WO1986003227A1

WO1986003227A1 - An assay for nucleic acid sequences, particularly genetic lesions

Info

Publication number: WO1986003227A1
Application number: PCT/US1985/002129
Authority: WO
Inventors: Floyd Taub
Original assignee: Dgi, Inc.
Priority date: 1984-11-23
Filing date: 1985-10-28
Publication date: 1986-06-05
Also published as: CA1258029A; US4820630A; NO862918L; AU591471B2; IL77078A0; JPS63501051A; DE3578190D1; NO862918D0; IL77078A; AU5195786A; JP2644215B2; EP0203143A1; EP0203143B1

Abstract

Lesions in genetic sequences, for example, the sickle cell anemia mutation in the beta globin gene, are detected by means of interactive labels in a nucleic acid hybridization assay. A signal is generated only if the labels are in physical proximity, which is made dependent on whether a predetermined normal or abnormal sequence is present by exposure to appropriate conditions such as restriction enzyme digestion or stringent hybridization.

Description

AN ASSAY FOR NUCLEIC ACID SEQUENCES, PARTICULARLY GENETIC LESIONS

BACKGROUND OF THE INVENTION

Embodiments of this invention were disclosed in Disclosure Documents 129717, dated August 2, 1984, recorded August 6, 1984, and 130094, dated August 14, 1984, recorded August 17, 1984, incorporated by reference, which the Patent and Trademark Office is requested to preserve.

In the past, genetic diseases were diagnosed based on clinical findings once the disease had developed. Various enzyme and protein tests were subsequently developed to confirm or provide more accurate diagnosis and to allow earlier diagnosis. Unfortunately, for many diseases no such tests are available.

Recently, it has become possible to analyze an individual's DNA (which is present in every cell) to determine if certain abnormal genes which will cause genetic diseases are present. These diseases include Huntington chorea, phenylketonuria, thalassemias, and sickle cell anemia. The abnormal genes are found by analyzing restriction site polymorphisms (RSPs) using "Southern blotting" (SB) (Southern, E. M. S., Molecular Biology, 1975, 98:503). This test is time consuming and expensive. However, it is an extremely important method, since it has allowed prenatal diagnosis and thus intervention to prevent birth of severely diseased individuals.

Kan and Dozy, The Lancet 910 (October 28, 1978) described a new approach to prenatal diagnosis of sickle cell anemia utilizing a "Southern blot" of DNA from a niotic fluid cells. When normal DNA was digested with the enzyme Hpa I, the beta-globin gene was contained in a 7.6 kb fragment. In variant DNA, the gene was found in fragments 7.0 kb (hemoglobin-A) or 13.0 kb (hemoglobin-S) in length. The polymorphic Hpa I site detected by this method was not located in the beta-globin gene itself, but rather in an adjacent sequence. Thus "this method of analysis is indirect and suitable only in those cases where the parents at risk can be shown to carry the appropriate linked polymorphism prior to amniocentesis . " Benz, Am. J. Ped. Hematol./Oncol. 6:59 (Spring 1984). (This was done by family studies.)

It is known that sickle cell anemia is caused by a single nucleotide base mutation in the beta globin gene which converts a glutamic acid codon (CAG) to one coding for valine (GTG) . Nienhuis, N. Engl. J. Med. 299:195 (1978) proposed direct analysis by means of a restriction enzyme whose recognition site is created or eliminated by the point mutation. His candidate, Mnl I, yielded small (60-80 bp) fragments that could not be resolved by blotting techniques at that time.

Wilson, et al. , US 4,395,486 (1983) found that direct diagnosis of sickle cell anemia was possible by restriction assay with an enzyme, such as Dde I, recognizing a CTNAG. The B-globin gene fragment was identified by a radiolabeled probe complementary to the 5' end of the gene. Individuals with normal hemoglobin had 175 bp and 201 bp bands; anemic individuals have a single 376 bp band. Unfortunately, the small Dde I generated fragments could be detected and distinguished only after sophisticated technical modification of the blotting techniques.

A new enzyme, Mst I, made possible the use of conventional techniques as described in Wilson, et al., PNAS (USA) 79:3628 (June 1982). The normal fragment was 1.14 bp long, while sickle cell individuals produced a 1.34 kb fragment.

These fragments are separated according to size by gel electrophoresis . Since many other fragments from the non-globin DNA are also present, a special procedure ( "Southern Blot") must be used to find the globin fragments . (Southern, PNAS [USA] 76 : 3683-3687 [ 1979 ] . ) After electrophoresis , the DNA is transferred to a filter support (ex. , nitrocellulose) ; then the filter is reacted with a radioactive probe which specifically binds to the globin sequences. This probe will stick to the glob in sequences and , following washing and autoradiography , it can be determined whether the patient has 1. 34 kb or 1. 14 kb length fragments or both. The process of electrophoresis, transfer, filter hybr id i z at i on , wa sh ing , and autoradiography is expensive, time consuming, and, for some size fragments, very difficult. •»

All of the aforementioned techniques for diagnosing SCA require that the disease create or destroy a restriction site.

