DNA sequencing by indexer walking

Clinical Chemistry

Volumn 51, Issue 9, 2005, Pages 1612-1618

  Gromek, Katarzyna ^a   Kaczorowski, Tadeusz ^a  

^a UNIVERSITY OF GDA SK   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA FRAGMENT; FLUORESCENT DYE; OLIGONUCLEOTIDE; RESTRICTION ENDONUCLEASE;

ANALYTIC METHOD; ANALYTICAL ERROR; ARTICLE; AUTOMATION; BACTERIAL STRAIN; DIAGNOSTIC ACCURACY; DNA DETERMINATION; DNA LIBRARY; DNA SEQUENCE; ESCHERICHIA COLI; GENE AMPLIFICATION; INDEXER WALKING; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID;

DNA PRIMERS; DNA RESTRICTION ENZYMES; DNA, BACTERIAL; ESCHERICHIA COLI; MOLECULAR SEQUENCE DATA; PLASMIDS; SEQUENCE ANALYSIS, DNA;

ESCHERICHIA COLI;

EID: 24144467479     PISSN: 00099147     EISSN: None     Source Type: Journal    
DOI: 10.1373/clinchem.2004.046599     Document Type: Article

References (41)

1. Bentley DR. Genomes for medicine. Nature 2004;429:440-5.
2. Bell J. Predicting disease using genomics. Nature 2004;429: 453-6.
3. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 1977;74:5463-7.
4. Strauss EC, Kobori JA, Siu G, Hood LE. Specific-primer-directed DNA sequencing. Anal Biochem 1986;154:353-60.
5. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995;269: 496-512.
6. Hardin SH, Jones LB, Homayouni R, McCollum JC. Octamer-primed cycle sequencing: design of an optimized primer library. Genome Res 1996;6:545-50.
7. Siemieniak DR, Slightom JL. A library of 3342 useful nonamer primers for genome sequencing. Gene 1990;96:121-4.
8. Studier FW. A strategy for high-volume sequencing of cosmid DNAs: random and direct priming with a library of oligonucleotides. Proc Natl Acad Sci U S A 1989;86:6917-21.
9. Szybalski W. Proposal for sequencing DNA using ligation of hexamers to generate sequential elongation primers (SPEL-6). Gene 1990;90:177-8.
10. Kieleczawa J, Dunn JJ, Studier FW. DNA sequencing by primer walking with strings of contiguous hexamers. Science 1992;258: 1787-91.
11. Azhikina TL, Veselovskaya SV, Myasnikov VA, Potapov VK, Ermolayeva O, Sverdlov ED. Strings of contiguous modified pentamers with increased binding affinity can be used for DNA sequencing by primer walking. Proc Natl Acad Sci U S A 1993;90:11460-2.
12. Kotler LE, Zevin-Sonkin D, Sobolev IA, Beskin AD, Ulanovsky LE. DNA sequencing: modular primers assembled from a library of hexamers or pentamers. Proc Natl Acad Sci U S A 1993;90: 4241-5.
13. Kaczorowski T, Szybalski W. Assembly of 18-nucleotide primers by ligation of three hexamers: sequencing of large genomes by primer walking. Anal Biochem 1994;221:127-35.
14. Kaczorowski T, Szybalski W. Genomic DNA sequencing by SPEL-6 primer walking using hexamer ligation. Gene 1998;223:83-91.
15. Lashkari DA, Hunicke-Smith SP, Norgren RM, Davis RW, Brennan T. An automated multiplex oligonucleotide synthesizer: development of high-throughput, low-cost DNA synthesis. Proc Natl Acad Sci U S A 1995;92:7912-5.
16. Rayner S, Brignac S, Bumeister R, Belosludtsev Y, Ward T, Grant OD, et al. MerMade: an oligodeoxyribonucleotide synthesizer for high throughput oligonucleotide production in dual 96-well plates. Genome Res 1998;8:741-7.
17. Unrau P, Deugau KV. Non-cloning amplification of specific DNA fragments from whole genomic DNA digests using DNA indexers. Gene 1994;145:163-9.
