DNA sequencing by stepwise ligation and cleavage

Details DNA sequencing by stepwise ligation and cleavage DNA sequencing by stepwise ligation and cleavage

1995-03-24

1997-02-04

Jones, W. Gary

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

435 911, 435 912, 435 9152, 435 9153, 536 243, 935 77, 935 78, C07H 2104, C12P 1934, C12Q 168

Patent

active

055996752

ABSTRACT:
The invention provides a method of nucleic acid sequence analysis based on repeated cycles of ligation to and cleavage of probes at the terminus of a target polynucleotide. At each such cycle one or more terminal nucleotides are identified and one or more nucleotides are removed from the end of the target polynucleotide, such that further cycles of ligation and cleavage can take place. At each cycle the target sequence is shortened by one or more nucleotides until the nucleotide sequence of the target polynucleotide is determined. The method obviates electrophoretic separation of similarly sized DNA fragments and eliminates the difficulties associated with the detection and analysis of spatially overlapping bands of DNA fragments in a gel, or like medium. The invention further obviates the need to generate DNA fragments from long single stranded templates with a DNA polymerase.

REFERENCES:
patent: 4237224 (1980-12-01), Cohen et al.
patent: 4293652 (1981-10-01), Cohen
patent: 4321365 (1982-03-01), Wu et al.
patent: 4683202 (1987-07-01), Mullis
patent: 4775619 (1988-10-01), Urdea
patent: 5002867 (1991-03-01), Macevicz
patent: 5093245 (1992-03-01), Urdea
patent: 5102785 (1992-04-01), Livak et al.
patent: 5114839 (1992-05-01), Bloker
patent: 5118605 (1992-06-01), Urdea
patent: 5126239 (1992-06-01), Livak et al.
patent: 5202231 (1993-04-01), Drmanac et al.
patent: 5242794 (1993-09-01), Whiteley et al.
patent: 5403708 (1995-04-01), Brennan et al.
patent: 5427911 (1995-06-01), Ruano
Cantor et al., Genomics 13:1378-1383, 1992.
Drmanac et al., J. Biomolecular & Struct. & Dyn. 8(5):1085-1102, 1991.
Khrapko et al., J. DNA Sequencing and Mapping 1:375-388, 1991.
Khrapko et al., Feb. 256, (1,2) 118-122, 1989.
Lysov et al., Doklady Akademii Nauk 555R 303 (6) 1508-1511, 1988 (Translated Version, pp. 436-438).
Southern et al., Genomics 13: 1008-1017, 1992.
Strezoska et al., P.N.A.S. 88:10089-10093, 1991.
Brenner and Livak, "DNA fingerprinting by sampled sequencing," Proc. Natl. Acad. Sci. 86:8902-8906 (1989).
Carrano et al, "A high-resolution, fluorescience-based, semiautomated method for DNA fingerprinting," Genomics, 4:129-136 (1989).
Szybalski et al, "Class-IIS restriction enzymes--a review," Gene, 100:13-26 (1991).
Kim et al, "Cleaving DNA at any predetermined site with adapter-primers and Class-IIS restriction enzymes," Science, 240:504-506 (1988).
Szybalski, "Universal restriction endonucleases: designing novel cleavage specificities by combining adapter oligonucleotide and enzyme moieties," Gene, 40:169-173 (1985).
Barany, "The ligase chain reaction in a PCR world," PCR methods and Applications, 1:5-16 (1991).
Wu and Wallace, "The ligase amplification reaction (LAR)--amplification of specific DNA sequences using sequential rounds of template-dependant ligation," Genomics, 4:560-569 (1989).
McGuigan et al, "DNA fingerprinting by sampled sequencing," Methods in Enzymology, 218:241-258 (1993).
Nelson et al, "Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases," Nucleic Acids research, 21:3139-3154 (1993).
Roberts and Macelis, "REBASE--restriction enzymes and methylases," Nucleic Acids Research, 21:3125-3137 (1993).
Syvanen et al, "A primer-guided nucleotide incorporation assay in the genotyping of apolipoprotein E," Genomics 8:684-692 (1990).
Broude et al, "Enhanced DNA sequencing by hybridization," Proc. Natl. Acad. Sci., 91:3072-3076 (1994).
Hultman et al, "Direct solid phase sequencing of genomic and plasmid DNA using magnetic beads as solid support," Nucleic Acids Research, 17:4937-4946 (1989).
Loakes et al, "5-Niroindole as an universal base analogue," Nucleic Acids Research, 22:4039-4043 (1994).
Nichols et al, "A universal nucleoside for use at ambiguous sites in DNA primers," Nature, 369:492 -493 (1994).
Nikiforov et al, "Genetic bit analysis: a solid phase method for typing single nucleotide polymorphisms," Nucleic Acids Research, 22: 4167-4175 (1994).
Berger, "Expanding the potential of restriction endonucleases: use of hapaxoterminstic enzymes," Anal. Biochem., 222:1-8 (1994).
Unrau et al, "Non-coding amplification of specific DNA fragments from whole genomic DNA digests using DNA `indexers,`" Gene, 145:163-169 (1994).
Syvanen et al, "Convenient and quantitative determination of the frequency of a mutant allele using solid-phase minisequencing application to aspartylglucosaminuria in Finland," Genomics, 12:590-595 (1992).
Wiaderkiewicz et al, "Mismatch and blunt to protruding end joining by DNA ligases," Nucleic Acids Research, 15:7831-7848 (1987).
Tsiapalis et al, "On the fidelity of phage T4-induced polynucleotide ligase in the joining of chemically synthesized deoxyriboligonucleotides," Biochem. Biophys. Res. Comm., 39:631-636 (1970).
Goffin et al, "Nicks 3' or 5' to AP sites or to mispaired bases, and one-nucleotide gaps can be sealed by T4 DNA ligase," Nucleic Acids Research, 15:8755-8771 (1987).

Affiliated with

Also associated with

Rating

DNA sequencing by stepwise ligation and cleavage does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with DNA sequencing by stepwise ligation and cleavage, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and DNA sequencing by stepwise ligation and cleavage will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFUS-PAI-O-677492