Another approach permits one to detect single base changes (point mutations) in geno ic DNA even where the change does not alter a restriction site . "Under appropriate hybridization conditions , only perfectly base-paired oligonucleotide-DNA duplexes will form; duplexes containing a single mismatched pair will not be stable . " Conner, et al . , PNAS (USA) 80 : 278 (January 1983 ) . In this method, an oligonucleotide complementary to the DNA of a normal (or afflicted) individual in the af fected region is synthesized , radiolabeled, and hybridized under stringent conditions. The duplexes are examined by autoradiography . Commenting on this approach , Orkin , BLOOD 63-249 (February 1984) writes: "In order to detect .globin DNA fragments or other single-copy sequences in blot hybridization of total DNA , the synthetic probe must be rendered highly radioactive. Our own experience indicates that this is the most troublesome part of the methodology. "

Thus, while more versatile than restriction mapping techniques, the stringent hybridization technique shares the disadvantageous requirements for radioactive probes, ge l el ectrophore s is , southern blotting , f ilter hybridization , washing and autoradiography. The present invention dispenses with these requirements.

It is known that radiolabeling of probes may be replaced by labeling with biotin, the biotin label than being detected by its affinity with avidin or its binding to an anti-biotin antibody (either then being linked to a reporter enzyme like peroxidase) . Renz, EMBO J. 2 : 817 (1983) . The art does not teach, however, us e o f int eractive labels whose interaction is differentially affected by treatment depending on the sequence to which they are bound.

Falkow , US 4 , 358 , 935 describes a method of diagnosing an infection utilizing a heterogeneous assay for pathogen DNA or RNA. The assay reagent is a labeled RNA or DNA probe. The patent states that "for the most part" the probe will be radiolabeled . It generally alludes to the use of labels known in the immunoassay art, but without expression of any preference for a particular nonradioactive label or any discussion of interactive labels. Nor does it mention use of adjacent probes that are differently labeled.

Taber, EP Appl 114 , 668 discloses a family of DNA probes each of which hybridizes to a different region of a s ingle chromosome of Salmonella bacteria . These probes are preferably radiolabeled , but also may be labeled with biotin. This reacts with avidin to which is bonded a fluorophore, an electron-dense compound, an antibody, or one member of a catalyst/substrate pair. While several probes are preferably used simultaneously, additively increasing the intensity of the resulting signal, there is no suggestion of any interaction among the multiple labels thus associated with the chromosomal DNA. The interactive labels of the present invention are more sensitive to the fine structure of sample DNA than Taber's noninteractive multiple labels.

Peterson, WO 83/03260 describes a method of determining the polymorphism of human MHC alleles which, like that of Wilson, is dependent on the fractionation of restriction fragments by size. While it recognizes alternatives to radioisotopic labels, such as enzymes, enzymatic substrates, co-factors, co-enzymes and luminescent substances, it does not refer to the use of interactive labels.

Ehrlich, EP Appl 84, 796 and Mach, EP Appl 103, 960, both relate to HLA (human lymphocyte antigen complex) diagnostic typing based on restriction site ploymorphism. As with Wilson, the DNA is restricted and fractionated prior to hybridization. The Mach reference refers to alternatives to radiolabeling of hybridization probes, but not to the use of interactive labels.

Ullman, US 3, 996, 345 teaches an immunoassay system utilizing a fluorescer-quencher pair. In one embodiment, the fluorescer is attached to a first receptor and the quencher to a second receptor for a polyepitopic ligand.

Maggio, US 4, 233, 402 describes the use of enzyme immunoassay utilizing a reactant label conjugated to an antibody to said analyte, and a signal producing label conjugated to an antibody to said analyte, where the reactant labels acts on a precursor compound to generate a signal mediator which in turn directly or indirectly acts on the signal producing label to generate a signal. Maggio teaches that one label must be attached to the analyte and the other to the receptor. Thus, he teaches against the use of two interactively labeled probes or of a doubly interactively labeled probe. Finally, Maggio does not suggest that interactive label may be used to distinguish a normal DNA sequence from a mutated sequence, let alone suggest a means whereby the difference in sequence operates to affect the interaction of the labels.

Other immunoassay patents of interest are Litman, US 4, 275, 149; Litman, US 4, 299, 916; Zuk, US 4, 208, 479; and Harris, US 4, 463, 090. The Harris patent deals with cascade amplification of immunoassay signals.

