UV) that eluted with the void volume of the column was collected in each case. The crude dye-DNA conjugates were then lyophilized, dissolved in water, and subjected to RP HPLC using the system described in Example 9. ~ linear gradient of 10%
buffer B/90% buffer A to 30~ buffer B/70~ buffer A
over thirty minutes was used (buffers A and B as des-cribed in Example 8), and a flow rate of 1 ml/minute.
In the case of the U(2'-NH-E'ITC)-containing oligo-nucleotide, two major peaks were observed. The starting 2'-amino oligonucleotide eluted at 18 minu-tes as ex-pected, while the fluorescent product dye-oligonucleo-tide conjugate eluted at 26 minutes (UV detection at 260 nm, fluorescent excitation at 240 nm and de-tection using a 525 nm band-pass filter). The fluo-rescent product accounted for about 50% of the total amount of amino-containing DNA present in the sample.
In the case of the U(2'-NHCOCH2NH-FITC)-containing oligonucleotide~ three major peaks were observed.
The starting 2'-amino oligonucleotide eluted at 20 minutes as expected. The second major peak at 20.5 .~ 3 ~

minutes was also observed as a contaminant in the chromatogram of the starting 2'-amino oligonucleotide.
The fluorescent product dye-oligonucleotide conjugate eluted at 28 minutes. In this case, however, the fluorescent product accounted Eor at least 90% of the total amount of amino-containing DNA in the sample.
The substantially higher degree of conjugation can be attributed to the presence of the glycine moiety on the 2'-amino group. Not surprisingly~ moving the reactive amino group away from the sugar ring and thus reducing the steric hindrance to its access by dye increases the amount of dye-DNA conjugate obtained.
Therefore, it is possible to control the degree of reactivity of the amino group by adjusting the length of the spacer, thus controlling its distance from the sugar ring.
Both purified fluorescent oligonucleotides had a UV absorbance maximum at 260 nm (characteristic of DNA) and a visible absorbance maxi~um at 496 nm (characteristic of fluorescein).
The above can also be carried out by using Texas Red, tetramethyl rhodamine isothiocyanate, eosin iso-thiocyanate, erythrosin isothiocyanate, rhodamine X isothiocyanate, lissamine rhodamine B sulfonyl chlo-ride, Lucifer Yellow, acridine-9-isothiocyanate, pyrene sulfonyl chloride, 7-diethylamino-4-methylcoumarin isothiocyanate, 4-fluoro- 7-nitrobenz-2-oxa-1,3~dia~ole, and 4-chloro-7-nitrobenz- 2-oxa 1,3-diazole.
Having fully described the invention, it is in-tended that it be limited solely by the lawful scope of appended claims.

Claims

1. Novel protected amino nucleoside phosphoramidites having the formula:

wherein B is selected from the group consisting of a nucleoside base, a nucleoside base analog, or their protected derivatives;
R1, R2 and R5 are defined as follows: R1, R2 and R5 are either H, OR, or NHR', with the proviso that at most only one of R1, R2 or R5 must be NHR', wherein R is a monovalent organic group containing up to 25 carbon atoms, R' is a nitrogen protecting group which is acid labile, or base labile protecting group selected from the group consisting of trifluoroacetylglycyl, 4-toluene-sulfonylethyl-oxycarbonyl, methylsulfonylethyl-oxycarbonyl, 2-cyano-t-butyl-oxycarbonyl; chloracetyl, aceto-acetyl, 2-nitro-benzoyl, dithiasuccinoyl, maleoyl, isonicotinyl,

2-bromoethyloxy-carbonyl, and 2,2,2-trichloroethyloxycarbonyl, with the proviso that when R1 or R2 is NHR', then R' is any of the foregoing groups, or trifluoroacetyl or 9-fluoroenylmethyloxy-carbonyl; R6 is lower alkyl or when (R6)2 is taken with the N of the P-N bond it forms a heterocyclic group; and R7 is lower alkyl, cyano-lower alkyl, halo-lower alkyl, or nitrophenyl lower alkyl.

