US20020025519A1 - Methods and oligonucleotides for detecting nucleic acid sequence variations - Google Patents

Methods and oligonucleotides for detecting nucleic acid sequence variations Download PDF

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US20020025519A1
US20020025519A1 US09/335,218 US33521899A US2002025519A1 US 20020025519 A1 US20020025519 A1 US 20020025519A1 US 33521899 A US33521899 A US 33521899A US 2002025519 A1 US2002025519 A1 US 2002025519A1
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primer
detector
nucleotide
target
detector primer
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David J. Wright
Maria Milla
James G. Nadeau
G. Terrance Walker
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Becton Dickinson and Co
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Becton Dickinson and Co
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Priority to US09/335,218 priority Critical patent/US20020025519A1/en
Assigned to BECTON, DICKINSON AND COMPANY reassignment BECTON, DICKINSON AND COMPANY ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: WALKER, G. TERRANCE, NADEAU, JAMES G., MILLA, MARIA A., WRIGHT, DAVID J.
Priority to DE60029876T priority patent/DE60029876T2/de
Priority to EP00108366A priority patent/EP1061135B1/de
Priority to CA002306055A priority patent/CA2306055A1/en
Priority to AU40852/00A priority patent/AU781136B2/en
Priority to JP2000182884A priority patent/JP2001057892A/ja
Priority to US09/778,175 priority patent/US20010039334A1/en
Priority to US09/778,168 priority patent/US7223536B2/en
Publication of US20020025519A1 publication Critical patent/US20020025519A1/en
Priority to US10/202,896 priority patent/US20030165913A1/en
Priority to US11/724,180 priority patent/US20090131647A1/en
Priority to JP2008120646A priority patent/JP2008200050A/ja
Priority to US12/419,737 priority patent/US8323929B2/en
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism

Definitions

  • the present invention relates to methods for detecting and identifying sequence variations in nucleic acids.
  • RFLP restriction fragment length polymorphism
  • PCR has been used to facilitate sequence analysis of DNA.
  • allele-specific oligonucleotides have been used to probe dot blots of PCR products for disease diagnosis. If a point mutation creates or eliminates a restriction site, cleavage of PCR products may be used for genetic diagnosis (e.g., sickle cell anemia).
  • General PCR techniques for analysis of sequence variations have also been reported. S. Kwok, et al. (1990. Nucl. Acids Res. 18:999-1005) evaluated the effect on PCR of various primer-template mismatches for the purpose of designing primers for amplification of HIV which would be tolerant of sequence variations.
  • Nucl. Acids Res. 17:2503-25166 report an improvement in PCR for analysis of any known mutation in genomic DNA.
  • the system is referred to as Amplification Refractory Mutation System or ARMS and employs an allele-specific PCR primer.
  • the 3′ terminal nucleotide of the PCR amplification primer is allele specific and therefore will not function as an amplification primer in PCR if it is mismatched to the target.
  • the authors also report that in some cases additional mismatches near the 3′ terminus of the amplification primer improve allele discrimination.
  • the present invention provides methods for detecting and identifying sequence variations in a nucleic acid sequence of interest using a detector primer.
  • the detector primer hybridizes to the sequence of interest and is extended by polymerase if the 3′ end hybridizes efficiently with the target.
  • the methods are particularly well suited for detecting and identifying single nucleotide differences between the target sequence being evaluated (e.g., a mutant allele of a gene) and a second nucleic acid sequence (e.g., a wild type allele for the same gene), as they make use of nucleotide mismatches at or near the 3′ end of the detector primer to discriminate between a first nucleotide and a second nucleotide which may occur at that site in the target.
  • the target sequence e.g., a mutant allele of a gene
  • a second nucleic acid sequence e.g., a wild type allele for the same gene
  • the reduced efficiency of primer extension by DNA polymerases when one or more nucleotides at or near the 3′ terminus of a primer do not efficiently hybridize with the target can be adapted for use as a means for distinguishing or identifying a nucleotide in the target which is at the site where the one or more nucleotides of the detector primer hybridize.
  • the efficiency of the extension reaction for a selected detector primer hybridized to a selected target is monitored by determining the relative amount of extended detector primer which is produced in the extension reaction.
  • FIGS. 1A, 1B, 1 C, 1 D and 1 E show the results of Example 1 for detection and identification of SNP's using a model target system and detector primers with a diagnostic 3′ terminal nucleotide and a nondiagnostic mismatch at N-3.
  • FIGS. 2A, 2B, 2 C, 2 D and 2 E show the results of Example 2 for detection and identification of SNP's using a model target system and detector primers with a diagnostic nucleotide at N-1 and no nondiagnostic mismatch.
  • FIGS. 3A, 3B and 3 C show the results of Example 3 for real-time simultaneous detection and identification of two alleles of exon 4 of the HFE gene.
  • FIGS. 4A, 4B and 4 C show the results of Example 4 for real-time simultaneous detection and identification of two alleles of exon 2 of the HFE gene.
