CA2179013C - Polymers for separation of biomolecules by capillary electrophoresis - Google Patents

Abstract

The invention provides uncharged water-soluble silica-adsorbing polymers for suppressing electroendoosmotic flow and to reduce analyte-wall interactions in capillary electrophoresis. In one aspect of the invention, one or more of such polymers are employed as components of a separation medium for the separation of biomolecules, such as polynucleotides, polysaccharides, proteins, and the like, by capillary electrophoresis. Generally, such polymers are characterized by (i)water solubility over the temperature range between about 20.degree.C to about 50.degree.C, (ii) concentration in a separation medium in the range between about 0.001 % toabout 10 % (weight/volume), (iii) molecular weight in the range of about 5 x 103to about 1 x 106 daltons, and (iv) absence of charged groups in an aqueous medium having pH in the range of about 6 to about 9. In one embodiment, polymers of the invention are selected from the group consisting of polylactams,such as polyvinylpyrrolidone; N_N disubstituted polyacrylamides; and N-substituted polyacrylamides. In accordance with the method of the invention, a sufficient amount of polymer adsorbs to the capillary surface to establish a zone of high viscosity that shields the analyte from the wall and impedes the movement of, anelectrical double layer under an electric field.

Description

SUN 3, '96 01:.42PM w&D 41S 63$ E071 - ~: =,,~,:=1 wo 95i 1691 t 2 ~ 7 ~ ~ ~ 3 YCI~'U59a113852 S

POLYMERS FOR SEpARATiON ~F BIOMOL>~CULES
BY CAPILLARY ELECTROPHORESIS
ao $~ated U . Applications This is a continuation-in-part application of application number 081170,078 filed 17 December 1993, now pending, which is hereby incorporated by referetu,e.
~,ld of the Invention _ The invention relates generahy to the field of capillary electrophoresis, and more particularly to materials and methods for suppressing electroendoosmotic flow and attalyte-wall interactions during separation of biomolecufes, especially potynucleotides, by capillary electrophoresis.
Backszround Capillary electrophoresis has been applied widely as an analytical technique baause of several technical advantages: (i) capillaries have high surface-to-volume ratios which ptrnsit mart e»'tcient heat dissipation which, in tum, petrna high electric fields to be used for more rapid separatiotu; (ii) the technique requires minimal sample volumes; (iii) superior resolution of most analytes is attainable; and (iv) the technique is amenable to automation) e.g. Carttitleri, editor, Capillary Electrophoresis: Theory and Practice (CRC Press, Boca Raton, 1943); and Grossman et al, editors, Capillary Electrophoresis (Academic Press, San Diego, WO 95116911 pCTIUS9:t/13852 1992). Because of these advantages, there has been great interest in applying capillary electrophoresis to the separation of biomolecules) particularly in nucleic acid analysis. The need for rapid and accurate separation of nucleic acids, particularly deoxyribonucleic acid (DNA) arises in the analysis of polymerise chain reaction (PCR) products and DNA sequencing fragment analysis, e.g. Williams, Methods 4: 227-232 (19920; Drossman et al, Anal. Chem., 62: 900-903 (1990);
Huang et al, Anal. Chem., 64: 2149-2154 (1992); and Swerdlow et al, Nucleic Acids Research, 18: 1415-1419 (1990).
Since the charge-to-frictional drag ratio is the same for different sized polynucleotides in free solution, electrophoretic separation requires the presence of a sieving medium. The initial sieving media of choice were gels, but problems of stability and manufacturability have led to the examination of non-gel liquid polymeric sieving media, such as linear polyacrylamide, hydroxyalkylcellulose, agarose, and cellulose acetate, and the like, e.g. Bode, Anal. Biochem., 83:

(1977); Bode, Anal. Biochem., 83: 364-371 (1977); Bode) Anal. Biochem.) 92: 99-110 (1979); Hjerten et al, J. Liquid Chromatography, 12: 2471-2477 (1989);
Grossman, U.S. patent 5,126,021; Zhu et al, U.S. patent 5,089111; Tietz et al, Electrophoresis, 13 : 614-616 ( 1992).
Another factor that complicates separations by capillary electrophoresis is the phenomena of electroendoosmosis. This phenomena, sometimes referred to as electroosmosis, is fluid flow in a capillary induced by an electrical field.
It has impeded the application of capillary electrophoresis to situations where high resolution separations are required, such as in the analysis of DNA sequencing fragments. The phenomena arises in capillary electrophoresis when the inner wall of the capillary contains immobilized charges which cause. the formation of a mobile layer of counter ions which, in turn, moves in the presence of an electrical field to create a bulk flow of liquid. Unfortunately, the magnitude of the electroendoosmotic flow can vary depending on a host of factors, including variation in the distribution of charges) selective adsorption of components of the analyte and/or separation medium, pH of the separation medium, and the like. Because this variability tends to reduce ones ability to resolve closely spaced bands analyte, many attempts have been made to directly or indirectly control such flow. The attempts have included covalent modification of the inner wall of the capillary to suppress charged groups, use of high viscosity polymers) adjustment of buffer pH and/or concentration, use of a gel separation medium covalently attached to the capillary wall, and the application of an electric field radial to the axis of the capillary, e.g.
Hayes et al, Anal. Chem., 65: 2010-2013 (1,993); Drossman et al (cited above);
Hjerten, U.S. patent 4,680,201; Van Alstine et al, U.S. patent 4,690,749;