2. Novel protected 5'-amino nucleoside phosphoramidites having the generic formula:

wherein B is selected from the group consisting of a nucleoside base, or a nucleoside base analog, or their protected derivatives; X1 is selected from p-anisyldiphenylmethyl, triphenylmethyl, and protected amino acyl having the formula-Y-NH-(CHR)n-CO
wherein Y is selected from the group consisting of trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-anisyldiphenylmethyl, and triphenylmethyl;
n is an integer from 1 to 100, R is an amino acid side chain or hydrogen when n = 1; and R is hydrogen when n is an integer from 2 to 100;
R1 is selected from the group consisting of lower alkyl (in which case m = 2) and heterocyclic which includes the nitrogen of the P-N bond (in which case m = 1), and R2 is selected from the group consisting of methyl, beta-cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl.

3. The compounds of Claim 2 wherein X1 is p-anisyldiphenylmethyl.

4. The compounds of Claim 2 wherein X1 is tri-phenylmethyl.

5. The compounds of Claim 2 wherein X1 is N-tri-fluoroacetylglycyl.

6. The compounds of Claim 2 wherein B is thymine.

7. The compounds of Claim 2 wherein B is uracil.

8. The compounds oE Claim 2 wherein R2 is methyl.

9. The compounds of Claim 2 wherein R2 is beta-cyanoethyl.

10. The compounds of Claim 2 wherein R1 is methyl.

11. The compounds of Claim 2 wherein R1 is isopropyl.

12. The compounds of Claim 2 wherein R1 is morpholino.

13. The compounds of Claim 2 wherein B is thymine and X1 is p-anisyldiphenylmethyl.

14. The compounds of Claim 2 wherein B is thymine and X1 is a triphenylmethyl.

15. The compounds of Claim 2 wherein B is thymine and X1 is N-trifluoroacetylglycyl.

16. The compounds of Claim 2 wherein B is uracil and Y is trifluoroacetyl.

17. The compounds of Claim 2 wherein B is uracil and Y is 9-fluoroenylmethyloxycarbonyl.

18. The compounds of Claim 2 wherein B is uracil and X1 is p-anisyldiphenylmethyl.

19. The compounds of Claim 2 wherein B is uracil and X1 is triphenylmethyl.

20. The compounds of Claim 2 wherein B is uracil and X1 is N-trifluoroacetylglycyl.

21. 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythymidine-3'-O-beta-cyanoethyl-N,N diisopropylamino phosphoramidite having the formula:

22. 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythymidine-3'-0-methyl-N,N-diisopropylamino phosphoramidite.

23. 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythymidine-3'-0-beta-cyanoethyl-N,N-dimethylamino phosphoramidite.

24. 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythymidine-3'-0-methyl-N,N dimethylamino phosphoramidite.

25. 5'-N-triphenylmethyl-5'-amino-5'-deoxythymidine-3'-0-beta-cyanoethyl-N,N-diisopropylamino phosphoramidite.

26. Novel protected 2'-amino-nucleoside phosphoramidites having the generic formula:

wherein B is selected from the group consisting of a nucleoside base, or a nucleoside base analog, or their protected derivatives; X1 is selected from trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-anisyldiphenylmethyl, triphenylmethyl, and protected amino acyl having the formula:
Y-NH-(CHR)n-CO

wherein Y is selected from the group consisting of trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-anisyldiphenylmethyl, and triphenylmethyl;
R is an amino acid side chain or hydrogen when n=1; and R is hydrogen when n is an integer from 2 to 100;
R1 is selected from the group consisting of lower alkyl (in which case m=2) and when m = 1 and R1 is taken in conjunction with the N of the P-N bond it forms a heterocyclic group, and R2 is selected from the group consisting of methyl, beta-cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl; and X2 is a hydroxyl protecting group selected from triphenylmethyl, p-anisyldiphenylmethyl, di-p-anisylphenylmethyl, and 9-phenyl-xanthenyl.

