Abstract:
Discrimination between RNAs which differ by as little as a single nucleotide is accomplished by having an excess of unlabeled non-complementary oligonucleotide present during hybridization with a labeled complementary nucleotide. The non-complementary oligonucleotide blocks hybridization of the labeled complementary oligonucleotide sequence without affecting hybridization of the labeled complementary oligonucleotide to the complementary sequence. The label may be an isotope, a fluorescent group or of any other type. The technique permits examination of the transcription of highly related allelic and non-allelic genes present in the same cell and the quantification of such transcripts by use of appropriate internal control. The technique is also useful in oligonucleotide hybridization to DNA sequences which differ only by a single nucleotide.

Description:
This application is a continuation-in-part of Itakura and Wallace application Ser. No. 825,903 filed Mar. 21, 1986 and abandoned Aug. 5, 1987, which is a continuation of Ser. No. 438,642 filed Nov. 3, 1982 and now abandoned. The full text of application Ser. No. 438,642 is incorporated herein by reference. 
    
    
     This invention provides a technique for discriminating between RNAs and DNAs which differ by as little as a single nucleotide. The technique is fully described in Nozari, Rahbar and Wallace, &#34;Discrimination among the transcripts of the allelic human β-globin genes β A , β S  and β C  using oligodeoxynucleotide hybridization probes,&#34; Gene, 43:23-28 (1986) which is incorporated herein by reference. A copy of the Gene reference is attached. 
     BACKGROUND OF THE INVENTION 
     The ability to discriminate between two genes that differ by only a single base pair has led to important applications, particularly in the diagnosis of certain human genetic diseases as well as to the screening of mutations created by site-directed mutagenesis. The most general approach to this discrimination has been through the use of specific synthetic oligo hybridization probes. Oligo:DNA duplexes containing single base pair mismatches are significantly less stable than those which are perfectly base-paired. Under appropriate conditions, oligo probes will only hybridize to their cognate sequence and not to a sequence containing one or more non-complementary nucleotide. Thus, oligo hybridization can be used to determine the sequence of a short region of a DNA molecule. 
     Until recently, it has not been possible to discriminate between RNA molecules which differ by only a single nucleotide. Although oligo probes have been used to discriminate between highly related RNAs, never have single nucleotide differences been probed. 
     It has been shown that G:T mismatches in oligo:DNA duplexes are less destabilizing than other mismatches. Similarly, G:U mismatches in RNA:RNA duplexes are more stable than other mismatches. To optimally discriminate two genes which differ by a single transition mutation, oligo probes can be synthesized such that they form an A:C mismatch with the DNA of the non-complementary allele. Due to the fact that RNA is single stranded, it is not always possible to avoid an oligo probe forming a G:T or G:U mismatch with a non-complementary RNA when hybridizing oligo probes to two RNA molecules which differ by a single nucleotide. To discriminate the two RNAs on the basis of oligo hybridization, one must attempt to optimize the destabilizing effect of the mismatch formed. 
     SUMMARY OF THE INVENTION 
     Discrimination between RNAs which differ by as little as a single nucleotide is accomplished by having an excess of unlabeled non-complementary oligonucleotide present during hybridization with a labeled complementary nucleotide. The non-complementary oligonucleotide blocks hybridization of the labeled complementary oligonucleotide sequence to the non-complementary sequence without affecting hybridization of the labeled complementary oligonucleotide to the complementary sequence. The label may be an isotope, a fluorescent group or of any other type. The technique permits examination of the transcription of highly related allelic and non-allelic genes present in the same cell and the quantification of such transcripts by use of appropriate internal control. The technique is also useful in oligonucleotide hybridization to DNA sequences which differ only by a single nucleotide. 
    