:l:.N D4 '?6 21' ~~'M r7EL. .1;5-638 6~~ 1 - , a.5% S1 WO 9511691 t 21 l 9 013 PCT~~59u13832 Wiktorowicz et al, Electrophoresis, I1: 7b9-773 {1990); I3elder et al, J. High Resolution Chromatography, 15: b86-693 (1992).
Most ofthese approaches have met with mixed success or have only been used in the separation of anafytes quite different chemically from nucleic acids. Ta particular, the use of capillary gels for DNA separations have been hampered by tnanufacturittg problems and problems of stability and reliability during use, e.g.
Swerdlow et al) Electrophoresis, 13' 475-483 (1992).
In view ofthe strong scientific and industrial interest in being able to conveniently sad accurately separate a variety ofbiomolecules, particularly polynucleotides, it would be desirable to have available a low viscosity electrophoretic separation medium capable of suppressing electroendoostnotic flow and of reducing analyto-wall interactions.
Summary of the dnvention The invention relates to the use of uncharged water-soluble si&ca-adsorbing polymers to suppress electroeadoesmotic flow and to reduce anaLyte-wall interactions in capillary electrophoresis. In ane aspect ofthe imrention, one or more of such polymers are employed as components of a separation medium for the separation of biomoleeules, prefrsably polynucleotides, by capillary electrophoresis.
Gtna'ally, such polymers are characterized by {i) water solubility over the temperature 1'ange betwcert about 20oC to about SOoC) (ii) concentration in a separarion medium in the range between about 0.001% to about 10°!0 (weightlvolume), (iii) molecular weight in the range of about 5 x 103 to about 1 x 106 daltons, and (iv) absence of charged groups in sa aqueous medium having pIi in the range of about 6 to about 9. Preferably, such polymers of the invention art ' substantially non-hydroxylic. In one etnbodiracnt, polymers of the itlventiaa are selected firm the group consisting of polyvinylactams, such as polyviuylpyrrolidone;
N,N-disubstituted polyacrylamides; and N-substituted polyacrylamides. More preferably, such polymers of the invetttion arc poly(N,N-dialethylacrylamide).
Ia accordance with the method of the invention, a sufficient amount of polymer adsorbs to the silica sur$tce to establish a zone of high viscosity at the silica surface that impedes the movement of an electrical double layer under an electric field and that shields the analyte from the wall.
The invention includes methods of using the polymers of the invention to separate biomolecules, especially polynucleotides, by capillary electrophoresis;
compositions comprising polymersofthe invention for eleccrophoretically separating biomolecules in capillaries; and methods of using the separation medium of the invention for sequencing DNA.
_3.