These i munoassays are used to measure trace amounts of organic compounds, not to elucidate fine structure. If the aforestated assays are used to detect a ligand-receptor complex comprising a DNA probe hybridized to sample DNA, they will not be effectual at detecting the lesion. Since stringent hybridization conditions are not used, and the duplex is not cleaved between the labels, the presence or absence of the resulting signal is not dependent on the presence of the lesion. Generally speaking, these immunoassay techniques require special adaptation to detect the fine difference in nucleic acid sequence with which the present invention is concerned.

Farina, US 4,378,428 relates to a homogeneous immunoassay in which one label is the S-peptide of ribonuclease A and the other is the S-protein of ribonuclease A. The S-peptide and S-protein are obtained from ribonuclease A by digesting the latter with subtilisin, a bacterial protease. My assay is a hybridization assay, not an immunoassay, and I digest a nucleic acid analyte, not a protein precursor of the labels employed. Gibbons, US 4,287,300 relates to a homogeneous immunoassay in which a charged label, by its electric field, modulates the signal producing activity of the second label.

Zuk, US 4,435,504 describes another homogeneous immunoassay of the product/ substrate type.

Campbell, US 4,478,817 teaches that a nucleic acid may be the antigen detected in an immunoassay utilizing a chemiluminescent or biolu inescent label. The nucleic acid is bound by an antibody, not by a complementary nucleic acid as in my invention.

Heller, EP Appl. 70,685 relates to the identification of "slow infection" diseases by a hybridization assay in which a first ss-polynucleotide reagent having a chemiluminescent catalyst and a second ss-polynucleotide reagent having an absorber/ emitter moiety are hybridized to essentially adjacent regions of target ss-polynucleotide at sites less than 100 angstroms apart. The two reagents may be obtained by cleavage of a source-polynucleotide.

The physical proximity, and hence, the ability to interact, of Heller's two reagents are not dependent on the presence of a lesion in the target polynucleotide. Nor does Heller recognize that interaction may be controlled by differential digestion or by stringent hybridization .

Furthermore, Heller does not teach use of his method to diagnose a genetic disorder, or, more particularly, to diagnose sickle cell anemia. He does not teach attaching two interactive labels to single probe, or attaching one interactive label to the target polynucleotide and the other to the probe. He does not teach use of scavenger means or of enzymatic labels, or particularly of two enzymatic labels where the product of the first enzymatic reaction is the substrate of another. He does not teach use of his method to determine the number of copies of a gene in a subject's DNA or to determine the family relationship between a first subject and second subject. Finally, he imposes a severe constraint on the distance separating the two labels.

Heller, EP Appl. 70,687 describes a heterogeneous hybridization assay in which an immobilized sample polynucleotide is hybridized with a luminescent-labeled polynucleotide reagent.

Malcolm, WO 84/03520 teaches that a polynucleotide probe may have a poly (dA) or poly (dT) tail and that an enzymatic label may be attached to this tail. He does not teach use of an antibody linker between the homopolymeric tail and the label.

Rabbani, EP Appl. 97,373 teaches that a genetic disorder may be diagnosed by preparing a labeled polynucleotide complementary to the sequence associated with the disorder and hybridizing it with the subject's DNA. There is no teaching of the use of i teractive labels.

While the discussion herein focused on prenatal diagnosis of sickle cell anemia, the method of the present invention is equally applicable to a variety of other disorders for which the locus of the lesion, and either the normal or mutated sequence about the lesion, are known or isolatable.

SUMMARY OF THE INVENTION In the diagnostic method of this invention, sample cells are collected, their DNA is isolated, purified, denatured, and hybridized. The sample DNA and/or probe DNA are labeled. At least two labels are utilized, and these labels are chosen so that they cooperate, when in physical proximity, to- yield a detectable signal. The labels are associated with the sample or probe DNA at locations such that their continued physical proximity is dependent on whether the sample DNA contains the sequence or lesion of interest.

These sequences may code for a protein, may regulate DNA expression, or otherwise be of interest. Lesions are single or multiple insertions, deletions, or substitutions, i.e. , mutations, of biological significance.

In another application of this invention, one may assay DNA for the degree of amplification of a particular sequence, such as a multi-drug resistance gene, in a cell. For example, Robinson, et al.. Nature 609-626, 628 (June 1984) report that a 1.1 Kb fragment was strongly amplified in certain multi-drug resistant tumor cell lines. The level of the signal generated by the method of this invention would be indicative of the degree of amplification. In a simple modification of this procedure, the mRNA transcribed from said gene is assayed instead of the gene itself. This provides an indication of the degree of expression of the gene in question. One may assay for cellular and viral oncogenes and other tumor markers besides multi-drug resistance. Another use would be to assay for abnormal number of chromosomes by assaying for a sequence normally present only on that chromosome in a known number of copies. This would be of value in the diagnosis of Klinef elter ' s , Turner's, and Down's Syndromes, as well as other conditions associated with chromosomal abnormalities.