27. The compounds oE claim 26 wherein X1 is trifluoroacetyl.

28. The compounds of claim 26 wherein X1 is 9-fluoroenylmethyloxycarbonyl.

29. The compounds of claim 26 wherein X1 is N-trifluoroacetylglycyl.

30. The compounds of claim 26 wherein B is uracil.

31. The compounds of claim 26 wherein R1 is methyl.

32. The compounds of claim 26 wherein R1 is isopropyl.

33. The compounds of claim 26 wherein R1 is morpholino.

34. The compounds of claim 26 wherein R2 is methyl.

35. The compounds of claim 26 wherein R2 is beta-cyanoethyl.

36. The compounds of claim 26 wherein B is uracil and X1 is trifluoroacetyl.

37. The compounds of claim 26 wherein B is uracil and X1 is 9-fluoroenylmethyloxycarbonyl.

38. The compounds of claim 26 wherein B is uracil and X1 is N-trifluoroacetylglycyl.

39. 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl 2'-amino-2'-deoxyuridine-3'-0-methyl N,N-diisopropylamino phosphoramidite having the formula:

40. 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetylglycyl)-2'-amino-2'-deoxyuridine-3'-0-methyl-N,N-diisopropylamino phosphoramidite having the formula:

41. 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxyuridine-3'-0-beta-cyanoethyl-N,N-diisopropylamino phosphoramidite.

42. 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetylglycyl)-2'-amino-2'-deoxyuridine-3'-0-beta-cyanoethyl-N,N-diisopropylamino phosphoramidite.

43. Novel protected 2'-amino-nucleoside phosphoramidites having the generic formula:

wherein B is selected from the group consisting of a nucleoside base, or a nucleoside base analog, or their protected derivatives; X1 is selected from trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-anisyldiphenylmethyl, triphenylmethyl, and protected amino acyl having the formula:
Y-NH-(CHR)n-CO
wherein Y is selected from the group consisting of trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-anisyldiphenylmethyl, and triphenylmethyl;
R is an amino acid side chain or hydrogen when n=1; and R is hydrogen when n is an integer from 2 to 100;
R1 is selected from the group consisting of lower alkyl (in which case m=2) and when m=1 and R1 is taken in conjunction with the N of the P-N bond it forms a heterocyclic group, and R2 is selected from the group consisting of methyl, beta-cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl; and X2 is a hydroxyl protecting group selected from triphenylmethyl, p-anisyl-diphenylmethyl, di-p-anisylphenylmethyl, and 9-phenylxanthenyl.

44. The compounds oE Claim 43 wherein Xl is trifluoroacetyl.

45. The compounds of Claim 43 wherein X1 is 9-fluoroenylmethyloxycarbonyl.

46. The compounds of Claim 43 wherein X1 is N-trifluoroacetylglycyl.

47. The compounds of Claim 43 wherein B is uracil.

48. The compounds of Claim 43 wherein R1 is methyl.

49. The compounds of Claim 43 wherein R1 is isopropyl.

50. The compounds of Claim 43 wherein R1 is morpholino.

51. The compounds of Claim 43 wherein R2 is methyl.

52. The compounds of Claim 43 wherein R2 is beta-cyanoethyl.

53. The compounds of Claim 43 wherein B is uracil and X1 is trifluoroacetyl.

54. The compounds of Claim 43 wherein B is uracil and X1 is 9-fluoroenylmethyloxycarbonyl.

55. The compounds of claim 43 wherein B is uracil and X1 is N-trifluoroacetylglycyl.

56. 5'-O-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxy-ara-uridine-3'-O-methyl-N,N-diisopropylamino phosphoramidite.

57. 5'-O-di-p-anisylphenylmethyl-2'-N-(N-trifluoroacetylglycyl)-2'-amino-2'-deoxy-ara-uridine-3'-O-methyl,-N,N-diisopropylamino phosphoramidite.