  • FIG. 5 illustrates a possible mechanism for generation of false-positive signals when multiple detector primers in an amplification reaction have the same 5′ tail sequence.
  • FIG. 6 shows the results of Example 5, comparing the performance of multiple detector primers in reactions when the multiple detector primers have the same or different 5′ tail sequences.
  • the methods of the invention are useful for detecting variants of a nucleic acid sequence contained in a target nucleic acid.
  • the methods of the invention are directed to detecting single nucleotide polymorphisms (SNPs) in a nucleic acid sequence of interest (e.g., alleles) and, optionally, to identifying such SNPs or alleles.
  • SNPs single nucleotide polymorphisms
  • Such nucleotide sequence variants may be detected directly in a sample to be analyzed during amplification of the target sequence.
  • the inventive methods are based upon the relative inefficiency of primer extension by DNA polymerases when there are mismatches at or near the 3′ end of a primer hybridized to an otherwise complementary sequence.
  • Applicants have found that by selecting nucleotides at or near the 3′ end of a detector primer such that one or more mismatches will occur when the detector primer is hybridized to a first allele of a target nucleic acid and correct base pairing will occur when the detector primer is hybridized to a second allele of the target nucleic acid, the difference in the efficiency of polymerase extension when the detector primer is hybridized to the two different alleles may be used to indicate which allele the target nucleic acid contains.
  • multiple detector primers are employed in the analysis, each with a different potential mismatch at or near the 3′ end.
  • the detector primer which is most efficiently extended provides the identity of the allele (i.e., the identity of the nucleotide present in the target sequence being analyzed). For example, if a set of detector primers comprising A, G, C and T at the site of the allele to be identified is hybridized to the target of interest and extended, the identity of the allele will be the complement of the nucleotide in the signal primer which was most efficiently extended by the polymerase. For identification of the allele in a single reaction, multiple detector primers are present in the reaction and each of the detector primers has a separately detectable label associated with it (e.g., different fluorophores which can be distinguished within the mixture of detector primers).
  • the detector primers of the invention are oligonucleotides which hybridize to the target sequence of interest and are extended by DNA polymerase during the isothermal amplification reaction.
  • the nucleotide sequence of the detector primer is selected such that it hybridizes specifically to the target nucleic acid of interest and the majority of the detector primer base-pairs correctly in typical Watson-Crick fashion with the target.
  • the nucleotide sequence of the detector primer at or near the 3′ end is selected to discriminate between different-SNPs or alleles of the target sequence (the diagnostic nucleotide position).
  • the diagnostic nucleotide is defined as the nucleotide in the detector primer which allows analysis (e.g., presence or identification) of a particular allele in a selected target. That is, the sequence of the 3′ end of the detector primer is selected such that hybridization with a first single nucleotide variation of the target sequence (e.g., a wild-type or mutant allele of a gene) results in correct Watson-Crick base-pairing at the site of the SNP and hybridization of the detector primer with a target containing a second single nucleotide variation of the target sequence at the same site (e.g., a second mutant allele of the gene) results in a mismatch between the detector primer and the target.
  • a first single nucleotide variation of the target sequence e.g., a wild-type or mutant allele of a gene
  • a detector primer having a C residue at the diagnostic nucleotide position produces a high signal indicative of efficient extension of the detector primer, this indicates that the target allele is G.
  • low signal for the extended detector primer indicates that the target allele is not G.
  • multiple detector primers containing A, T and G at the site of the SNP may be used to identify the allele in the target, i.e., the detector primer which produces a high signal associated with detector primer extension product contains the nucleotide which is the complement of the SNP in the target.
  • the potentially mismatched nucleotide of the detector primer is placed at the 3′ terminus or about one to four nucleotide residues from the 3′ terminus (i.e., at the N, N-1, N-2, N-3 or N-4 position).
  • the second, nondiagnostic mismatch often improves the level of discrimination between the SNPs being detected or identified and is preferably selected based on a region of the target sequence which is not expected to vary so that the nondiagnostic mismatch will occur regardless of the target allele being analyzed.
  • the second mismatch may occur at any site within the detector primer which produces a positive effect on allele discrimination, but typically produces the greatest improvement when it is near the diagnostic nucleotide.
  • the second, nondiagnostic mismatch has a positional effect rather than a general effect on the T m of the detector primer, based on the observation that as the nondiagnostic mismatch is moved away from the diagnostic mismatch its positive effect on allele discrimination diminishes.
  • Those skilled in the art are capable of determining through routine experimentation the appropriate placement of the nondiagnostic mismatch in a detector primer by evaluating its effect on allele discrimination using the detector primer.
  • the detector primers of the invention are typically about 12-50 nucleotides in length. When only a diagnostic nucleotide is present, the detector primer is preferably about 12-24 nucleotides long, more preferably about 12-19 nucleotides long. For detector primers containing both a diagnostic and a nondiagnostic nucleotide, lengths of about 12-50 nucleotide are preferred, 15-36 nucleotides are more preferred and 18-24 nucleotides are most preferred.