Still another use would be to determine t family relationship of two subjects by assaying for marker genes. Preferably, one would assay for the presence of several markers. Source of Sample DNA

Sample DNA may be isolated from cells present in the amniotic fluid, or from peripheral blood lymphocytes, as taught by Wilson, et al., US 4, 395, 486 (1983) and others. Other convenient sources of DNA may be present in a particular situation and it is not intended that this invention be construed to be limited to any particular source or manner of isolating sample DNA. Source of Probe DNA

Probes may be prepared by conventional techniques, including chemical synthesis, reyerse transcription from mRNA, or restriction-and isolation of DNA of known content or sequence. It is not intended that this invention be construed to be limited to any particular manner of preparing the probe.

The probe prepared is one having a sequence complementary to a region proximate to the lesion. By "proximate" is meant either "adjacent", or "including", or both, as may be desirable. Finally, the probe prepared may be complementary to either the coding or anticoding strand of the gene, as desired. Example of Labels

These may include but are not limited to enzymes, enzyme substrates, proenzymes, proenzy e activators (including cofactors and coenzymes) , reagents to alter the microenvironment such as various polar or nonpolar or other chemicals or polymers, fluorescent labels, biolu inescent labels, or any other labels that may interact with each other to enhance, alter, or diminish a signal. In some situations it may be desirable to use more than two interactive labels (for example an enzyme cascade or chain might be used) . In some instances it may be desirable to use more than two probes also. The density of the label(s) on the probe, as well as its (their) location may be varied. Examples of Signals

These may include but are not limited to:

A. P rodu ct ion o f luminescent ( including fluorescent) products.

B. Alteration of the luminescence ( including amplitude, polarization, and other properties) of one label by the other.

C . Chemiluminescence.

D. Light absorbent (colored) products.

E. pH Changes.

F. NMR changes.

G. Alteration in the absorption or emission of electromagnetic radiation by the label or other component, generally.

H. Gravimetric , volumetric, or electrochemical changes .

I . Precipitation or agglutination, generally.

The term "signal* is also used broadly herein to include the discontinuance of an existing signal .

A "signal" may constitute a rate of change in a detectable parameter rather than an absolute value of a parameter.

The s ignal may b e mon i to red individually , automatically, or semi-automat iσally.

Presently , the use o f en zymatic labels is preferred. Attachment of Labels to Probes

The labels may be attached to the probes, directly or indirectly, by a variety of techniques. They may be covalently bound or held to the probe by a variety of associations. Depending on the precise type of labels used they might be located at the ends of the probes throughout the length of the probes or attached to linkers of various sizes and compositions to facilitate interactions. One form of attachment would be to label an antibody specific to a homopolymeric DNA strand, and utilize a probe having a homopolymeric tail. The label would then be attached to the probe by the antibody linker by antigen-antibody binding.

The label may be specifically attached to the probes following hybridization. In this case the probes might contain small tags, such as biotin or mercury and the specific labels would be attached selectively based on the affinity for these tags at any time even after hybridization. (The advantage of this system would be the minimization of steriσ hindrance of the hybridization reaction.) Additional bases, or other moieties, might be added to the ends of the probes (1) as sites of label attachment, (2) to facilitate the interaction by spatial or steric effects or (3) to help bring the labels together. For example a short sequence of complementary bases attached to the two probes might facilitate interaction of the labels after the probes were bound to - the genomic DNA. The attraction of sequences attached to the labels would of course be kept below that required for stable binding in the absence of sample nucleic acid.

A preferred technique of labeling DNA is given by Renz and Kurz, Nucleic Acids Research 11:3435 (1984). They describe the use of polyethylenimine as a cross linking agent to bind enzymes to DNA probes.

The size and composition of the DNA sequences (probes) to which the labels are attached will depend on the specific sequence being analyzed.

DESCRIPTION OF THE SEVERAL EMBODIMENTS In the first embodiment of the method of this invention, a first labeled probe, complementary to a region 5' of the site of interest, and a second labeled probe, complementary to a region 3' of the site of interest, are utilized. If the site constitutes a recognition/restriction site for an enzyme, digestion of the sample DNA with that enzyme and hybridization of the restriction fragments to the labelled probes will separate the two labels and thus hinder their interaction to produce a signal.