58. 5'-O-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxy-ara-uridine-3'-O-beta-cyanoethyl-N,N-diisopropylamino phosphoramidite.

59. 5'-O-di-p-anisylphenylmethyl-2'-N-(N-trifluoroacetylglycyl-2'-amino-2'-deoxy-ara-uridine-3'-O-beta-cyanoethyl-N,N-diisopropylamino phosphoramidite

60. 5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxythymidine having the formula:

61. 5'-N-(N-benzyloxycarbonyl-6-aminohexanoyl)-5'-amino-5'-deoxythymidine having the formula:

62. 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxyuridine having the formula:

63. 5'-0-di-p-anisylphenylmethyl-2'-N-(N-trifluoro-acetylglycyl)-2'-amino-2'-deoxyuridine having the formula:

64. 5'-0-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxy-ara-uridine having the formula:

65. 5'-O-di-p-anisylphenylmethyl-2'-N-(N-trifluoroacetylglycyl)-2'-amino-2'-deoxy-ara-uridine having the formula:

66. An improved method of the synthesis of 5'-amino oligonucleotides which comprises reacting a phosphoramidite compound having the formula:

wherein B is selected rom the group consisting of a nucleoside base, a nucleoside base analog, or their protected derivatives; R1, R2 and R5 are defined as follows: R1 and R2 can be H or OR and R5 is NHR', wherein R is a monovalent organic group containing up to 25 carbon atoms, R' is a nitrogen protecting group which is acid labile, or base labile protecting group selected from the group consisting of trifluoroacetylglycyl, 4-toluene-sulfonylethyl-oxycarbonyl, methylsulfonylethyl-oxycarbonyl, 2-cyano-t-butyl-oxycarbonyl; chloracetyl, aceto-acetyl, 2-nitro-benzoyl, dithiasuccinoyl, maleoyl, isonicotinyl, 2-bromoethyloxy-carbonyl, and 2,2,2- trichloroethyloxycarbonyl; R6 is lower alkyl or when (R6)2 is taken with the N of the P-N bond it forms a heterocyclic group; R7 is lower alkyl, cyano-lower alkyl, halo-lower alkyl, or nitrophenyl-lower alkyl; in the last coupling step in solid phase oligonucleotide synthesis with an oligonucleotide bound to a solid support.

67. An improved method of the synthesis of 5'-amino oligonucleotides which comprises reacting a phosphoramidite compound having the general formula:

wherein B is selected from the group consisting of a nucleoside base, or a nucleoside base analog, or their protected derivatives; X1 is selected from p-anisyldiphenylmethyl, triphenylmethyl, and protected amino acyl having the formula:
Y-NH-(CHR)n-CO
wherein Y is selected from the group consisting of trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-anisyldiphenylmethyl, and triphenylmethyl;
R is an amino acid side chai.n or hydrogen when n=1; and R is hydrogen when n is an integer from 2 to 100;
R1 is selected from the group consisting of lower alkyl (in which case m=2) and when m=1 and R1 is taken in conjunction with the N of the P-N bond it forms a heterocyclic group, and R2 is selected from the group consisting of methyl, beta-cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl;
in the last coupling step in solid phase oligonucleotide synthesis with an oligonucleotide bound to a solid support.