  • the detector primers may be employed in a variety of ways in the isothermal amplification methods of the invention.
  • the detector primer may be an amplification primer for use in a nucleic acid amplification reaction. That is, the detector primer may perform two functions in the amplification reaction—amplification of the target sequence of interest and detection or identification of SNPs within the target sequence (a “detector/amplification primer”).
  • amplification primers for SDA, 3SR, NASBA, TMA and other isothermal amplification reactions are well known in the art and it is within the ordinary skill in the art to adapt these amplification primers for use as detector primers in the present invention by selecting the 3′ nucleotide sequence as taught herein.
  • amplification primers for PCR generally consist only of target binding sequences.
  • the amplification primers comprise specialized sequences and structures necessary for the amplification reaction to occur.
  • amplification primers for 3SR and NASBA comprise an RNA polymerase promoter near the 5′ end. The promoter is appended to the target sequence and serves to drive the amplification reaction by directing transcription of multiple RNA copies of the target.
  • Amplification primers for SDA comprise a recognition site for a restriction endonuclease near the 5′ end.
  • restriction site is appended to the target sequence and becomes hemimodified and double-stranded during the amplification reaction.
  • Nicking of the restriction site once it becomes double stranded drives the SDA reaction by allowing synthesis and displacement of multiple copies of the target by polymerase.
  • the detector/amplification primer forms a mismatch with the target at or near it's 3′ end, amplification efficiency is reduced and the accompanying reduction in signal upon detection of the extended detector/amplification primer (i.e., the amplification product or amplicon) indicates the presence or the identity of an SNP at the nucleotide position in the target where the diagnostic mismatch with the detector/amplification primer occurred.
  • the detector/amplification primer is tagged with a label which produces a signal change when the detector/amplification primer has been extended (as discussed below), the extension products may be detected in real-time as amplification of the target occurs, thus eliminating the additional steps of post-amplification detection of extension products.
  • a single mismatch at N-1 or N-2 in the detector/amplification primer in general may provide more efficient allele discrimination than a single mismatch at the 3′ terminus. Therefore, a 3′ terminal mismatch is not preferred when the detector primer is an amplification primer for an isothermal amplification reaction. This is in contrast to the teaching of the prior art for temperature cycling amplification reactions, where a 3′ terminal mismatch on the PCR amplification primer reportedly gave adequate allele discrimination (see Kwok, et al., supra).
  • the detector primer is used in an isothermal amplification reaction as a signal primer (also referred to as a detector probe) as taught in U.S. Pat. No. 5,547,861, the disclosure of which is hereby incorporated by reference.
  • the signal primer hybridizes to the target sequence downstream of an amplification primer such that extension of the amplification primer displaces the signal primer and its extension product.
  • the signal primer includes the downstream sequence which is the hybridization site for the second amplification primer.
  • the second amplification primer hybridizes to the extended signal primer and primes synthesis of its complementary strand.
  • a signal primer which has the sequence characteristics of a detector primer (a detector/signal primer) also facilitates detection and/or identification of SNP's within the target sequence.
  • a diagnostic mismatch at either the 3′ terminus (N) or at N-1 to N-4 provides excellent allele discrimination. Allele discrimination is further improved with the use of a second nondiagnostic mismatch as previously described, particularly when using longer detector primers where the difference in hybridization efficiency between matched and mismatched primers is small. This finding was unexpected, as a 3′ terminal diagnostic mismatch alone produced poor allele discrimination in detector/amplification primers.
  • detector/signal primer in an isothermal amplification reaction also allows detection of extension products and analysis of SNPs in real-time (i.e., concurrently with amplification) when the detector/signal primer is labeled with a reporter group which produces a detectable change in the signal when the detector/signal primer is extended.
  • the detector/signal primer may be used post-amplification or without amplifying the target for detection of SNPs.
  • the detector signal primer is hybridized to the target downstream from any primer which is extendible by polymerase such that extension of the second primer displaces the detector/signal primer and any detector/signal primer extension products which may be produced.
  • Applicants hypothesize that the different results obtained with a diagnostic mismatch at the 3′ terminus of a detector/signal primer as compared to a diagnostic mismatch at the 3′ terminus of a detector/amplification primer may be at least partially due to a kinetic effect. If a signal primer is not efficiently extended on a target to which it is hybridized (e.g., when it contains mismatches), it will be quickly displaced from the template by extension of the upstream amplification primer. If the signal primer is efficiently extended, extension will occur before the signal primer is displaced from the target. That is, the upstream amplification primer (which is typically perfectly matched and efficiently extended) imposes a “time-limit” for extension on the detector/signal primer.
  • the amplification primer in an isothermal amplification reaction typically does not have a time-limit for extension imposed upon it by additional components of the isothermal amplification reaction or by thermocycling. Therefore, with sufficient time available, a detector/amplification primer may eventually be extended even when the extension reaction is inefficient. This phenomenon could reduce discrimination between alleles when a detector/amplification primer with a 3′ terminal mismatch is employed in isothermal amplification reactions.