J~N04 '~6 -~t:,,~M RBL.~.1_5 e.3~ =0'!-- ._.....
WO x5116911 ~ ~ ~ pCTIUS9s113g52 The invention enhances the precision of biomolecule separation by electrophoresis in a capillary by dynanucally suppressing electroendoosmotic flow and wall~analyte interactions through the adsorption of the uncharged polymers of the invemion onto the surface of the capillary. Suppression is dynamic in the sense that throughout the separation process polymers of the invention adsorb and desorb from the surface of a capillary is equilibrium with polymer in solution in the separation medium. Thus, a constant degree of suppression is maintained net only during a separation tun, but also from separation run to separation run.
IO BriefDescrintionofthaFi ~r ~
l;igure 1 diagrammatically illustrates an apparatus for carrying out capillary electrophoresis.
Figure 2 is an ele~apherogram of a 100 basepair DNA ladder separated is a 3% poly(dimethyacrylamide) solution (RM8) in a glycylglycine buffer.
IS Figure 3 is an elaccropherogram of a 100 basepair DNA ladder separated in a 3% poly(ditnethyacrytatnide) solution (RM18) in a glyeylglycine buffer.
Figure 4 is an electropherogram of a 100 basepair DNA ladder separated in a 3°!° poly(ditnethyacrylatttide) solution (RM18) in a TBF buffer.
lagtun 5 it an electropherogram of a i00 basepair DNA ladder separated in a 20 binary polymer solution comprising 3% polyacrylamide and 0.05%
poly(dunethylacrylamide) (RMlB) in a glycylglycine bufFa.
Figures 6A to 6F are eleciropherograms of a 100 basepair DNA ladder separated in various binary polymer solutions.
Figures 7A to 7J is an electropherogram of a commercially available DNA
25 sequencing fragment standard separated in a separation medium containing a 6.5%
solution ofpoly(dimethylacrylantida).
Fgure 8 is an alectropherogtam showing the separation and sequencing of a 4-color sequencing standard in a separation medium coatainiag a 6.5% solution of poly(dimethylacrylamide). The numbers above the peaks refer to the base mmtbar in 30 the sequence, end the Ictters above each peak refer to the identity of the base.
Defin~tians_ The tam "capillary" as used herein refers to a tube or channel or other 33 structure capable of supporting a volume of separation medium for carrying out electrophoresis. The geometry of a capillary rosy vary widely and includes tubes with circular, rectangular or square cross-sections, channels, groves, plates, and the like, and may be fabricated by a wide range oftechnologies. An importam feature of WO 95/16911 PGT/US9:t113852 a capillary for use with the invention is the surface-to-volume ratio of the surface in contact with the volume of separation medium. High values of this ratio permit better heat transfer from the separation medium during electrophoresis.
Preferably, values in the range of about 0.4 to .04 are employed. These correspond to the surface-to-volume ratios of tubular capillaries with circular cross-sections having inside diameters in the range of about 10 ~m to about 100 l,un. Preferably) capillaries for use with the invention are made of silica, fused silica, quartz, silicate-based glass, such as borosilicate glass, phosphate glass, alumina-containing glass, and the Iike) or other silica-like materials.
The term "biomolecule" means a molecule typically synthesised by a biological organism that is water soluble and charged in the pH range of from about 6 to about 9. Preferably, the term biomolecule includes proteins, glycoproteins, natural and synthetic peptides, alkaloids, polysaccharides, polynucleotides, and the like. More preferably, the term biomolecule refers to polynucleotides.
The term "polynucleotide" as used herein refers to linear polymers of natural or modified nucleoside monomers, including double and single stranded deoxyribonucleosides, ribonucleosides, a-anomeric forms thereof; and the like.
Usually the nucleoside monomers are linked by phosphodiester bonds or analogs thereof to form polynucleotides ranging in size from a few monomeric units) e.g. 8-40, to several thousands of monomeric units. Whenever a polynucleotide is represented by a sequence of letters, such as "ATGCCTG," it will be understood that the nucleotides are in 5'->3' order from left to right and that "A" denotes deoxyadenosine, "C" denotes deoxycytidine, "G" denotes deoxyguanosine, and "T" denotes thymidine, unless otherwise noted. Analogs of phosphodiester linkages include phosphorothioate, phosphorodithioate, phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate, phosphoranilidate, phosphoramidate) and the like.
As used herein, "nucleoside" includes the natural nucleosides, including 2'-deoxy and 2'-hydroxyl forms, e.g. as described in Kornberg and Baker, DNA
Replication, 2nd Ed. (Freeman, San Francisco, 1992). "Analogs" in reference to nucleosides includes synthetic nucleosides having modified base moieties and/or modified sugar moieties, e.g. described generally by Scheit, Nucleotide Analogs (John Whey, New York, 1980).
The term "electroendoosmosis" or "electroendoosmostic flow" as used herein refers to the bulk flow of liquid due to the influence of an electric field on the layer of mobile counter ions adjacent to fixed, or immobile, charges on a surface) such as a capillary wall. Electroendoosmotic flow is typically measured as the mobility (cm2/sec-volts) of a test analyte through a capillary tube under a standard WO 95/16911 PCTIUS9:1/13852 set of conditions) e.g. determining buffer concentration and type, tube length, electrical field strength, and the like:
The term "polymer" is a large molecule composed of smaller monomeric subunits covalently linked together in a characteristic fashion. A
"homopolymer" is a polymer made up of only one kind of monomeric subunit. A "copolymer" refers to a polymer made up of two or more kinds of monomeric subunits. As used herein the term "polymer" includes homopolymers and copolymers. A "monodisperse"
polymer solution means that the polymer molecules in solution have substantially identical molecular weights. A "polydisperse" polymer solution means that the polymer molecules in solution have a distribution of molecular weights.
The term "non-hydroxylic" as used herein in reference to polymers means that the monomers used in the synthesis of a polymer contain no hydroxyl substituents.
Detailed Description of the Invention The invention provides a convenient means for suppressing electroendoosmotic flow and wall-analyte interactions during the separation of biomolecules, particularly DNA, by capillary electrophoresis. As used herein, the term "separation medium" refers to the medium in a capillary in which the separation of analyte components takes place. Separation media typically comprise several components, at least one of which is a charge-carrying component, or electrolyte.
The charge-carrying component is usually part of a buffer system for maintaining the separation medium at a constant pH. Media for separating polynucleotides) or other biomolecules having different sizes but identical charge-frictional drag ratios in free solution, further include a sieving component. In addition to such conventional components, the separation medium of the invention comprise a surface interaction component. In the case of polynucleotide separations, the sieving component may be the same or different than the surface interaction component, but is usually different. The surface interaction component comprises one or more uncharged water-soluble silica-adsorbing polymers having the physical properties set forth above. Preferably, such one or more uncharged water-soluble silica-adsorbing polymers are non-hydroxylic. In further preference for polynucleotide separations, the sieving component of the separation medium of the invention comprises one or more uncrosslinked, particularly linear, polymers. Preferably, the components of tfie separation medium of the invention are selected so that its viscosity is low enough to permit rapid re-filling of capillaries between separation runs. For typical capillaries, e.g. 20-100 ~m inside diameter and 40-b0 cm in length, in the absence of a sieving component, viscosity is preferably less than 1000 centipoise, and more preferably, WO 95116911 PCTlUS9aI13852 between about 1 to about 300 centipoise. In the presence of a sieving component) viscosity is preferably less than 5000 centipoise, and more preferably, less than 1000 centipoise.
Polymers for use as the surface interaction component of the separation medium may belong to a variety of chemical classes) such as those described in the following references: Molyneux, Water-Soluble Synthetic Polymers: Properties and Behavior, Volumes I and II (CRC Press, Boca Raton, 1982); Davidson, Editor, Handbook of Water-Soluble Gums and Resins (McGraw-Hill, New York, 1980);
Franks, editor, Water: A Comprehensive Treatise (Plenum Press, New York, 1973);
and the like. Preferably, the uncharged water-soluble silica-adsorbing polymers of the invention include; but not limited to) N,N-disubstituted polyacrylamides, N-monosubstituted polyacrylamides, polymethacryiamide, polyvinylpyrrolidone, and the like. Exemplary substituents of the polyacrylamides include C 1 to C 12 alkyl;
halo-substituted C 1 to C 1 Z alkyl; methoxy-substituted C 1 to C 12 alkyl;
hydroxyl-substituted C 1 to C 12 alkyl and the like. Preferably, the halo substituent is fluoro and the hydroxyl-substituted C 1 to C 12 alkyl is monosubstituted. It is understood that the above monomer substituents are selected so that the resulting polymer is water soluble. For example, it is clear that C 12 alkyl-containing mononer could only be present as a small fractional component of a copolymer. More preferably, exemplary substituents are selected from the group consisting of C 1 to C3 alkyl;
halo-substituted C 1 to C3 alkyl; methoxy-substituted C 1 to C3 alkyl; and hydroxyl-substituted C1 to C3 alkyl.
Such polymers are synthesized by conventional techniques) e.g. as disclosed in Odian, Principles of Polymerization, Third Edition (John Wiley, New York, 1991 ). An important feature of the invention is that the polymer of the surface interaction component be uncharged. Preferably, polymers of the invention are synthesized under non-aqueous conditions so that uncharged initiators can be used.
Such conditions also preclude the incorporation of charged initiators into the product. The polymers comprising the surface interaction component of the separation medium may be present at a concentration of from about .001% to about 10% (w:v). Preferably, such polymers are present at a concentration in the range of about .01 % to about 6%.
The silica-adsorbing quality of the preferred polymers can be measured in a number of well-known ways, such as by ellipsometry, determining changes in the hydrodynamic properties of adsorbent test particles, determination of adsorption isotherms, or like methods. Such techniques are described in Malmsten et al, Macromolecules, 25: 2474-248 I ( I 992); Rob and Smith, European Polymer J., 10:
1005-1010 (1974); Vincent et al Surf. Colloid Sci., 12: I-117 (1982);
Takahashi et _7_ WO 95/16911 PCTIUS9a/13852 al, Advances in Polymers Science, 46: 1-65 (1982), and like references. An .
adsorption isotherm is a graphical presentation of the adsorption exerted by an adsorbent on a solution of a given substance at a fixed temperature. The determination of adsorption isotherms require the preparation of solutions of known concentrations of the material whose adsorption is to be measured (the adsorbate).
The adsorbate solutions are combined with known quantities of the material (the adsorbent) whose surface the adsorbate adheres to. Once an equilibrium is reached between the adsorbate in solution and the adsorbate on the surface of the adsorbent, the concentration of the adsorbate. solution is determined. The reduction in concentration of the solution is a measure of the degree of adsorption of the adsorbate under the standard conditions.
The degree of adsorption may also be measured indirectly by observing the reduction of electroendoosmotic flow under a set of standard values of the following parameters: buffer type and concernration, temperature, electric field strength, capillary type, diameter, and length, and test analyte. An exemplary standard for such measurement is as follows: Uncoated fused silica capillary 40 cm in total length, 20 cm to detector (LJV), 75 pm inside diameter; 0.1 M glycylglycine buffer (pH 8.0); marker solution of 0.92 mM mesityl oxide and 1 mM p-toluenesulfonic acid (p-TSA); electrophoresis at 30oC under 10 kV. The polymer being tested is .
added to the buffer. With no surface interaction component, the electroendoosmotic flow is approximately 6 x 10-'1 cm2/sec-volts. Preferably, in such a separation medium, a cuff cient concentration of polymer of the invention is employed to reduce electroendoosmotic flow to less than about 2 x 10-5 cm2/sec-volts.
For polynucleotide separations, the silica-adsorbing quality of a polymer of the invention is preferably characterized by the relationship between resolving power and polynucleotide length for a selected "ladder" of polynucleotides under a standard set of conditions. Resolving power is conveniently expressed in terms of the number of theoretical plates, N, of the test system. N=(L/a~ where L is the average path length of a test analyte under a peak from injection port to detector (usually position of peak maximum) and Q is the variance of the peak. Preferably, polymers of the invention provide a substantially linear relationship between number of theoretical plates and size of polynucleotide over the range of from about 100 to about nucleotides; more preferably, the 'relationship is linear over the range of from about 20 to about 600 nucleotides. A standard set of conditions for generating theoretical plates versus polynucleotide length curves is described below.
