DNA extension and analysis with rolling primers

Details DNA extension and analysis with rolling primers DNA extension and analysis with rolling primers

1996-03-05

1998-07-14

Jones, W. Gary

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

435 912, 935 77, 935 78, C12Q 168, C12P 1934, C12N 1500

Patent

active

057802319

ABSTRACT:
A novel "primer walking" method for DNA sequencing is provided that comprises repeated cycles nucleotide identification by selective extension and primer advancement along a template by template mutation. An important feature of the invention is providing a set of primers, referred to herein as "rolling primers" that contain complexity-reducing nucleotides for reducing the number of primers required for annealing to every possible primer binding site on a sequencing template. Another important feature of the invention is the systematic replacement of at least one of the four nucleotides in the target polynucleotide with its cognate complexity-reducing nucleotide or complement thereof. Sequencing is initiated by annealing rolling primers differing only in their terminal nucleotides to a primer binding site of a sequencing template so that only the rolling primer whose terminal nucleotide forms a perfect complement with the template leads to the formation of an extension product. After amplifying the double stranded extension product to form an amplicon, the terminal nucleotide, and hence its complement in the template, is identified by the identity of the amplicon. The primer binding site of the template of the successfully amplified polynucleotide is then mutated by, for example, oligonucleotide-directed mutagenesis so that a subsequent rolling primer may be selected from the set that forms a perfectly matched duplex with the mutated template at a site which is shifted towards the direction of extension by one nucleotide relative to the binding site of the previous rolling primer. The steps of selective extension, amplification and identification are then repeated. In this manner, the primers "roll" along the polynucleotide during the sequencing process, moving a base at a time along the template with each cycle.

REFERENCES:
patent: 4293652 (1981-10-01), Cohen
patent: 4942124 (1990-07-01), Church
patent: 4994370 (1991-02-01), Silver et al.
patent: 5102785 (1992-04-01), Livak et al.
patent: 5149625 (1992-09-01), Church
patent: 5310893 (1994-05-01), Erlich et al.
patent: 5405746 (1995-04-01), Uhlen
patent: 5407799 (1995-04-01), Stuidier
patent: 5413909 (1995-05-01), Bassam et al.
patent: 5427911 (1995-06-01), Ruano
patent: 5496699 (1996-03-01), Sorenson
patent: 5508169 (1996-04-01), Deugau et al.
Gramegna et al., Research in Virology 144:307-309 (1993).
Martin, Genome 31:1073-1080 (1989).
McBride et al., Clinical Chemistry 35(11):2196-2201 (1989).
Berg et al., Biotechniques 17(5):896-901 (1994).
Kasai et al., Nucleic Acids Research20(24): 6509-6515 (1992).
Boles et al., Current Genetics 28: 197-198 (1995).
Wu et al., PNAS 86:2757-2760 (1990).
Scharf et al., PNAS 86:6215-6219 (1990).
Okayama et al., J. Laboratory and Clinical Medicine 114(2): 105-113 (1989).
Szybalski, Gene 135: 279-290 (1993).
International Application PCT/GB93/01452 (Publ. No. wo 95/05182) Inventor Sibson Title Process for categorizing nucleotide sequence population Publication Date 20 Jan. 1994.
International Application PCT/GB95/00109 (Publ. No. wo 93/20053) Inventor Sibson Title Sequencing of nucleic acids Publcation Date 27 Jul. 1995.
International Application PCT/US93/01552 (Publ. No. wo 93/17126) Inventor Chetverin and Kramer Title Novel oligonucleotide arrays and their use for sorting, isolating, sequencing, and manipulating nucleic acids Publication Date 2 Sept. 1993.
International Application PCT/US92/01905 (Publ. No. wo 92/15712) Inventor Goelet et al Title Nucleic acid typing by polymerase extension of oligonucleotides using terminator mixtures Publication Date 17 Sept. 1992.
International Application PCT/US94/07086 (Publ. No. wo 94/05182) Inventor Caskey et al Title Parallel primer extension approach to nucleic acid sequence analysis Publication Date 5 Jan. 1995.
European patent Application 90107066.4 Publ. No. 0 392 546 A2 Inventor Drmanac and Crkvenjakov Title Process for determination of a complete or a partial contents of very short sequences in the samples of nucleic acids connected to the discrete particles of microscopic size by hybridization with oligonucleotide probes Publication Date 17 Oct. 1990.
Roberts and Macelis, "REBASE-restriction enzymes and methylases", Nucleic Acids Research, 21: 3125-3137 (1993).
Hasan et al., "A novel multistep method for generating precise unidirectional deletions using BspMI, a class-IIS restriction enzyme", Gene, 82: 50: 55-62 (1986).
Hasan et al., "An Mboll/Fokl trimming plasmid allowing consecutive cycles of precise 1-to 12-base-pair deletions in cloned DNA", Gene, 82: 305-311 (1989).
Szybalski et al., "Class-IIS restriction enzymes--a review", Gene, 100: 13-26 (1991).
Kwok et al., "Effects of primer--template mismatches on the polymerase chain reaction: Human immunodeficiency virus type 1 model studies", Nucleic Acids Research, 18;999-1005 (1990).
Huang et al., "Extension of base mispairs by Taq DNA polymerase: implications for single nucleotide discrimination in PCR", Nucleic Acids Research 20 :4567-4573 (1992).
Short Technical Reports, "Priming Efficiency", BioTechniques, 18: 84-89 (1995).
Martin and Castro, "Base pairing involving deoxyinosine: implications for probe design", Nucleic Acids Research, 13: 8927-8938 (1985).
Kawase et al., "Studies on nucleic acid interactions I. Stabilities of mini-duplexes (dG.sub.2 A.sub.4 XA.sub.4 .cndot.dC.sub.2 T.sub.4 YT.sub.4 C.sub.2) and self-complementary d(GGGAAXYTTCCC) containing deoxyinosine and other mismatched bases", Nucleic Acids Research, 14: 7727-7736 (1986).
Case-Green and Southern, "Studies on the base pairing properties of deoxyinosine by solid phase hybridization to oligonucleotides", Nucleic Acids Research, 22: 131-136 (1994).
Ausubel et al., "Mutagenesis of Cloned DNA", Current Protocols in Molecular Biology, Chapter 8, John Wiley & Sons, 1995.
Mormeneo ey al., "Precise nucleotide sequence modifications with bidirectionally cleaving class-IIS excision linkers", Gene, 61: 21-30 (1987).
Unrau and Deugau, "Non-Cloning amplification of specific DNA fragments from whole genomic DNA digests using DNA `indexers`", Gene, 145: 163-169 (1994).
Kato, "Description of the entire mRNA population by a 3'end cDNA fragment generated by a 3'end cDNA fragment generated by class IIS restriction enzymes", Nucleic Acids Research, 23: 3685-3690 (1995).
Zoller et al., "Oligonucleotide-Directed mutagenesis of DNA Fragments Cloned into M13 Vectors", Recombinant DNA Methodology, Chapter 30, Academic Press, Inc., 1989.

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