  • a time limit may be imposed prior to amplification if a second primer binds upstream from the amplification primer, as described in U.S. Pat. No. 5,270,184 (e.g., the “external” or “bumper” primer).
  • extension of the upstream primer places a time limit on extension of the amplification primer. If extension of the amplification primer is retarded by a mismatch at or near the 3′ end, the amplification primer may be displaced by elongation of the upstream primer before it is extended. This kinetic effect is expected to enhance the ability of amplification primers to discriminate between matched and mismatched targets prior to amplification when there is an upstream primer to displace them. If mispriming occurs, however, the ability of amplification primers to correct a mismatch with the target may result in an amplification product which is not a faithful copy of the original target. Amplification primers produce amplicons that are perfectly matched with the amplification primers which produced them, thus eliminating the basis of allele discrimination. In contrast, such “correction” does not occur with signal primers.
  • Whether hybridization of the detector primer results in correct base-pairing or a mismatch at the diagnostic nucleotide position of the target being analyzed is determined by evaluating the relative efficiency of detector primer extension by DNA polymerase. This determination may be quantitative or qualitative. Detector primer extension is less efficient in the presence of a mismatch at or near the 3′ end and more efficient when the entire 3′ end is correctly base-paired with the target. That is, relatively more extended detector primer product is produced with correct base-pairing near the 3′ terminus.
  • the extended detector primer is typically detected by means of a label associated with the detector primer. The label may be directly detectable or detectable only after subsequent reaction as is known in the art.
  • the detector primer itself may be unlabeled and the extension product detected by hybridization to a labeled probe or in a subsequent reaction such as treatment with ethidium bromide for visualization on a gel.
  • the relative amount of signal from the label which is associated with the extended detector primer as compared to the amount of signal associated with the unextended primer serves as an indication of the amount of extension product produced and the efficiency of the extension reaction.
  • the extension products of the detector primer may be detected and/or quantified by their increased size, for example by separation from unextended detector primer by gel elecrophoresis or by selectively capturing the extended detector primer on a solid phase.
  • the detector primers are labeled with a reporter group which is detectable only when the detector primer has been extended or a label which produces a change in signal only when the detector primer has been extended.
  • fluorescent dyes which undergo changes in fluorescence polarization when the oligonucleotides to which they are linked have been hybridized to and extended on a target sequence.
  • a second example of labels which undergo a detectable change in signal indicative of primer extension are fluorescent donor/quencher dye pairs.
  • the quencher dye may also be fluorescent but need not be. When the donor and quencher are in close proximity, fluorescence of the donor is quenched. As the dyes are moved farther apart, quenching is reduced and donor fluorescence increases.
  • the use of such donor/quencher dye pairs in a variety of mechanisms for increasing the distance between the dyes in the presence of target for detection of target nucleic acids is described in U.S. Pat. No. 5,846,726; U.S. Pat. No. 5,691,145, and; EP 0 881 302.
  • the detector primers of the invention may be labeled with donor/quencher dye pairs and employed for detection and/or identification of SNP's in the target as is known in the art.
  • detector primers may be labeled with structures containing fluorescent reporter groups as taught in the foregoing references and the extension product detected by changes in fluorescence polarization or fluorescence quenching.
  • the detector primer may be unlabeled and its extension product detected by hybridization to a labeled primer/probe with detection of changes in fluorescence polarization or fluorescence quenching of the primer/probe as taught in these references.
  • oligonucleotides differing by only a single nucleotide were prepared as follows: Four oligonucleotides containing identical sequences except at one position were synthesized. The variant position of the oligonucleotide contained either adenosine (A), cytosine (C), guanine (G) or thymine (T). A fifth oligonucleotide complementary to the 3′ termini of the four variant oligonucleotides was also synthesized. Each of the four variant oligonucleotides was mixed with the fifth oligonucleotide, heated for 2 min.
  • oligonucleotide and the fifth oligonucleotide were then extended in a primer extension reaction comprising 14 mM deoxycytidine ⁇ -(O-1-thio)-triphosphate, 2 mM deoxyadenosine triphosphate, 2 mM deoxyguanosine triphosphate, 2 mM thymidine triphosphate and 40 units of exonuclease deficient Klenow DNA polymerase.
  • the primer extension reactions were allowed to proceed for 45 min. at 37° C., following which the Klenow polymerase was inactivated by incubating the reactions at 70° C. for 10 min. in a dry incubator. This produced four double-stranded DNA model target sequences differing only at one nucleotide position.
  • the targets were designated A, C, G and T targets.
  • a second set of four oligonucleotides which hybridize to the model target sequences with their 3′ termini at the polymorphic nucleotide position were also synthesized for use as detector primers.
  • Each of the four detector primers had one of the four nucleotide bases (A, C, G or T) at its 3′ terminus (N, the diagnostic nucleotide) and an “A” nucleotide at the position three bases from the 3′ terminus which formed a mismatch with the model target sequence (N-3, the nondiagnostic nucleotide).