Exemplary ladders of different-sized polynucleotides in the above-mentioned size ranges are available in commercially available kits, e.g. the 100 basepair double stranded DNA ladder from BRL-GIBCO, the Taq DNA Sequencing Standard from _g-WO 95116911 PCT/US9d/13852 Applied Biosystems, Inc., or the like. A standard separation medium can be prepared as follows: 0.60 g of acrylamide (ultrapure, ICN, Costa Mesa, CA) is dissolved in 10 ml lx TBE) 30% formamide, 3.5 M urea buffer, filtered (0.2 pm pore size)) and degassed. The monomer solutions are polymerized by addition at S room temperature of 1 E.11 of 100% N,N,N,N-tetramethylethylenediamine (TEMED) and 2 pl ammonium persulfate, 10% w:v in water (APS), per ml of monomer solution (to give a final concentration of 0.02% w:v APS and 0.1% v:v TEMED).
The above separation medium is loaded into a 55 cm uncoated fused silica capillary tube) 50 Etm inside diameter, 40 cm to defector. The capillary may be used in a commercially available capillary electrophoresis apparatus having fluorescence detection capability. Fluorescence detection systems for detecting fluorescently labelled analyzes in capillaries is well known in the art, e. g. Mathies et al, U. S. patent 5,091,652; Mathies et al, International Application No. PCT/US93/01607; Ruiz-Martinez et al, Anal. Chem. 65: 2851-2858 (1993); and the like. The DNA
fragments from the standard are denatured and loaded electrokinetically as follows: The dried sample is resuspended in a mixture of 5 mM aqueous EDTA (0.5 l,tl) and formamide (6 l,tl). The suspension is heated at 90oC for 2 minutes then transferred to an ice bath.
The ladder is loaded by placing the cathode and catholic end of the capillary into the above solution then applying 6 kV across the tube for 5 seconds. Separation of the DNA fragments in the ladder commences by returning the cathode and catholic end of the capillary into the cathode reservoir and applying a running voltage of 12 kV.
Apparatus for carrying out capillary electrophoresis is well-known and is not a critical feature of the invention. Many references are available describing the basic apparatus and several capillary electrophoresis instruments are commercially available, .
e.g. Applied Biosystems (Foster City, CA) model 270A instrument. Exemplary references describing capillary electrophoresis apparatus and their operation include Jorgenson, Methods, 4: 179-190 (1992); Colburn et al, Applied Biosystems Research News, issue 1 (winter 1990); Grossman et al (cited above); and the like.
Figure 1 is a schematic representation of an exemplary capillary electrophoresis system 20 suitable for practicing the invention. However, as mentioned above, a wide variety of systems are amenable for use with the invention in addition to that represented in the figure, e.g. as described in Harrison et al, Science, 261: 895-897 (1993); Pace, U.S.
patent 4,908,112; Kambara et al, U.S. patent 5,192,412; Seiler et al, Anal. Chem., 65: 1481-1488 (1993); and the like. In the figure, capillary tube 22 preferably has a length between about 10 to 200 cm, typically less than about 100 cm, and a preferred inner diameter in the range of about 10. to 200 Vim, and more typically in the range of about 50 to 75 pm, .e.g. available from Polymicro Technologies (Phoeniz, AZ).
Preferably, there is no coating on the inside.surface of the tube. A catholic reservoir 26 in system PCTIUS9aI13852 20 contains a separation medium 28, described further below. The cathodic end 22a of capillary tube 22 is sealed within reservoir 26 and is immersed in the separation medium during electrophoresis. Second tube 30 in reservoir 26 is connected to a finely controlled air pressure system which can be used to control the pressure in the head space above the separation medium, e.g. for loading separation medium into the capillary tube by positive pressure. Sample reservoir 31 contains the sample mixture to be loaded into the cathodic end of capillary 22. The anodic end 22b of capillary 22 is immersed in separation medium 32 contained in anodic reservoir 34. A second tube 36 in reservoir 34 can be included to control the pressure above separation medium 32. I~gh voltage supply 40 is connected to the cathodic and anodic reservoirs by electrodes 41 and 42: I~gh voltage supply 40 produces a constant potential across the electrodes in the range of a few kilovolts (kV) to 60 kV, with a potential in the range of about 10 to 30 kV being typical. Currents through the capiDary are generally in the microamp range, typically between a few to 100 ~A, with 20 ~A being typical.
Detector 44 positioned adjacent to capillary 22 monitors sample peaks migrating through optical detection zone 45 of the capillary. Typically, optical detection zone 45 comprises a region of capillary 22 in which the ususal polyimide coating has been removed to permit UV and/or visible light, e.g. fluorescence, detection of the separated analyte. A wide variety of detection schemes are amenable for use with the invention, including UV absorption, fluorescence emission, conductance, radioactive emission, and the like. For example, detection systems for fluorescent analyzes are described in Zare et al, U.S. patent 4,675,300 and Folestad et al) U.S. patent 4,548,498.
As mentioned above, separation medium of the invention generally comprises three components: a charge-carrying component) a sieving component, and a.
surface interaction component. fldditional components may also be included in particular embodiments, such as~ denaturants when it is desirable to prevent the formation of duplexes or secondary structures in polynucleotides. Preferred denaturants include formamide, e.g. 40-90%, urea, e.g. 6-8 M, commercially available lactams, such as pyrrolidone, and the like. Guidance for their use in electrophoresis can be found in well known molecular biology references, e.g.
Sambrook et al, Molecular Cloning: A Laboratory Manual, Second Edition (Cold Spring Harbor Laboratory, New York, 1989).
Typically, a buffer system for controlling pH is employed as the charge-carrying component. Exemplary buffers include aqueous solutions of organic acids, such as citric, acetic, or formic acid; zwitterionics, such as TES (N-tris[hydroxymethylJ-2-aminoethanesulfonic acid, BICINE (N,N-bis[2-hydroxyethyl]glycine, ACES (2-[2-amino-2-oxoethyl)-aminoJethanesulfonic acid), run oa w~ al:aeP~~ aah_av~ sae soW
WO 95116911 FCT~'U59~'I385:
i or glycylglycinc; inorganic acids, such as phosphoric; and organic bases, such as Tris (Tris[hydroxymethy!]aminomethane) buffers, e.g, available from Sigma. Hu~'er concentration can vary widely, for example between about 1 mM to 1 M, but are typically about 20 mM. Exemplary buffer solutions for conventional capillary electro~ :oresis appGeations include the following: (i) 0.1 M Tris, 0.25 M
boric acid, J M urea wish a pH of J.6 for single stranded polynucleotide separations; or (ii) 0.089 M Tris, 0.089 M boric acid, 0.005 M F.L1TA for double stranded polynucleotide separations. For non-zwitttrionic buH'cr SystGtls, prefezably 1'DMA
or polyvitrylpyrrolidone are employCd as the surface interaction component.
Sieving components of etectrophoretic separation media are well known in the art and are disclosed in 2hu etnl, U.S. patent 5,089,111; Ruiz-Martinet et a1, Anal. Chem., 65: 2851-2858 (1993); ~lliams, Methods, 4: 227-232 (1942); end tike references. Preferably, the sieving component of the separation medium of the invention is a lowwiscosity tntati~led polymer solution as taught by Grossman, U.S.
patent 5) 126,021. A low viscosity separation medium is preferred so that capillaries can be readily re-filled in automated systems, e,g. for large-scale DNA
sequencing applications. The rate of solution Bow through the capillary determines how mush time is required to replace the separation medium between successive analyses.
Guidance for synthesirittg entangled polymers with a range ofviscosities suitable for DNA sieving agplications is provided by Grossman, which is incorporated by reference. Generally, the viscosity of a pcrlymcr) or copolymer, solution is deternitled by the molecular weight (MVO and concentration of the polymer or copolymer componems of the separation medium. The molecular weight of a polymer or copolymer can be adjusted during symhesis in a member of ways well 2S known in the art, e. g. as reviewed in ~dian, Principles of Polymesi~ation, Third Edition (John v~>ley, New York, 1941)) or like references.
A socond approach for controlling the average MW of a polymer or copolymer used in the invention is by fractionating a polydisperse polymer product into diPfererrt MW fractions followed by pacification. Typical ftaciionation techniques include gel pcmteation chromatography, dialysis using membranes having specific MW cutoffs, fractional precipitations in water-miscabie solvents, such as methanol, and the like.
For apparatus employing conveationa! capillary tubes, it is clear that the upper limits of polymer or copolymer MW andlor concentration is dictated prima.7ly by the upper viscosity that can be pushed or putted through the tubes. For example, if short capillaries (length of about 20 cm) with large inside diameters (Das) (e.g.
radius of about 0.01 cm) are empioyed, a solution with a viscosity of as much as 38,000 centipoise could be pushed through the capillary in 30 minutes at high WO 95/16911 pCT/US9a/13852 pressure, e.g. 100 psi. For more conventional capillary tubes, e.g. 50 dun ID
and 50 cm in length, a viscosity in the range of about 10-1000 centipoise permits separation medium to be replaced within about 30 minutes using a pressure differential across the tube of between about 50-100 psi.
Exemplary sieving polymers include linear polyoxides; polyethers, such as polyethylene oxide and polypropylene oxide; polyacrylamide;
polymethacrylamide;
polyvinyipyrrolidone; polyvinyloxazolidone; and a variety of water-soluble hydroxylic polymers, such as water-soluble natural gums, such as dextrin;
water-soluble cellulose compounds, such as methylcellulose and hydroxyethylcellulose, and copolymers and blends of these polymers. Preferably, such polymers are used at a concentration in the range between about .5% and 10% w:v.
Double stranded polynucleotides, e.g. DNA fragments from PCR or LCR
amplifications) enzyme digests, or the like) are separated by standard protocols, or manufacturer's suggested protocols where a commercial capillary electrophoresis instrument is employed, e.g. a model 270-HT instrument (Applied Biosystems, Inc., Foster City). The only exception to such standard or suggested protocols is that the separation medium of the invention.is employed.
DNA sequencing in accordance with the invention requires the separation of single stranded polynucleotides prepared by DNA sequencing protocols, e.g. described in Sambrook et al, Molecular Cloning: A Laboratory Manual, Second Edition (Cold Spring Harbor Laboratory, New York, 1989);
Ausubel et al, Current Protocols in Molecular Biology (John wley & Sons, Media, PA); or the like.
The important feature of currently available DNA sequencing protocols is the generation of a "nested series" or "ladder" of single stranded polynucleotides, or DNA sequencing fragment, that must be separated by size.
The basic steps of the chain-termination approach to DNA sequencing are (1) providing an oligonucleotide primer and a template nucleic acid containing, as a subsequence, a target nucleic acid whose sequence is to be determined, (2) hybridizing the oligonucleotide primer to the template nucleic acid) (3) extending the primer with a nucleic acid polymerise, e.g. T7 DNA polymerise) SequenaseTM, a reverse transcriptase) or the like, in a reaction mixture containing nucleoside triphosphate precursors and at least one chain terminating nucleotide to form a nested series of DNA fragment populations, such that every shorter DNA fragment is a subsequence of every longer DNA
fragment and such that each DNA fragment of the same size terminates with the same chain-terminating nucleotide) (4) separating the DNA fragment populations according to size, and (5) identifying the chain-terminating nucleotide associated with each DNA fragment population. As used herein, the term "nucleoside triphosphaie precursors" refers to deoxyadenosine triphosphate (ATP), deoxycytidine triphosphate (CTP), deoxyguanosine triphosphate (GTP), and thymidine triphosphate (TTP), or analogs thcreof, such as deoxyinosine triphosphata (ITP), 7-deazadeoxyguanosine triphosphate, and the like.
A template is provided in accordance with the teachings in the art, e.g.
Technical Manual for Model 370A DNA Sequencer (Applied Biosystems) Inc., Foster City, CA). For example) the target sequence may be inserted into a suitable cloning vector, such as the replicative form of an M 13 cloning vector, which is then propagated to amplify the number of copies of the target sequence. The single-stranded form of M 13 is isolated for use as a template.
Alternatively, a template can be provided by polymerise chain reaction (PCR) as taught in the art, e.g. Innis et al, (cited above); Wilson et al, Biotechniques, Vol. 8, pgs. 184-189 (1990); Gyllensten, Biotechniques, Vol. 7) pgs. 700-708 (1989); and the like. ARer amplification, the template can be used in the polymerization reactions) either in liquid phase or attached to a solid phase support, e.g. as taught by Stahl et al, Nucleic Acids Research, Vol: 16, pgs.
. 3025-3038 (1988); Hultman et al) Nucleic Acids Research, Vol. 17, pgs. 4937-4946 ( 1989); or the like.
Once the nested series DNA fragments are generated, they are separated by capillary electrophoresis using the separation medium of the invention.