Many combinations of interactive labels are possible. In one preferred combination, the first label is the enzyme glucose oxidase, which, acting on a glucose substrate, generates hydrogen peroxide, and the second label is the enzyme horseradish peroxidase, which catalyzes the chemiluminescent reaction of the hydrogen peroxide with luminol. In a second preferred combination, one label is hexokinase and the other is glucose-6-phosphate dehydrogenase . Litman, et al.. Anal Biochem. 106: 223 - 229 (1980) . A number of useful enzymatic labels and reactions are taught in tables IV through VIII of Litman, US 4, 275, 149 (1981).

It is not necessary to utilize two enzymatic labels . One label may be, for example, aminobutylethyl-isoluminol (ABEI) , and the other fuorescein. The ABEI is a chemiluminescent substance which exhibits a spectral shift as a result of interaction with the fluorescein. Patel and Campbell, Clin. Chem. 29: 1604-1608 (1983).

In still another combination, the DNA probe is labeled with beta galactosidase, and macromolecular o-nitrophenyl-beta-galactoside, a positively charged substrate for that enzyme, is bound by electrical attraction to (negatively charged) sample DNA. The interaction of substrate and enzyme is detectable by monitoring the rate of increase in light scattering. Gibbons, et. al., Clin. .Chem. 29: 1602-1608 (1983). In a refinement of this method, a "scavenger" enzyme is used to hinder interaction between labels attached to unlinked DNA fragments. For example, the enzyme catalase may be used to destroy free hydrogen peroxide in the peroxidase system. Phosphofructokinase may be used as a scavenger in the hexokinase system. Other methods of limiting diffusion of free components of the signal generating system or to diminish the signal generated by such components may be used.

In another refinement of this method, a "cascade* of more than two enzymes may be used in the signal-generating system. Such multiple enzyme cascades, culminating in signal generation, are known from Harris, US 4,463,090 where they are used in enzyme immunoassays .

In a second embodiment of this invention, a single doubly-labelled probe is used which is complementary to the region of interest. The points of attachment of the first and second labels are then sufficiently far apart so as to be left on separate fragments if a restriction enzyme acts upon the mutated site.

In a third embodiment of this invention, a single labelled probe is used, but an interactive label is also attached to the sample DNA.

In a fourth embodiment of the invention, a single label is attached to the probe, or the sample DNA, and this label generates a signal which is altered upon hybridization. For example, the fluorescent polarization of a fluorescent-labeled probe may be altered when the probed is hybridized to the sample DNA.

In a fifth embodiment of this invention, interactive labels are utilized to assay point mutation which do not create or destroy a recognition/restriction site. One label is attached to an oligonucleotide complementary to the normal DNA sequence, and the other label is attached to the sample DNA or to another poly or oligonucleotide complementary to a proximate region of the sample DNA. As taught by Conner, et al., PNAS (USA) 80:278 (1983), under appropriate hybridization conditions the normal sequence will hybridize but the mutated sequence will not. Thus, the labels will interact effectively only if the sequences match perfectly.

The precise size and composition of the synthetic probes would depend on many factors including the specific sequence being analyzed and any alterations in the formation and stability of the hybrids that might result from the attachment of labels or tags for label attachment.

As taught by Orkin, BLOOD 63:249 (February 1984), the hybridization conditions may be established with cloned mutant and normal genes and then extended to total genomic digests.

Of course, it is possible to utilize a probe which is complementary to the mutated rather than the normal sequence, in which case the signal is indicative of the genetic disorder.

In a sixth embodiment of this invention, an enzyme is utilized which preferentially attacks single stranded DNA, such as SI nuclease or Mung-bean nuclease. (Brief descriptions of these enzymes may be found in Maniatis, Molecular Cloning 140-141, 1982.) If the probes are perfectly homologous to a region of the sample DNA, no point of attack is offered by the duplex. If, however, a mutation (deletion, insertion or substitution) prevents perfect binding, the honomologous regions would be attacked and cut. One might use a doubly labeled probe, the interacting labels 5'and 3', respectively, of the expected point of attack. Alternatively, one label could be placed on the probe, and the other on the sample DNA; or both labels could be placed on the sample DNA; so long as the labels would be on separate fragments if enzymatic attack was effective.

While the discussion above utilizes sample DNA and

DNA probes by way of example, the methods of this invention may readily be adapted to the examination of sample RNA or the use of RNA probes.

While the methods of this invention are of great advantage in the detection of DNA lesions associated with genetic disorders, they may readily be adapted to the detection of the preservation or alternation of a predetermined sequence, and the term "gene" therefore should be read broadly. The method is not limited to human genes, but may be applied to the assay of nucleic acid sequences of human, animal, plant, microbial, or viral origin, whether natural or synthetic, for instance, for diagnostic purposes. The sample nucleic acid may be attached to support means.