  • the four detector primers were radiolabeled in 25 ⁇ l reactions containing 1 ⁇ M detector primer, 25 units of T4 polynucleotide kinase (PNK), 175 ⁇ Ci of ⁇ -[ 32 P]-adenosine triphosphate ( 32 P-ATP), and PNK buffer at 1 ⁇ concentration. Labeling reactions were initiated by addition of PNK to a solution containing the other components. The reactions were incubated for 20 min. at 37° C., than heated in a boiling water bath for 5 min. to inactivate the PNK.
  • PNK polynucleotide kinase
  • the detector primers were used as signal primers in the amplification reaction.
  • a 5 ⁇ l aliquot of each of the labeled detector primer preparation was added to a separate SDA reaction for each target (50 ⁇ l comprising 40 mM KH 2 PO 4 /K 2 HPO 4 pH 7.6; 10% v/v glycerol; 7.5 mM magnesium acetate; 0.5 ⁇ M each amplification primer; 1.4 mM deoxycytidine ⁇ -(O-1-thio)-triphosphate; 0.5 mM deoxyadenosine triphosphate; 0.5 mM deoxyguanosine triphosphate; 0.5 mM thymidine triphosphate; 0.1 mg/ml bovine serum albumin; 0.5 ⁇ g human placental DNA, 104 A, C, G or T target DNA molecules; 100 nM radiolabeled detector primer; 160 units BsoBi restriction endonuclease and 25 units Bst DNA polymerase large fragment
  • the SDA reactions were assembled without the BsoBI and Bst, and the target DNA duplexes were denatured by heating these reaction mixes for 3 min. in a boiling water bath.
  • the reaction mixtures were equilibrated to 55° C. for 3 min. in a dry incubator and SDA was initiated by adding 160 units of BsoBI and 25 units of Bst polymerase large fragment to each reaction (total volume of enzymes was 2 ⁇ l, adjusted with 50% v/v glycerol).
  • SDA was allowed to proceed for 30 min. at 55° C. Aliquots of each reaction (5 ⁇ l) were removed at 5 min. intervals during the reaction and added to 5 ⁇ l of sequencing stop solution to quench the SDA reaction.
  • FIGS. 1A, 1B, 1 C and 1 D show the results obtained for extension of each of the four detector primers on each of the four different model target sequences.
  • the detector primer with the 3′ nucleotide that was the correct match for the polymorphic nucleotide in the target DNA sequence was preferentially extended during SDA by the DNA polymerase as compared to the detector primers which did not contain the correct 3′ match for the polymorphic nucleotide in the target, as evidenced by greater amounts of the correct detector primer after amplification.
  • the 3′A detector primer was preferentially extended only in the SDA reactions containing the T target sequence (FIG. 1A).
  • N/N-3 detector/signal primers according to the invention can be used in isothermal amplification reactions to identify the nucleotide present at a selected position in a target nucleic acid sequence, whereas N/N-3 detector/amplification primers for isothermal amplification reactions do not effectively discriminate between alleles.
  • Example 1 was repeated except that the detector/signal primers were synthesized so that the variant, diagnostic nucleotide was positioned one nucleotide from the 3′ terminus of the detector primer (N-1) and the overall length of the detector primer was shortened by 4 nucleotides at the 5′ end.
  • the detector primers also made a perfect match with the target DNA at the position three nucleotides from the 3′ terminus of the detector primer.
  • Each of the four detector primers was added to separate SDA reactions containing 10 4 molecules of each of the target sequences. The targets were amplified and detected as previously described.
  • FIGS. 2A ⁇ 1A detector primer
  • 2 B ⁇ 1C detector primer
  • 2 C ⁇ 1G detector primer
  • 2 D ⁇ 1T detector primer
  • the detector primer was preferentially extended on the target which contained the perfect match at the variant position.
  • Signals obtained with the perfectly matched detector primer and target were 30- to 100-fold higher than signals obtained with any of the mismatched detector primer/target pairs. This difference in signal allowed unambiguous identification of the polymorphic nucleotide in the target and is in contrast to the results reported for PCR by Kwok, et al., supra, where an N-1 mismatch had no effect on the yield of PCR amplicons.
  • FIG. 2E shows that the signal obtained with the singly mismatched target was over five-fold higher than that obtained with any of the doubly mismatched targets and that the C allele could be easily distinguished from the T, G and A alleles of the target.
  • SDA was generally performed as described in U.S. Pat. No. 5,846,726, except that each reaction mixture contained two detector/signal primers according to the invention (one specific for the mutant allele and one specific for the wild-type allele) and BsoBI was substituted for AvaI.