18. Szybalski W, Kim SC, Hasan N, Podhajska AJ. Class-IIS restriction enzymes - a review. Gene 1991;100:13-26.
19. Orskov I, Orskov F, Rowe B. Three new Escherichia coli O antigens O154, O155 and O156, and one new K antigen, K94. Acta Pathol Microbiol Scand [B] 1973;81:59-64.
20. Sambrook J, Fritsch EF, Maniatis T. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory, 1989;1.38-1.39: Appendix A1.
21. Roberts RJ, Vincze T, Pósfai J, Macelis D. REBASE: restriction enzymes and methyltransferases. Nucleic Acids Res 2003;31: 418-20.
22. Cheng S, Fockler C, Barnes WM, Higuchi R. Effective amplification of long targets from cloned inserts and human genomic DNA. Proc Natl Acad Sci U S A 1994;91:5695-9.
23. Weiss B, Jacquemin-Sablon A, Live TR, Fareed GC, Richardson CC. Enzymatic breakage and joining of deoxyribonucleic acid. VI. Further purification and properties of polynucleotide ligase from Escherichia coli infected with bacteriophage T4. J Biol Chem 1968;243:4543-55.
24. Smith DR. Ligation-mediated PCR of restriction fragments from large DNA molecules. PCR Methods Appl 1992;2:21-7.
25. Wu DY, Wallace RB. Specificity of the nick-closing activity of bacteriophage T4 DNA ligase. Gene 1989;76:245-54.
26. Barnes WM. PCR amplification of up to 35-kb DNA with high fidelity and high yield from λ bacteriophage templates. Proc Natl Acad Sci U S A 1994;91:2216-20.
27. Cline J, Braman JC, Hogrefe HH. PCR fidelity of Pfu polymerase and other thermostable DNA polymerases. Nucleic Acids Res 1996;18:3546-51.
28. Henikoff S. Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene 1984;28:351-9.
29. Glaser V. Market expands for custom oligonucleotides. Genet Eng News 2003;23:26-9.
30. Wright WE. Partial-digest DNA sequencing. Biotechniques 1992; 13:772-9.
31. Kato K. RNA fingerprinting by molecular indexing. Nucleic Acids Res 1996;24:394-5.
32. Guilfoyle RA, Leeck CL, Kroening KD, Smith LM, Quo Z. Ligation-mediated PCR amplification of specific fragments from a class-II restriction endonuclease total digest. Nucleic Acids Res 1997; 25:1854-8.
33. Nishigaki K, Akasaka K, Hasegawa T. Random PCR-based genome sequencing: a non-divide-and-conquer strategy. DNA Res 2000;7: 19-26.
34. Kato K. Description of the entire mRNA population by a 3′ end cDNA fragment generated by class US restriction enzymes. Nucleic Acids Res 1995;23:3685-90.
35. Jones DH. An iterative and regenerative method for DNA sequencing. Biotechniques 1997;22:938-46.
36. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 2000; 18:630-4.
37. Yamashita R, Matsubara K, Kato K. A comprehensive collection of mouse zinc finger motifs compiled by molecular indexing. Gene 2001;274:101-10.
38. Rosenthal A, Jones DSC. Genomic walking and sequencing by oligo-cassette mediated polymerase chain reaction. Nucleic Acids Res 1990;18:3095-6.
39. Heitman J, Model P. Site-specific methylases induce the SOS DNA repair response in Escherichia coli. J Bacteriol 1987;169:3243-50.
40. Perkins EL, Sterling JF, Hashem VI, Resnick MA. Yeast and human genes that affect the Escherichia coli SOS response. Proc Natl Acad Sci U S A 1999;96:2204-9.
41. Bzymek M, Lovett ST. Instability of repetitive DNA sequences: the role of replication in multiple mechanisms. Proc Natl Acad Sci U S A 2001;98:8319-25.