Although several embodiments of the invention have been described, it will be appreciated that many combinations, modifications and variations are possible in the light of the above, teachings. It is, therefore, to be understood that this invention is not limited to the specific embodiments described.

The following experimental examples illustrate the practicality of this assay methodology.

Example 1: Homogeneous Solution Hybridization Assay for Nucleic Acid

Conjugates of polyribonucleotides (Poly I, C, U) to peroxidase (P) or Glucose oxidase (G) were made by the Renz technique using concentrations and amounts as specified in Renz. Nuc. Acids Res. 12:3435. .omplexes of RNA and enzymes were isolated according to size by S300 gel filtration, which separated them from the large amounts of enzymes that- were not conjugated to RNA. In particular, free peroxidase and glucose oxidase were separated from the complexes by this gel filtration.

In this manner, complexes of Poly I to peroxidase (complex PIP) , Poly C to glucose oxidase (complex PCG) , and Poly U to glucose oxidase (complex PUG) were formed. In addition, both glucose and peroxidase were simultaneously conjugated to Poly U in a single tube to form a single preformed complex (complex PUPG) .

In order to test for specific hybridization of Poly I to Poly C the following were mixed in tubes as indicated:

Complex 1 Complex 2

Tube 20 ul 20 ul Expected Interacti

A PIP PCG Poly I and Poly should hybridi placing peroxid near glucose oxida

B PIP PUG Poly I and Poly s h o u l d n hybridize. Enzy s h o u l d a independently .

PUGP This preform complex should h glucose oxidase peroxidase near e other. Following 45 minutes hybridization (37 deg. C, 0.1M Na. ⁺ , pH 6.5, 0.6 mg/ l Poly A carrier to prevent non-specific sticking) without separation of bound and free probe or any additional steps, an enzyme development reagent (orthophenyldiamine [OPD] lmg/ml; sodium acetate 50mM, pH 5.1; 4% glucose) was added. For the reaction to occur, the glucose oxidase must synthesize H₂0₂ (from the glucose) . The peroxidase can then use the H2O2 to create a change in the OPD substrate.

In tube C, where the interactive complex was preformed, color development occurred in 15 to 60 minutes. In tube A, where hybridization caused the glucose and peroxidase to interact closely, color development also occurred to a similar extent. Initially some color also developed in tube B. However, this appeared lighter than in tube A and tube C. Following overnight enzyme development, crystals had grown in tube C indicating interaction of peroxidase and glucose oxidase. Crystals had also grown in tube A. Tube B, however, had no evidence of crystals. Control reactions containing no complexed enzymes also had no crystal development. Crystals were brown in transmitted or reflected light and showed red orange birefringence in polarized light.

To my knowledge this is the first demonstration that a solution (or any) hybridization can be performed and analyzed without cumbersome methods to separate free from bound nucleic acid. Further, it is the first demonstration of a non-radioactively labeled probe directly monitoring a solution hybridization. In addition, the development of crystals as well as color differences may provide a novel and potentially useful assay. (As will be indicated in the next experiment, substrate conditions may be varied to alter the form of the final product.)

Example 2: Use of Catalase as a Scavenger in a

Homogeneous Assay of Nucleic Acid Hybridization

In order to confirm and extend the results of Example 1, and to decrease the background seen when nonhybridizing nucleic acids containing G. and P. were mixed in B (above) , a similar experiment was designed. but with catalase added to the development mix. This would minimize the diffusion of H θ₂ from the glucose oxidase to the peroxidase unless the two enzymes were in close proximity. Free catalase was present as scavenger in the color development reagent. The catalase was capable of destroying H₂0₂ freely diffusing in the mixture. The color development reagent was otherwise identical to that of example 1 except for the presence of additional glucose substrate. The color development mix contained 25% rather than 4% glucose to supply adequate substrate and generate soluble colored rather than crystalline products. Three different amounts of catalase were tested in each panel of enzyme complexes - 7.5, 15, and 30 units/ml. The tubes of Panel A contained 50 ul Poly I labeled with peroxidase (PIP) and 50 ul complementary polynucleotide C labeled with the interacting glucose oxidase (PCG) . The tubes of Panel B contained 50 ul of PIP complex and. 50 ul of the noncomplementary PUG complex. The tubes of panel C contained 50 ul of PIP complex and 50 ul of a preformed complex of Poly U, enzyme label G and enzyme label P (PUGP) . Hybridization conditions were 30 deg. C, 0.1M NaCl, pH 6.5, and 0.6 mg/ml Poly A.