  • the final concentrations of components in each 100 ⁇ L reaction were 50 mM KiPO 4 (pH 7.5), 6.0 mM MgOAc, 0.2 mM each DTTP, dGTP, dATP, 1.4 mM dCTP ⁇ S, 5 ⁇ g/mL acetylated BSA, 15% (v/v) glycerol, 400 ng salmon sperm DNA, 20 units exo Klenow Bst polymerase, 160 units BsoBI and either 0 or 10 5 copies of target DNA.
  • target DNA consisted of PCR products generated from DNA cloned from either normal or mutant HFE exon 4 DNA.
  • Normal HFE exon 4 DNA contains a G at nucleotide position 845 of the HFE wild-type gene and the mutant HFE exon 4 DNA contained an SNP at that position in which the nucleotide was A.
  • Each sample also contained two detector/signal primers (SEQ ID NO:1 and SEQ ID NO:2 below), two unlabeled bumper primers (SEQ ID NO:3 and SEQ ID NO:4 below) and two unlabeled SDA amplification primers (SEQ ID NO:5 and SEQ ID NO:6 below).
  • Underlined sequences indicate complementarity to the target sequence.
  • the base A at position N-3 which is not underlined is not complementary to the corresponding nucleotide in the target sequence.
  • C* represents the 3′ terminal nucleotide (position N of the detector primer) which pairs with the G at position 845 of the wild-type target.
  • T* represents the 3′ terminal nucleotide which pairs with A at nucleotide position 845 of the mutant target (the G845A mutation).
  • Italicized sequences represent restriction enzyme recognition sites (RERS).
  • RERS restriction enzyme recognition sites
  • the RERS provides the nicking site which drives SDA.
  • the RERS is flanked by a two dyes which form a donor/quencher dye pair.
  • the RERS As the detector/signal primer is extended, displaced and rendered double-stranded the RERS also becomes double-stranded and cleavable by the restriction enzyme.
  • the reaction products are treated with the appropriate restriction enzyme to cleave the RERS of the detector primer. Quenching of the fluorescent dye decreases as the double-stranded products are cleaved and the dye pair is separated.
  • the increase in fluorescence is an indicator of the amount of extended, double-stranded detector primer produced. If the detector primer is not efficiently extended the RERS remains single-stranded, is not cleaved by the restriction enzyme and the fluorescent dye remains quenched. Failure to detect an increase in fluorescence therefore indicates that the detector primer was not efficiently extended on the target.
  • SEQ ID NO:1 Detector primer specific for nucleotide G at position 845 (wild-type):
  • SEQ ID NO:2 Detector primer specific for nucleotide A at position 845 (mutant):
  • SEQ ID NO:3 first bumper primer for exon 4:
  • SEQ ID NO:4 second bumper primer for exon 4:
  • SEQ ID NO:5 first SDA amplification primer for exon 4:
  • SEQ ID NO:6 second SDA amplification primer for exon 4:
  • Each SDA reaction included both detector primers, each labeled with a different fluorophore as shown above.
  • the reactions were assembled in microwells to contain all reagents except Bst and BsoBI and amplification was initiated after heat denaturation and equilibration to 55° C. by addition of the enzymes.
  • the microwells were sealed and placed into a Cytofluor IITM which had been modified to permit temperature control.
  • Bandpass filters were used to limit excitation to one wavelength range characteristic of fluorescein (475-495 nm) and a second range specific for ROX (635-655 nm). For each well, one fluorescein and one ROX reading were made every 45 seconds. Reactions were typically monitored for 90 min. Control reactions contained no target DNA.
  • an alternative detector primer specific for the wild type allele was tested and its performance compared to the SEQ ID NO:1 detector primer.
  • the alternative detector primer had a diagnostic nucleotide at N-2 and a second nondiagnostic nucleotide at N-3 (an N-2/N-3 detector primer; FAM-TC CTC GAG T(dabcyl)AT GGG TGC TCC ACC TGA C*AC; SEQ ID NO:14).
  • amplification primer SEQ ID NO:5 was replaced with SEQ ID NO:15 (ACG CAG CAG CAC ACA TTC TCG GGG MG AGC AGA GAT ATA CGT)
  • SEQ ID NO:14 ACG CAG CAG CAC ACA TTC TCG GGG MG AGC AGA GAT ATA CGT
  • SEQ ID NO:14 Two samples were tested using SEQ ID NO:14—one containing only wild type target and the other containing only mutant target. Each test reaction contained SEQ ID NO:14 for detection of the wild type allele and SEQ ID NO:2 for detection of the mutant target.
  • the SEQ ID NO:1/SEQ ID NO:2 detector primer system served as a control reaction. Both fluorescein and rhodamine fluorescense were monitored and the fluorescence readings for each sample were plotted.
  • the N-2/N-3 detector primer was converted, resulting in a three-fold increase in fluorescein emission.
  • the mutant-specific detector primer remained unconverted and the rhodamine emission was essentially unchanged.
  • the pattern was reversed.
  • the N-2/N-3 detector primer was not converted, as indicated by no change in fluorescein emission, but rhodamine emission from the mutant-specific detector primer increased about three-fold.