WO 95/16911 PCT/US9a/13852 Ezample 1 ~,~nthesis of PDMA in dioxane using AIBN
Poly(N,N-dimethylacrylamide) (pDMA) is synthesized using conventional techniques, e.g. as disclosed in Trossarelli et al, J. Polymer Sci., 57:445-452 ( 1962).
Known amounts of dimethylacrylamide (DMA), dioxane, and azobisisobutyronitrile (AIBN) were mixed in an Erlenmeyer flask and argon gas was bubbled through the solution for 10 minutes at room temperature. Polymerization was initiated by raising the temperature to SSoC. Polymerization times ranged from 10 to 25 minutes depending on the concentration of monomer: After polymerization, the resulting polymer was purified by three cycles of precipitation in hexane and dissolution in CH2Cl2. Finally, the~hexane precipitate was dried overnight in a vacuum desiccator then lyophilized. The table below summarizes the reaction conditions for the various experiments.
Estimated Monomer Average Concentration Molecular hatch No. °/ w/v Dioxane lccl AIBN (mel(mel Weisht*
RM 1 70 14.3 12 79 kd RM2 60 17.0 14 92 kd RM3 50 20.0 16 99 kd RM4 40 25.0 21 97 kd RMS 30 33.3 27 83 kd RM6 20 50.0 41 --RM7 10 100.0 82 69 kd RM8 5 200.0 164. 54 kd * Estimated by gel permeation chromatography (peak mol. wt.).
Eiample 2 Synthesis of PDMA in t-butyl alcohol using ~N
Further polymerizations were carried out with t-butyl alcohol (t-BuOFl7 using the following protocol: Known amounts of DMA monomer, t-butyl alcohol) and AIBN were combined, and argon gas was bubbled through the solutions for 20 minutes. The mixtures were brought to SSoC and allowed to polymerize for 15 minutes. The resulting polymers were isolated as described in Example 1. The table below summarizes the reaction conditions for the various experiments.