After 30 minutes of color development, the (positive control) preformed complex (Panel C) showed a dark reaction at all levels of catalase. The amount of color generated by the non-hybridizing nucleotides in tube B was lighter at all concentrations of catalase, showing inhibition by catalase. As anticipated, the hybridized complexes of panel A were intermediately inhibited by catalase. At each concentration of catalase. Panel A is darker than Panel B, indicating that the polynucleotides hybridized to reduce the peroxide diffusion distance for G and P interaction. Best results were achieved with 15 units/ml of catalase, though 10 units/ml is now preferred.

Thus, the system of interactive labels can be used to monitor solution phase hybridizations in a simple rapid manner by formation of colored (or crystalline) products. In addition, the presence of scavenger enzymes facilitates the observation of enzyme interaction.

Claims

I claim: 1. A method of detecting a lesion in a genetic sequence which comprises (a) isolating sample nucleic acid containing said sequence (b) associating said sample nucleic acid with a signal generating system comprising at least two labels capable of interacting to generate a signal when in physical proximity, (c) stimulating said signal generating system under conditions in which the physical proximity of the labels is dependent on the presence of the lesion, and (d) attempting to detect the signal.

The method of claim 1 in which one label is attached to one nucleic acid probe, the other label is attached to another nucleic acid probe, one probe hybridizing to the region 5' of the lesion, and the other probe hybridizing to the region 3' of the lesion. The method of claim 1 in which both labels are attached to a single nucleic acid probe, one label has a point of attachment 5' of the locus of the lesion, and the other label has a point of attachment 3' of the locus of the lesion, said probe being complementary to said sample nucleic acid in a region proximate to said lesion.

The method of claim 1 in which one label is attached to the sample nucleic acid and the other label is attached to a nucleic acid probe complementary to said sample nucleic acid in a region proximate to said lesion. The method of claim 1 wherein the conditions of step (c) are conditions under which single stranded nucleic acid is cut. 6. The method of claim 4 wherein said sample nucleic acid and said nucleic acid probe are hybridized under conditions sufficiently stringent so that hybridization requires perfect homology between said sample nucleic acid and said nucleic acid probe.

7. The method of claim 1 wherein said lesion creates or destroys a recognition site for a restriction enzyme, and the conditions of step (c) include exposure to said restriction enzyme.

8. The method of claim 7 in which the sample DNA is associated with a signal generating system comprising at least one labeled probe by hybridizing it to the probe after digesting the sample DNA with said restriction enzyme.

9. The method of claim 7 in which the sample DNA is associated with a signal generating system comprising at least one labeled probe by hybridizing it to the probe before digesting the sample DNA and the probe with said restriction enzyme.

10. The method of claim 1 in which the sample DNA is associated with a signal generating system comprising at least one probe-attached label and the probe is perfectly homologous to a normal subsequence of said sequence.

11. The method of claim 1 in which the sample DNA is associated with a signal generating system comprising at least one probe-attached label and the probe is perfectly homologous to a subsequence of said sequence containing a predetermined lesion.

12. The method of claim 1 in which the resulting signal is quantified. 13. The method of claim 1 in which one label is a proen zyme activator wh ich acts upon a proenzyme to yield an activate.d form which interacts more strongly with a second label to generate a signal .

14. The method of claim 1 in which a first label is an enzyme which acts on a substrate to generate a messenger species which in turn interacts with a second label to generate a signal .

15. The method of claim 14 in which the signal generating system further comprises scavenger means operating on said messenger species to diminish its interaction with the second label.

16. The method of claim 1 in which the signal generating system comprises a cascade of at least three stages.

17. The method of claim 1 in which the genetic sequence is the human beta globin gene and the lesion is the presence of a codon coding for valine at codon position 6.

18. The method of claim 14 in which the labels are selected from the group consisting of (a) glucose oxidase/horseradish peroxidase and (b) hexokinase/glucose-6-phosphate dehydrogenase .

19. The method of claim 18 in which the scavenger means is selected from the group consisting of ( a ) catalase and (b) phosphofructokinase , respectively. 20. A method of diagnosis in a subject of a genetic disorder of known genetic determination which comprises (a) obtaining cells from the subject, (b) isolating nucleic acid from said cells bearing the gene whose normality is in question, and (c) distinguishing a normal gene from an abnormal gene by means of a signal generated by a signal generating system comprising a plurality of interactive labels whose interaction after treatment of said nucleic acid is dependent on the normality of said gene.

21. The method of claim 1 in which a nucleic acid molecule is labeled by attaching a label to it be cross-linking means.

22. The method of claim 21 in which the cross-linking means includes polyethylenimine.

23. The method of claim 20 for prenatal diagnosis in which said cells are of fetal origin.

24. An assay for the presence of a nucleic acid region of interest in a sample nucleic acid, comprising:

(a) preparing a first nucleic acid probe complementary to a first subregion of said region and a second nucleic acid probe complementary to a second subregion, said subregions being adjacent and non-overlapping;

(b) labeling said first probe with a first enzymatic label and said second probe with a second enzymatic label, said first and second labels being capable of interacting by diffusion of a chemical species to generate a signal, said signal being stronger when the labels are in physical proximity;

(c) hybridizing said probes to the sample nucleic acid whereby said labels are brought into and maintained in physical proximity; and

(d) monitoring said signal.