    
     DESCRIPTION OF THE FIGURES 
     FIG. 1--Effect of competitor oligo on the hybridization specificity of oligo probes to β-globin mRNA. RNA was prepared from blood cells of individuals which are either homozygous for the normal β-globin gene (AA) or heterozygous for the normal and β C  -globin genes (AC). The RNA was denatured, subjected to electrophoresis on an agarose gel and transferred to a GeneScreen filter. The filter was hybridized with Hβ19C&#39;[ 32  P] probe in the absence (FIG. 1A) or presence (FIG. 1B) of a 10-fold molar excess of unlabeled Hβ19A&#39;. The hybridizing band was the same mobility as commercially available rabbit globin mRNA (Bethesda Research Laboratories). 
     FIG. 2--Discrimination among the transcripts of the allelic globin genes β A , β S  and β C  by oligo hybridization. RNA was isolated from blood cells of individuals with the genotypes SS, AS, AC and AA. The RNA was denatured, electrophoresed and blotted as described in FIG. 1. The filter was hybridized sequentially as follows: 
     FIG. 2A. Hybridized with Hβ19A&#39;[ 32  P] probe in the absence of unlabeled non-complementary-oligo (non-c-oligo). 
     FIG. 2B. Hybridized with Hβ19A&#39;[ 32  P]probe in the presence of unlabeled Hβ19A&#39; as the non-c-oligo. 
     FIG. 2C. Hybridized with Hβ19A&#39;[ 32  P]probe in the presence of unlabeled Hβ19A&#39; as the non-c-oligo. 
     Hybridized probe was removed between hybridizations by washing the blot in 1×SSC at 50° C. for 15 min., then in 0.1×SSC at 50° C. for 15 min., and finally in 0.01×SSC at 68° for 30 min. The filter was autoradiographed overnight to check that hybridized probe was completely removed. 
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     RNA Preparation 
     RNA was prepared from 20 ml of heparinized blood obtained from various individuals of differing β-globin genotypes. Red cells were lysed by resuspending the washed cell pellet in 0.144M NH 4  Cl, 3 mM dithiothreitol (DDT), followed by the addition of 0.1 vol. of 0.01M NH 4  HCO 3 . To the lysate is added 0.1 vol. of 1.5M sucrose, 0.5M KCl and 0.5% sodium dodecyl sulfate (SDS), and the solution was centrifuged at 3000×g for 20 min. at 4° C. The ribonucleoprotein was recovered from the supernatant by precipitation at pH 5 using 10% acetic acid followed by centrifugation at 3000×g for 20 min. at 4° C. The pellet was dissolved in 0.1M Tris-HCl pH 9, 0.1M NaCl, 1 mM EDTA and 0.1% SDS, and extracted first with phenol-chloroform and then with chloroform-isoamyl alcohol followed by ethanol precipitation. 
     Oligo Probe Design 
     The sequences of the oligos used in this study are given in Table I. 
     
                                           TABLE I__________________________________________________________________________Oligonucleotide Probes for the Discrimination of β.sup.A,β.sup.S and β.sup.C mRNA                                          Mismatches withβ-Globinaa No.    3   4   5   6.sup.a                      7   8     9   10    β.sup.A                                             β.sup.S                                                   β.sup.C__________________________________________________________________________β.sup.A. . .    Leu Thr Pro  Glu  Glu Lys   Ser Ala . . .mRNA 5&#39;  CUG ACU CCU  GAG  GAG AAG   UCU GCC3&#39;H 19A&#39;   3&#39;  GA  GGA  CTC  CTC TTC   AGA CG 5&#39; -- T:U   C:Aβ.sup.S. . .    Leu Thr Pro  Val  Glu Lys   Ser Ala . . .mRNA 5&#39;  CUG ACU CCU  GUG  GAG AAG   UCU GCC3&#39;H 19S&#39;   3&#39;  GA  GGA  CAC  CTC TTC   AGA CG 5&#39; A:A                                             --    C:A + A:Aβ.sup.C. . .    Leu Thr Pro  Lys  Glu Lys   Ser Ala . . .mRNA 5&#39;  CUG ACU CCU  AAG  GAG AAG   UCU GCC3&#39;H 19C&#39;   3&#39;  GA  GGA  TTC  CTC TTC   AGA CG 5&#39; T:G                                             T:G + T:U                                                   --__________________________________________________________________________ .sup.a The codon affected by the mutation is underlined. 
    