WO 95/16911 PGTIUS9:iI13852 hatch Monomer t-BuOH AIBN Monomer Estimated No. (ccl Concentration ~mg) ~ Average / w/v Molecular Wei t RM17 50 20.0 16 10 81 kd RM18 50 60.0 50 30 107 kd RM19 70 14.0 12 10 99 kd RM21 70 72.0 60 50 112 kd * Estimated by gel permeation chromatography (peak mol. wt.).
Ezampte 3 ~t,~nge in Electroendoosmotic Flow in Test System ~v Various Poly(dimethyl~lamide Solutions The effect of various formulations of PDMA on electroendoosmotic flow in a test system was measured. The test system consisted of an Applied Biosystems model 270 HT capillary electrophoresis instrument configured in the following manner: Uncoated fused silica capillary 40 cm in total length, 20 cm to detector (U'V), 75 ~m inside diameter was installed; the separation medium consisted of a 0.1 M glycylglycine buffer (pH 8.0) with the test PDMA polymer added; a marker solution consisted of 0.92 mM mesityl oxide; and electrophoresis took place at 30oC
under 10 kV after electrokinetic loading as described above. The results are listed in the table below:
Electroendo-osmotic PDMA Concentration Flow*

RM8 0.1% (w:v) 7.38 x 10-5' RM16 0.1% (w:v) 2.73 x 10-5 RM18** 0.01% (w:v) 1.98 x 10-5 * cm2/sec-volts * * p-TSA ( 1 mM in H20) used as marker.

WO 95!16911 PCT/US9:t/13852 Eiample 4 ~lg,~,~~phoresis of 100 basepair DNA ladder usin,~ 3% RMS
in a 0.1 M Glycvlgl_ycine Buffer A 3% (w:v) RM8 PDMA polymer in a 0.1 M glycylglycine buffer was used to separate the components of a commercial double stranded DNA ladder ( 100 by DNA ladder, GIBCO-BRL). An Applied Biosystems model 270 HT was fitted with a 75 l,un inside diameter uncoated fused silica capillary having 60 cm total length and 40 cm from the sample injection port to detector. Electrophoresis was carried out under 10 kV and 13 ~A at 30oC. .The sample was electrokinetically injected under 5 kV and 6 ~A for 5 seconds. An electropherogram of the analyze (showing IJV
absorption at 260 nm) is illustrated in Figure 2.
Ezample 5 Electro~resis of 100 baseaair DNA ladder using 3% RM18 ~n a 0.1 M Glvcvlglycine Buffer A 3% (w:v) RM18 PDMA polymcr in a 0.1 M glycylglycine buffer pH 8.0 was used to separate the components of the double stranded DNA ladder of Facample 4. An Applied Biosystems model 270 HT was fitted with a 75 ~m inside diameter uncoated fused silica capillary having 60 cm total length and 40 cm from the sample injection port to detector. Electrophoresis was carried out under 10 kV
and 13 pA at 30oC. The sample was electrokinetically injected under 5 kV and 7 p A for 5 seconds. An electropherogram of the analyte (showing UV absorption at 260 run) is illustrated in Figure 3.
Ezample 6 electrophoresis of 100 basepair DNA ladder using 3% RMl 8 in a 90 mM TBE Buffer A 3% (w:v) RM18 PDMA polymer in a 90 mM TBE buffer pH 8.3 was used to separate the components of the double stranded DNA ladder of Example 4. An Applied Biosystems model 270 HT was fitted with a 75 ltm inside diameter uncoated fused silica capillary having 60 cm total length and 40 cm from the sample injection port to detector. Electrophoresis was carried out under 10 kV and 8 ~A at 30oC. The sample was electrokinetically injected under 5 kV and 8 ~A for 5 seconds. An electropherogram of the analyte (showing UV absorption at 260 nm) is illustrated in Figure 4.

Ezample 7 F=lectronhore~is of 100 base~,r DNA ladder using 3% Polvacrvlamide with and without 0 OS% PDMA (RM181 in a 0 1 Glvcvlelvcine Buffer A 3% (w:v) linear polyacrylamide solution in a 0.1 M glycylglycine buffer pH
8.0 was used to separate the components of the double stranded DNA ladder of Example 4. An Applied Biosystems model 270 HT was fitted with a 75 pm inside diameter uncoated fused silica capillary having 60 cm total length and 40 cm from the ample injection port to detector. Electrophoresis was carried out under 10 kV
and 17 EtA at 30oC. The sample was electrokinetically injected under 5 kV and 8 ~tA
for 5 seconds. After 30 minutes no peaks were detected indicating that there was no separation of ladder components.
A second separation was conducted under identical conditions, except that the polymer solution used was a mixture of 3% linear polyacrylamide and 0.05%
PDMA (RM18). An electropherogram of the analyte (showing LTV absorption at 260 nm) is illustrated in Figure 5.