  • Comparison of the results to the control reaction demonstrated that the target specificity for SEQ ID NO:14 is approximately equivalent to the target specificity for SEQ ID NO:1.
  • a wild-type specific detector primer having the sequence FAM-TA GCA GTC CCG AGA CTG CT(dabcyl)A TGG GTG CTC CAC CAG GC* (SEQ ID NO:16) provides more sensitive detection of the wild-type allele than SEQ ID NO:1, although it is slightly less specific.
  • Example 3 The experimental protocol of Example 3 was repeated except that a pair of amplification primers specific for exon 2 of the HFE gene and detector/signal primers for detection and identification of wild-type and mutant alleles in exon 2 were used.
  • the wild-type allele is C at nucleotide 187.
  • the mutant allele has a G in this position, resulting in a histidine to lysine change at amino acid 63 in the protein.
  • These detector primers were designed to hybridize to the allele contained in the non-coding strand of exon 2.
  • SEQ ID NO:7 Detector primer for wild-type allele at nucleotide position 187 (C187, i.e., G on the complementary strand):
  • SEQ ID NO:8 Detector primer for mutant allele at nucleotide position 187 (G187, i.e., C on the complementary strand):
  • SEQ ID NO:9 First bumper primer for exon 2:
  • SEQ ID NO:10 Second bumper primer for exon 2:
  • SEQ ID NO:11 First amplification primer for SDA:
  • SEQ ID NO:12 Syncond amplification primer for SDA:
  • SEQ ID NO:7 did not contain a nondiagnostic mismatch with the target.
  • SEQ ID NO:8 did not contain an RERS, as the ROX/Dabcyl dye pair dequenches upon formation of the extended, double-stranded detector primer product. Cleavage with a restriction enzyme is not necessary to observe the increase in fluorescence.
  • FIGS. 4A, 4B and 4 C The results are shown in FIGS. 4A, 4B and 4 C for SDA reactions containing 10 7 copies of target DNA derived from either wild-type or mutant exon 2.
  • fluorescence increased strongly with time in the emission wavelength range for fluorescein, indicating the presence of the wild-type allele.
  • fluorescence in the emission wavelength range for rhodamine remained low for these samples, indicating the absence of the mutant allele.
  • the fluorescence profile was reversed for samples containing DNA derived only from mutant exon 2 (FIG. 4B). In this case, ROX fluorescence increased strongly and FAM fluorescence remained low.
  • fluorescence from both fluorophores increased strongly, indicating the presence of both alleles in a single sample.
  • an amplification primer having the sequence CGA TAC GCT CCT GAC TTC TCG GGA CM ACG GCG ACT CTC AT (SEQ ID NO:17) for SEQ ID NO:12 in the reaction provides more efficient amplification of the exon 2 target.
  • an N-1 detector primer having the sequence Rox-TA GCG CCC GAG CGC T(dabcyl)AT GTT CGT GTT CTA TGA TC*A (SEQ ID NO:18) provides improved allele discrimination when used in combination with the alternative amplification primer SEQ ID NO:17.
  • This example illustrates the use of 5′ tail sequences in detector primers to modulate cross-reactivity of multiple allele-specific probes in nucleic acid amplification reactions.
  • SDA S-specific primers
  • Similar results are expected for other amplification methods known in the art, including PCR, NASBA, 3SR, etc., which involve extension of a labeled probe or primer to discriminate between two alleles.
  • Examples 3 and 4 describe SDA reactions which contain two differentially labeled detector/signal primers, one specific for the wild-type allele and the other specific for a mutant allele.
  • each reaction mixture is capable of detecting either the mutant allele, the wild-type allele or both alleles simultaneously.
  • the ability to analyze one sample for either allele is more convenient and reliable, requires less sample and is less expensive than the alternative approach of splitting the sample sample and performing two separate single-detector primer assays.
  • reaction mixtures containing two or more differentially-labeled detector primers an increased level of spurious, cross-reactive signal may be generated by one detector primer when the target of a second detector primer is present.
  • cross-reactivity is caused or exacerbated by the simultaneous presence of both detector primers in the same reaction mixture, as cross-reactivity is diminished or absent in single-detector primer reaction mixtures. It has been discovered that the cross-reactivity can be substantially diminished in such multiple detector primer reaction mixtures by designing detector primers so that the 5′ tail sequences of the two detector primers are substantially different. This result was unexpected, as the 5′ tails are not complementary to the original target sequences and the allele-specific nucleotides are located away from the 5′ tails at or near the 3′ ends of the detector primers.
  • FIG. 5 illustrates the possible source of this unexpected cross-reactivity, using SDA as an illustrative example.
  • the “wild-type” target depicted contains a C at the nucleotide position to be diagnosed.
  • the detector primer for this allele therefore contains a 3′ terminal G, as shown.
  • the “mutant” allele (not shown) contains a T at the diagnostic position, and its detector primer contains a 3′ terminal A. Both detector primers are present in the amplification reaction.