68. The improved method of Claim 67 wherein X1 is p-anisyldiphenylmethyl.

69. The improved method of Claim 67 wherein X1 is triphenylmethyl.

70. The improved method of Claim 67 wherein X1 is N-trifluoroacetylglycyl.

71. The improved method of Claim 67 wherein B is thymine.

72. The improved method of Claim 67 wherein B is uracil.

73. The improved method of Claim 67 wherein R2 is methyl.

74. The improved method of Claim 67 wherein R2 is beta-cyanoethyl.

75. The improved method of Claim 67 wherein R1 is methyl.

76. The improved method of Claim 67 wherein R1 is isopropyl.

77. The improved method of Claim 67 wherein R1 is morpholino.

78. The improved method of Claim 67 wherein B is thymine and X1 is p-anisyldiphenylmethyl.

79. The improved method of Claim 67 wherein B is thymine and X1 is triphenylmethyl.

80. The improved method of Claim 67 wherein B is thymine and X1 is N-trifluoroacetylglycyl.

81. The improved method of Claim 67 wherein B is uracil and Y is trifluoroacetyl.

82. The improved method of Claim 67 wherein B is uracil and Y is 9-fluoroenylmethyloxycarbonyl.

92 6829g-92

83. The improved method of Claim 67 wherein B is uracil and X1 is p-anisyldiphenylmethyl.

84. The improved method of Claim 67 wherein B is uracil and X1 is triphenylmethyl.

85. The improved method of Claim 67 wherein B is uracil and X1 is N-trifluoroacetylglycyl.

86. An improved method of the synthesis of 2'-amino oligonucleotides which comprises reacting a phosphoramidite compound having the general formula:

where B is selected from the group consisting of a nucleoside base, or a nucleoside base analog, or their protected derivatives;
X1 is selected from trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-anisyldiphenylmethyl, triphenylmethyl, and protected amino acyl having the formula:
Y-NH-(CHR)n-CO
wherein Y is selected from the group consisting of trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-anisyldiphenylmethyl, and triphenylmethyl;
R is an amino acid side chain or hydrogen when n=1; and R is hydrogen when n is an integer from 2 to 100;
R1 is selected from the group consisting of lower alkyl (in which case m=2) and when m=1 and R1 is taken in conjunction with the N of the P-N bond it forms a heterocyclic group, and R2 is selected from the group consisting of methyl, beta-cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl; and X2 is a hydroxyl protecting group selected from triphenylmethyl, p-anisyl-diphenylmethyl, di-p-anisylphenylmethyl, and 9-phenylxanthenyl;
in one or more coupling step(s) in solid phase oligonucleotide synthesis with an oligonucleotide bound to a solid support.

87. The improved method of Claim 86 wherein X1 is trifluoroacetyl.

88. The improved method of Claim 86 wherein X1 is 9-fluoroenylmethyloxycarbonyl.

89. The improved method of Claim 86 wherein X1 is N-trifluoroacetylglycyl.

90. The improved method of Claim 86 wherein B is uracil.

91. The improved method of Claim 86 wherein R1 is methyl.

92. The improved method of Claim 86 wherein R1 is isopropyl.

93. The improved method of Claim 86 wherein R1 is morpholino.

94. The improved method of Claim 86 wherein R2 is methyl.

95. The improved method of Claim 86 wherein R2 is beta-cyanoethyl.

96. The improved method of Claim 86 wherein B is uracil and X1 is trifluoroacetyl.

97. The improved method of Claim 86 wherein B is uracil and X1 is 9-fluoroenylmethyloxycarbonyl.

98. The improved method of Claim 86 wherein B is uracil and X1 is N-trifluoroacetylglycyl.

99. An improved method of the synthesis of 2'-amino oligonucleotides which comprises reacting a phosphoramidite compound having the general formula:

wherein B i3 selected from the group consisting of a nucleoside base, or a nucleoside base analog, or their protected derivatives; X1 is selected from trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-anisyldiphenylmethyl, triphenylmethyl, and protected amino acyl having the formula:
Y-NH-(CHR)n-CO
wherein Y is selected from the group consisting of trifluoroacetyl, 9-fluoroenylmethyloxycarbonyl, p-anisyldiphenylmethyl, and triphenylmethyl;
R is an amino acid side chain or hydrogen when n=1; and R is hydrogen when n is an integer from 2 to 100;
R1 is selected from the group consisting o lower alkyl ( in which case m=2) and when m=1 and R1 is taken in conjunction with the N of the P-N bond it forms a heterocyclic groupl and R2 is selected from the group consisting of methyl, beta-cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl; and X2 is a hydroxyl protecting group selected from triphenylmethyl, p-anisyldiphenylmethyl, di-p-anisylphenylmethyl, and 9-phenylxanthenyl;
in one or more coupling step(s) in solid phase oligonucleotide synthesis with an oligonucleotide bound to a solid support.