25. The assay of claim 24 in which the species is hydrogen peroxide.

26. The assay of claim 24 where said sample nucleic acid is obtained from a cell or virus, and the nucleic acid region is functionally related to the cell or virus' ability to function or grow in a particular environment.

27. The method of claim 1, in which the label is attached to the probe by an antibody linker which binds specifically to a region of the probe.

28. The method of claim 27, in which said region is a homopolymeric tail.

29. A test kit for the diagnosis of sickle cell anemia comprising a probe, complementary to the normal or variant human beta globin gene in the vicinity of codon 6 for sufficient number of bases 3' and 5' of codon 6 to avoid significant hybridization to a foreign region, said probe being labeled 5' and 3' to codon 6 with labels which interact when in physical proximity to generate a signal.

30. The test kit of claim 29 wherein said labels are substances having respectively the enzymatic activities of glucose oxidase and horseradish peroxidase. 31. The test kit of claim 29 further comprising s c avenger means interf ering with the generation of signals by labels which are not in physical proximity.

32. The test kit of claim 30 also comprising a substance having the enzymatic activity of catalase as a scavenger for hydrogen peroxide.

33. The assay of claim 24 in which the sample DNA is attached to a support means.

34. A test kit for the diagnosis of a genetic disorder in a subj ect characterized by a lesion in the subject's DNA which comprises a first nucleic acid probe complementary to a region upstream of said lesion and having a f irst label , and a second nucleic probe complementary to a region downstream of said les ion and having a second label , said labe l s being capable of interaction to generate a signal, said signal being stronger when the labels are in physical proximity resulting from the hybridization of said probes to said complementary regions.

35. The test kit of claim 33 wherein said first label is glucose oxidase and said second probe is horseradish peroxidase.

36. The test kit of claim 34 further comprising catalase.

37. A me tho d o f d i a gn o s i n g a c o n d i t i o n characterized by a chromosomal abnormality which comprises identifying a gene present in a fixed number of copies in the normal complement of cellular DNA and determining the number of copies of said gene in a subject's DNA by utilizing the method of claim 1. 38. The method of claim 37 in which the condition is selected from the group consisting of Klinefelter's Syndrome, Turner's Syndrome, and Down's Syndrome.

39. A method of determining the family relationship between a first subject and a second subject which comprises assaying the DNA of said subjects for the presence of at least one nucleic acid region of interest by

(b) labeling said first probe with a first label and said second probe with a second label, said first and second labels being capable of interacting to generate a signal, said signal being stronger when the labels are in physical proximity;

(c) hybridizing said probes to the sample nucleic acid whereby said labels are brought into and maintained in physical proximity;

(d) measuring said signal; and

(e) determining the likelihood of a family relationship between said subjects from the magnitude of said signal.

40. The test kit of claim 31 in which said labels are attached to said probes by linker means.

41. The method of claim 20 in which the signal is quantified. 42. The method of claim 20 in which the treatment is stringent hybridization conditions, one label is attached to the sample nucleic acid, and another label is attached to a probe capable of perfect hybridization to either the normal gene or the abnormal gene, but not to both.

43. The method of claim 20 in which the treatment is digestion with a restriction enzyme and the abnormality is associated with the creation or destruction of a recognization site for said enzyme.

44. The method of claim 1 in which a first label is a chemiluminescent substance and a second label is a fluorophore interacting therewith.

45. The method of claim 44 in which the first label is ABEI and the second label is fluorescein.

46. The method of claim 2 wherein said sample nucleic acid and said nucleic acid probe are hybridized under conditions sufficiently stringent so that hybridization requires perfect homology between said sample nucleic acid and said nucleic acid probe.

47. The test kit of claim 29, further including a restriction enzyme whose recognition site is created or destroyed by the sickle cell anemia lesion at codon 6 of the beta globin gene.

48. The test kit of claim 34, further including a restriction enzyme whose recognition site is created or destroyed by the sickle cell anemia lesion at codon 6 of the beta globin gene.

49. The method of claim 1 in which a first label is a substrate and a second label is an enzyme acting on said-substrate to generate a signal. 50. The method of claim 49 in which the first label is a macromolecular beta-galactoside and the second label is beta-galactosidase.

51. The method of claim 14 in which the number of said identical regions in said sample is determined from the signal level.