WO 95/16911 PCTlUS9sl13852 Eiample 8 ElectrQ~horesis of 100 basepair DNA ladder usine Polymer Solutions of Polyethylene oxide and Polv-N-vinvl~vrrolidone in 0.1 M Glv,~yl_elycine Buffers A 3% (w:v) solution of poly-N-vinylpyrrolidone (PVP) (average MW 360 kD) and a 5% (w:v) solution of polyethylene oxide (PEO) (average MW 35 kD) were prepared in 0.1 M glycylglycine buffers pH 8Ø The DNA ladder of Example 4 was electrophoretically separated in six separate experiments using the same apparatus and under the same conditions as used in Examples 4-7 with the exception that different polymer solutions were employed. The polymer solutions are listed in the table below with reference to the Figures illustrating the degree of separation accomplished. The poly(dimethylacrylamide) used was RM18.
Po(~rmer Solution Sep,~rat'gLn Figure 3% PVP Yes 6A
6% PVP Yes 6B
3% PVP + 0.5% PDMA Yes 6C

5% PEO No No figure 5% PEO + 0.5% PDMA Yes 6D
0.5% PDMA Yes 6E
5% PEO + 0.05% PDMA Yes 6F
Ezample 9 Separation of DNA Sequencin~Fra~ments in Polytdimethylacrvlamide) ~y Ca i~r~ElectroQhoresis Fluorescently labelled DNA sequencing fragments were obtained from Applied Biosystems, Inc. (Foster City, CA) (The fragments used were the "C"-terminated fragments used to make up the 4-color sequencing standard supplied by Applied Biosystems as Part No. 400993, Taq DNA Sequencing Standard). 8 pl of the mixture containing fragments terminating with dideoxycytidine and labelled with fluorescein (FAM-C fragments) was added to a 500 pl centrifuge tube and dried in a speed vac using moderate heating. ~ After adding 0.5 ml 50 mM EDTA solution and 6 ml recrystalized formamide to the dried FAM-C fragments, the mixture was heated at 95oC for 2 min then placed on ice.
A separation medium for electrophoresis was prepared as follows: A stock buffer was prepared by mixing 20 ml methanol 110 ml water and 2.8 g Tris followed by titration with 85% phosphoric acid to pH 8Ø The separation medium was prepared by mixing 3.6 ml stock buffer, 3.6 ml water, 4.8 g urea, and 0.65 g poly(dimethylacrylamide) prepared as described above (RM21 ) to give a total volume of approximately 10 ml. The resulting mixture was stirred for 3 hours then filtered through a 0.45 pm syringe filter.
An uncoated 50 prn inside diameter Polymicro Technologies fused silica capillary (Cat. No. 2000017) of total length 54 cm was prepared so that there was 40 cm between the injection inlet and the detection zone. Prior to the first use, the capillary was flushed with 20 column volumes of 1.0 M NaOH) 20 column volumes of water, then filled with separation medium. In subsequent runs with the same capillary, prior to use, the capillary was flushed with 20 column volumes of water, column volumes tetrahydrofuran (Tl~)) 20 column volumes 1 M NaOH, 20 column volumes of water, then filled with separation medium.
The FAM-C firagment sample was electrokinetically loaded into the capillary under 1.8 kV at 0.69 pA for 25 sec, taking care to keep the electrode and the end of 20 capillary as far apart as possible. The fragments were separated under 220 V/cm at 4.41 ~A. Both sample injection and electrophoresis took place at 22oC.
Fragment bands were illuminated at the detection window with an excitation beam from an argon ion laser (model 221-40MLA, Cyonics, San Jose, CA) operating at 1.5 mW.
The excitation beam was passed through a 0.5 optical density neutral density filter (#FNG 085, Melles Groit, Irvine, CA) and into a set of focusing optics composed of a 64 mm focal length 7 mm diameter positive lens and an 85 mrn focal length.5 mm diameter negative lens, resulting in a beam diameter of approximately 100 pm focused on the capillary detection window. Fluorescence erriission was collected at right angles by a 12 mm focal length 14 diameter aspheric collector lens and passed through a 530 run ItDF bandpass filter (Omega Optical, Brattleboro, VT) and to a Fabry set composed of a 48 mm focal length 19 mm diameter aspheric Fabry lens followed by a 17 mm 10 mm diameter spherical Fabry lens. The light was then imaged on a photomultiplier tube (#R98-21; Hamamatsu, San Jose, CA) for detection. The electropherogram of the separated fragments is shown in Figures 7A-7J. The numbers adjacent to;,the peaks indicate the fragment size.
Example 10 4-Color DNA Seauencing Analysis in Poly(dimethylacrvlamidel WO 95/16911 PCT/US9a113852 ~y Capillary Electrophoresis Fluorescently labeled DNA sequencing fragments were obtained from Applied Biosystems, Inc. (Foster City) CA) (Part No. 400993, Taq DNA
Sequencing Standard). To the dry Sequencing Standard were added 30 ~l of a sample loading reagent made up of 0.15% hydroxyethyicellulose (QP 1 OOMH Union Carbide) dissolved in a water-pyrrolidone. (75:25 (vol:vol)) solvent. The sample was then divided into two 15 I,.tl aliquots, heated at 95 °C for 2 min, and placed on ice.
The separation medium was prepared by dissolving 0.65 g poly(dimethylacrylamide) prepared as described above (RM21 ) and 4. 8 g urea in a solution of 1.0 ml 1.0 M TAPS (N-tris[Hydroxymethyl]methyl-3-aminopropanesulfonic acid), pH 8.0, and 6.2 ml water. The polymer solution was stirred overnight then filtered through a 0.45 Eun syringe filter. The viscosity of the final polymer solution was approximately 75 cp at 25 °C as measured in a Brookfield viscometer Model DV-II using spindle #00 at a speed of approximately 50 rpm (Brookfield Engineering Laboratories) Stoughton, MA).
An uncoated 50 Etm inside diameter fused silica capillary (Polymicro Technologies, Tucson) AZ Cat. No. 2000017) of total length 51 cm was prepared so that there was 40 cm between the injection inlet and the detection zonc. Prior to the first use, the capillary was flushed with greater than 20 column volumes of water, followed by greater than 20 column volumes of 0.1 M NaOH, followed by greater than 20 column volumes of water; then filled with separation medium.
The 4-color detection system used herein is similar to well known systems in the art of DNA analysis and is not a critical feature of the present invention, e.g., K~rger et al., Nucleic Acids Research 19( 18): 4955-62 ( 1991 ). The 4-color detection system utilizes an argon ion laser as a fluorescence-excitation light source that emits light at wavelengths of 488 and 514 nm. Typically the laser was operated at a total laser power of 9.9 mW. The laser light passes through a bandpass filter to remove the laser tube's cathode glow, the filter passing light having a wavelength of between approximately 485 nm and 515 nm. Next) a plano-convex lens diverges the light beam, the lens having a focal length of 100 mm and a diameter of 8 mm, e.g., Melles Griot part no. O1LPK041/078 (Melles Griot, Irvine, CA). The laser light then passes through a dichroic mirror which passes light having wavelengths 3 5 of between approximately 485 nm and 515 nm, then passes through a microscope objective and into the detection region of the separation capillary. The emission light is reflected off of the dichroic mirror and directed toward a spectrograph. To reduce the amount of scattered laser light passing onto the spectrograph, the w0 95/16911 PCTlUS9~113852 emission light passes through a long-pass filter having a cutoff of approximately 520 nm and is then focused onto an entrance slit of the spectrograph by a re-imaging lens having an 85 mm focal length, e.g., Melles Griot part no.
O1LPK035.
The spectrograph utilizes a 40~rg/mm) 450 nm blaze grating with a dispersion of 17 nm/mm. After passing through the spectrograph, the light then falls onto a charged coupled device (CCD) detector. The output signal from the CCD is transmitted to electronic computer for subsequent data analysis and presentation. The software used for data analysis was the Sequencing Analysis version 2.1.OB 1, which is similar to commercially utilized sequence analysis software (Applied Biosystems Model DNA Sequencer), the basic algorithm of which is generally described elsewhere, e.g., Smith et al, Methods in Enzymology Vol. 155 pages 260-301, Academic Press (1991).
The sample was electrokinetically loaded info the capillary using a field of 60 V/cm for 25 sec. The fragments were separated under a field of 160 V/cm at 3.0 ~A at a temperature of 42 °C. The run was allowed to proceed for approximately two hours.
The resulting electropherogram is shown in Fig. 8.
E~cample 11 4-Color DNA S uencing~,alysis in PolvvinylRyrrolidone b~Capillarv Electro hp oresis The separation medium was prepared by dissolving 1.0 g polyvinylpyrrolidone (Povidone , United States Pharmacopia) BASF, Kollidon 90 F) and 4.8 g urea in a solution of 1.0 ml 1.0 M TAPS (N-tris[HydroxymethyiJmethyi-3=aminopropanesulfonic acid), pH 8.0, and 6.2 ml water. The polymer solution was stirred overnight then filtered through a 0.45 ~m syringe filter.
The DNA sequencing fragments, the fragment sample preparation, the electrophoresis capillary, the 4-color detection system, the sample injection protocol, and the electrophoresis run conditions were all essentially the same as those used in Example 10.
The resulting electropherogram is shown in Fig. 9.
No dye mobility correction was applied to the data shown in Fig. 9. Because the addition of fluorescent dyes to the DNA sequencing extension products alters the electrophoretic mobility of the asociated DNA fragments, and because different dyes cause different mobility shifts, a "mobility correction" is required to normalize the electrophoretic mobility of fragments containing different dyes. Because the data in Fig. 9 has not been corrected for these mobility shifts, the order of the peaks is offset WO 95116911 PCT/US9:tI13852 somewhat. However, it is still possible to see that the requisite resolution of neighboring fragments has been achieved using the polyvinylpyrrolidone material.