  • the C-specific detector primer hybridizes to the target and is extended and converted to the double-stranded form which is cleavable to separate the donor/quencher dye pair.
  • the linear amplification product may hybridize to the appropriate C-specific detector primer and be converted to cleaved product as before, further enhancing the C-specific signal.
  • the linear amplification reaction product may hybridize spuriously to the T-specific detector primer. Tthe single mismatch at the 3′ end of the T-specific detector primer would not be sufficient to prevent such errant hybridization.
  • the 5′ tail sequences of the T-specific and C-specific detector primers are identical hybridization could occur and the spuriously-hybridized T-specific detector primer would be converted quickly into a cleaved fluorescent product without the need for extension of the A:C mismatch. This results in a signal falsely indicative of the presence of a T nucleotide at the diagnostic position. If, however, the T-specific and C-specific detector primers contain different 5′ tail sequences, spuriously hybridized T-specific detector primer will not undergo cleavage, as the 5′ tail cannot be converted to double-stranded form by hybridization to the linear amplification product.
  • the detector primer would then remain uncleaved even if errantly hybridized to wild-type target and no false-positive signal would be produced.
  • the fact that the two detector primers have the same restriction site would not be sufficient to allow the tails to hybridize provided the rest of the 5′ tail sequence was different.
  • FIG. 5 illustrates a mechanism for spurious generation of false-positive signals in SDA, similar reactions will occur in other amplification methods.
  • a single-stranded C-containing detector primer extension product is generated in PCR, NASBA, 3SR, TMA or any other amplification reaction, it may hybridize to either the C-specific detector primer (correctly) or to the T-specific detector primer (incorrectly).
  • the extension product will be complementary to either one at its 5′ end and the RERS will be double-stranded and cleavable. If the two detector primers have different 5′ tail sequences the double-stranded RERS will not be generated when the detector primer hybridizes to the incorrect target and no false-positive signal will be generated.
  • reaction mixtures also contained either wild-type (reactions 1 and 3) or mutant (reactions 2 and 4) target DNA (10 5 copies per reaction) derived from exon 4 of the HFE gene (see Example 3).
  • the reactions were carried out as in Example 3 except that only fluorescein fluorescence emissions were detected.
  • Reaction 1 produced a strong increase in fluorescein fluorescence, indicative of the presence of the wild-type allele in the target.
  • Reaction 2 which contained mutant DNA only, produced a diminished but substantial fluorescence increase even though no wild-type DNA was present.
  • This signal represented spurious conversion of the wild-type “specific” detector primer, possibly through the mechanism illustrated in FIG. 5, as the 5′ tail sequences of the two detector primers present in the reaction were identical.
  • the 5′ tail sequence of the wild-type detector primer was changed (SEQ ID NO:1), the cross-reacting signal was suppressed (reaction 4) without substantially affecting the target-specific signal (reaction 3).

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US09/335,218 US20020025519A1 (en) 1999-06-17 1999-06-17 Methods and oligonucleotides for detecting nucleic acid sequence variations
DE60029876T DE60029876T2 (de) 1999-06-17 2000-04-17 Verfahren und Oligonukleotide zum Nachweis von Nukleinsäuresequenzvariationen
EP00108366A EP1061135B1 (de) 1999-06-17 2000-04-17 Verfahren und Oligonukleotide zum Nachweis von Nukleinsäuresequenzvariationen
CA002306055A CA2306055A1 (en) 1999-06-17 2000-04-19 Methods and oligonucleotides for detecting nucleic acid sequence variations
AU40852/00A AU781136B2 (en) 1999-06-17 2000-06-14 Methods and oligonucleotides for detecting nucleic acid sequence variations
JP2000182884A JP2001057892A (ja) 1999-06-17 2000-06-19 核酸配列変異を検出するための方法とオリゴヌクレオチド
US09/778,168 US7223536B2 (en) 1999-06-17 2001-02-07 Methods for detecting single nucleotide polymorphisms
US09/778,175 US20010039334A1 (en) 1999-06-17 2001-02-07 Methods and oligonucleotides for detecting nucleic acid sequence variations
US10/202,896 US20030165913A1 (en) 1999-06-17 2002-07-26 Methods for detecting nucleic acid sequence variations
US11/724,180 US20090131647A1 (en) 1999-06-17 2007-03-15 Methods for detecting nucleic acid sequence variations
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CA2306055A1 (en) 2000-12-17
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US8323929B2 (en) 2012-12-04
US20090131647A1 (en) 2009-05-21
JP2008200050A (ja) 2008-09-04
DE60029876T2 (de) 2007-02-01
JP2001057892A (ja) 2001-03-06
US20090246792A1 (en) 2009-10-01
US20010039334A1 (en) 2001-11-08
EP1061135B1 (de) 2006-08-09
AU781136B2 (en) 2005-05-05
US20010009761A1 (en) 2001-07-26
US7223536B2 (en) 2007-05-29
DE60029876D1 (de) 2006-09-21
AU4085200A (en) 2000-12-21

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