100. The improved method of Claim 99 wherein X1 is trifluoroacetyl.

101. The improved method of Claim 99 wherein X1 is 9-fluoroenylmethyloxycarbonyl.

102. The improved method of Claim 99 wherein X1 is N-trifluoroacetylglycyl.

103. The improved method of Claim 99 wherein R1 is methyl.

104. The improved method of Claim 99 wherein R1 is isopropyl.

105. The improved method of Claim 99 wherein R1 is morpholino.

106. The improved method of Claim 99 wherein R2 is methyl.

107. The improved method of Claim 99 wherein R2 is beta-cyanoethyl.

108. The desired oligonucleotides produced by the method of any one of Claims 68 to 99.

109. The method of any one of Claims 66 to 107 wherein the oligonucleotide is subsequently cleaved from the support.

110. The method of Claim 67 wherein the X1 moiety is acid labile, the R2 moiety is beta-cyanoethyl, and after the phosphoramidite is attached to the oliyonucleotide bound to the solid support in the last coupling step in oligonucleotide synthesis, the beta-cyanoethyl protecting group is removed, the acid labile protecting group is removed, the free amino group is reacted with a detectable moiety, and then the derivatized oligonucleotide is cleaved from the support.

111. A conjugate, comprising oligonucleotides produced by the method of any one of Claims 66 to 107 and a detectable moiety.

112. The conjugate of Claim 111 wherein the detectable moiety is fluorescent.

113. The conjugate of Claim 111 wherein the detectable moiety is absorptive or colored.

114. The conjugate of Claim 111 wherein the detectable moiety is a protein.

115. The conjugate of Claim 111 wherein the detectable moiety is an enzyme.

116. The conjugate of Claim 111 wherein the detectable moiety contains radioactive I-125.

117. The conjugate of Claim 111 wherein the detectable moiety is selected from a group consisting of Texas Red, tetramethyl rhodamine isothiocyanate, eosin isothiocyanate, erythosin isothiocyanate, rhodamine X isothiocyanate, lissamine rhodamine B
sulfonyl chloride, pyrene sulfonyl chloride, 7-diethylarnino-4-methylcoumarin isothiocyanate, 4-fluoro-7-nitro-benz-2-oxa-1,3-diazole, 4-chloro-7-nitrobenz-2-oxa-1,3-diazole, fluorescein-5-isothiocyanate, acridine-9-isothiocyanate, and Lucifer Yellow.

118. Novel protected amino nucleosides having the formula:

wherein B is selected from the group consisting of a nucleoside base, a nucleoside base analog, or their protected derivatives;
R1, R2, R3, R4 and R5 are defined as follows: R3 = H, R4 = OH, and R1, R2 and R5 are either H, OR, or NHR', with the proviso that at most only one of R1, R2 or R5 must be NHR', wherein R is a monovalent organic group containing up to 25 carbon atoms, R' is a nitrogen protecting group which is acid labile, or base labile protecting group selected from the group consisting of trifluoroacetylglycyl, 4-toluene-sulfonylethyl-oxycarbonyl, methylsulfonylethyl-oxycarbonyl, 2-cyano-t-butyl-oxycarbonyl;
chloracetyl, aceto-acetyl, 2-nitro-benzoyl, dithiasuccinoyl, maleoyl, isonicotinyl, 2-bromoethyloxy-carbonyl, and 2,2,2-trichloroethyloxycarbonyl, with the proviso that when R1 or R2 is NHR', then R' is any of the foregoing groups, or trifluoroacetyl or 9-fluoroenylmethyloxy-carbonyl.