Claims (13)

Claims:

1. A method of suppressing electroendoosmotic flow in capillary electrophoresis, the method comprising providing a separation medium containing one or more uncharged water-soluble silica-adsorbing polymers having (i) water solubility in a temperature range between about 20°C and about 50°C, (ii) a concentration in the separation medium in a range between about 0.001% and about 10% (weight/volume), and (iii) an absence of charged groups in an aqueous medium having a pH in the range between about 6 and about 9, and performing capillary electrophoresis in such medium.

2. The method of claim 1 wherein said one or more uncharged water-soluble silica-adsorbing polymers are substantially non-hydroxylic.

3. The method of claim 2 wherein at least one of said one or more uncharged water-soluble silica-adsorbing polymer is a polylactam.

4. The method of claim 3 wherein at least one of said one or more uncharged water-soluble silica-adsorbing polymer is polyvinylpyrrolidone.

5. The method of claim 1 wherein at least one of said one or more uncharged water-soluble silica-adsorbing polymer is an N,N-disubstituted polyacrylamide or an N-substituted polyacrylamide, wherein said nitrogen substituents are selected from the group consisting of C1 to C3 alkyl; halo-substituted C1 to C3 alkyl;
methoxy-substituted C1 to C3 alkyl; and hydroxyl-substituted C1 to C3 alkyl.

6. The method of claim 5 wherein said nitrogen substituents are selected from the group consisting of C1 to C3 alkyl; halo-substituted C1 to C3 alkyl; and methoxy-substituted C1 to C3 alkyl.

7. The method of claim 6 wherein said at least one of said one or more uncharged water-soluble silica-adsorbing polymer is poly(dimethylacrylamide).

8. The method of claim 7 wherein said electroendoosmotic flow is less than about 2 x 10-5 cm2/sec-volts.

9. The method of claim 7 wherein said one or more uncharged water-soluble silica-adsorbing polymers provides a substantially linear relationship between number of theoretical plates and size of polynucleotide in the size range of between about 100 and about 500 nucleotides.

10. A composition for separating polynucleotides by capillary electrophoresis, the composition comprising:
a charge-carrying component;
a sieving component; and a surface interaction component consisting of one or more uncharged water-soluble silica-adsorbing polymers having (i) water solubility in a temperature range between about 20°C and about 50°C, (ii) a concentration in the separation medium in a range between about 0.001%
and about 10% (weight/volume), and (iii) an absence of charged groups in an aqueous medium having a pH in the range between about 6 and about 9.

11. The composition of claim 10 having a viscosity less than about 5000 centipoise.

12. A method of separating different-sized polynucleotides by electrophoresis in an uncoated silica capillary, the method comprising the steps of:
providing an uncoated silica capillary having a first end and a second end, the uncoated silica capillary containing one or more uncharged water-soluble silica-adsorbing polymers having (i) water solubility in a temperature range between about 20°C and about 50°C, (ii) a concentration in the separation medium in a range between about 0.001% and about 100 (weight-volume), and (iii) an absence of charged groups in an aqueous medium having a pH in the range between about 6 and about 9;
loading a sample of different-sized polynucleotide in the uncoated silica capillary; and applying an electrical field between the first and second ends of the uncoated silica capillary so that the different-sized polynucleotides in the sample migrate through the uncoated silica capillary.

13. The method of claim 1 wherein the separation medium is located in an uncoated capillary tube.