     The position and length of the sequences is based on several considerations: 
     (1) The length of 19 nucleotide has been previously shown to give a probe that recognizes a unique sequence in the human genome. See Connor, et al., Proc. Natl. Acad. Sci. USA 80:278-282 (1983). 
     (2) The mismatches are centrally located to optimize thermal destablization. 
     (3) All sequences are anti-sense and are thus complementary to the mRNA. 
     (4) Each oligo is complementary to one allele of the β-globin gene and forms either one or two mismatches with the other alleles. Hβ19A&#39; is specific for the β A  allele, Hβ19S&#39; for the β S  allele and Hβ19C&#39; for the B C  allele. 
     Probe Labeling 
     The three 19-nucleotide oligos Hβ19A&#39;, Hβ19S&#39; and Hβ19C&#39; (see Table I) were synthesized on a Systec Microsyn 1450 automated DNA synthesizer. The oligos were radiolabeled at their 5&#39;-ends using [ν- 32  P]ATP and T4 polynucleotide kinase and purified by electrophoresis on a 19.35% acrylamide, 0.65% bisacrylamide, 7M urea gel. 
     Gel Electrophoresis and Blotting 
     RNA was denatured by dissolving in 6M glyoxal and 50% dimethyl sulfoxide and heating at 50° C. for 60 min. The denatured RNA was subjected to electrophoresis in a 1.5% agarose gel using 0.01M sodium phosphate pH 7 buffer. Electrophoresis was at 3.5 V/cm for 3 h. RNA was transferred to GeneScreen (New England Nuclear) by capillary blotting using 20×SSC buffer. The blots were dried at room temperature and baked in vacuo at 80° C. for 2 h. 
     Hybridization 
     The blots were prehybridized in 10× Denhardt&#39;s solution (0.2% bovine serum albumin, 0.2% polyvinylpyrrolidone and 0.2% Ficoll) and 0.1% SDS for 1 h at 60° C. The blots were then washed in 2×SSC and hybridized with the labeled oligo (1×10 6  cpm/ml) in 5× Denhardt&#39;s, 5×SSPE and 0.1% SDS for 3 h at 60° C. (58° C. in the case of Hβ19C&#39;). For the hybridizations where unlabeled competitor oligo is included, it is added in a 10-fold molar excess over the labeled one. After hybridization the filters were washed three times with 6×SSC at room temperature for 15 min followed by one wash with 6×SSC at 57° C. for one min. The filter is then exposed to Kodak XAR X-ray film with two Dupont Quantum III intensifier screens at -70° C. for 0.5-3 h. 
     Effect of G:T Mismatch 
     To decrease the hybridization of non-c-oligos forming a G:T mismatch to the non-complementary target sequence, hybridizations were attempted using labeled c-oligo in the presence of a 10-fold molar excess of unlabeled non-c-oligo. The presence of the competitor oligo effectively suppressed any hybridization of the labeled oligo to its non-complementary target sequence. 
     FIG. 1 shows the effect of having the competitor oligo present during hybridization. mRNA was isolated from blood cells of individuals which were either homozygous for the normal β-globin gene (AA) or heterozygous for the normal and β C  allele (AC). The RNA was glyoxylated in the presence of dimethylsulfoxide (DMSO), subjected to electrophoresis on an agarose gel and transferred to GeneScreen. Duplicate Northern blots containing the two RNAs were hybridized with [ 32  P]Hβ19C&#39; in the absence (FIG. 1A) or presence (FIG. 1B) of a 10-fold molar excess of unlabeled Hβ19A&#39;. In both cases, the Hβ19C&#39; probe hybridizes strongly with the β-globin mRNA present in the AC RNA. In the absence of the competitor however, there was a low level of binding of the Hβ19C&#39; probe to the normal β-globin RNA in the AA sample. This residual hybridization could only be reduced by long high-criteria washes (65° C. in 6×SSC) which also resulted in the loss of signal from the AC lane. In the presence of non-c-oligo competitor (FIG. 1B), there is essentially no binding of the Hβ19C&#39; oligo to the β A  -globin mRNA. 
     Specific Hybridization of Allele-Specific Probes to B A , B S  and B C  mRNA 
     RNA was isolated from the blood cells of individuals with the following β-globin genotypes: AA, AC, AS and SS. The total RNA was denatured, subjected to electrophoresis and blotted onto a GeneScreen filter as described for FIG. 1. The blot containing the four RNA samples was hybridized first with Hβ19A&#39;[ 32  P]probe in the absence of unlabeled non-c-oligo (FIG. 2A). After the hybridized probe was removed, the filter was rehybridized with Hβ19S&#39;[ 32  P]probe in the presence of unlabeled Hβ19A&#39; oligo (FIG. 2B). The hybridized probe was once more removed and the filter was again rehybridized with Hβ19C&#39;[ 32  P] probe in the presence of unlabeled Hβ19A&#39; oligo (FIG. 2C). As can be seen, each probe only hybridized to RNA samples containing the homologous β-globin mRNA and not to samples containing non-homologous allelic transcripts. Thus, the allele-specific oligo probe can unambiguously distinguish among the transcripts of allelic genes both in the case where the genes differ by a single tranversion mutation as for β A  vs. β S  (compare the SS, AS and AA lanes in FIGS. 2A and 2B) as well as in the case where the genes differ by a single transition mutation as for β A  vs. β C  (compare the AC and AA lanes in FIGS. 2A and 2C).