Direct sequencing of bacterial artificial chromosomes (BACs) and prokaryotic genomes by biotin-capture PCR

Journal of Biotechnology

Volumn 60, Issue 1-2, 1998, Pages

  Sterky, Fredrik ^a   Holmberg, Anders ^a   Alexandersson, Gunnar ^a   Lundeberg, Joakim ^a   Uhlén, Mathias ^a  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

Biotin capture; Genome sequencing; PCR; Solid phase technology

Indexed keywords

BACTERIA; CELL IMMOBILIZATION; CHROMOSOMES;

BIOTIN CAPTURE; GENOMES;

DNA SEQUENCES;

BIOTIN; SINGLE STRANDED DNA;

ARTICLE; BACTERIAL GENE; CHROMOSOME; DNA SEQUENCE; ESCHERICHIA COLI; GENE SEQUENCE; GENOME; JURISPRUDENCE; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROKARYOTE;

BASE SEQUENCE; BETA-GALACTOSIDASE; BIOTIN; CHROMOSOMES, BACTERIAL; DNA, BACTERIAL; ELECTROPHORESIS, AGAR GEL; ESCHERICHIA COLI; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 0345214533     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-1656(97)00196-X     Document Type: Article

References (28)

1. Copley, C.G., Boot, C., Bundell, K., McPheat, W.L., 1991. Unknown sequence amplification: application to in vitro genome walking in Chlamydia trachomatis L2. Biotechnology (NY) 9, 74-79.
2. Devon, R.S., Porteous, D.J., Brookes, A.J., 1995. Splinkerettes - improved vectorettes for greater efficiency in PCR walking. Nucleic Acids Res. 23, 1644-1645.
3. Espelund, M., Jakobsen, K.S., 1992. Cloning and direct sequencing of plant promoters using primer-adapter mediated PCR on DNA coupled to a magnetic solid phase. Biotechniques 13, 74-81.
4. Fors, L., Saavedra, R.A., Hood, L., 1990. Cloning of the shark Po promoter using a genomic walking technique based on the polymerase chain reaction. Nucleic Acids Res. 18, 2793-2799.
5. Frohman, M.A., Dush, M.K., Martin, G.R., 1988. Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc. Natl. Acad. Sci. USA 85, 8998-9002.
6. Holmberg, A., Fry, C., Uhlén, M., 1994. Automatic preparation of DNA templates for sequencing on the ABI catalyst robotic workstation. In: Adams, M.D., Fields, C., Venter, J.C. (Eds.), Automated DNA Sequencing and Analysis. Academic Press, London, pp. 139-145.
7. Hultman, T., Ståhl, S., Hornes, E., Uhlén, M., 1989. Direct solid phase sequencing of genomic and plasmid DNA using magnetic beads as solid support. Nucleic Acids Res. 17, 4937-4946.
8. Hultman, T., Bergh, S., Moks, T., Uhlén, M., 1991. Bidirectional solid-phase sequencing of in vitro-amplified plasmid DNA. Biotechniques 10, 84-93.
9. Jones, D.H., Winistorfer, S.C., 1992. Sequence specific generation of a DNA panhandle permits PCR amplification of unknown flanking DNA. Nucleic Acids Res. 20, 595-600.
10. Lagerström, M., Parik, J., Malmgren, H., Stewart, J., Pettersson, U., Landegren, U., 1991. Capture PCR: efficient amplification of DNA fragments adjacent to a known sequence in human and YAC DNA. PCR Methods Appl. 1, 111-119.
11. Liu, Y.G., Whittier, R.F., 1995. Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics 2535, 674-681.
12. Loh, E.Y., Elliott, J.F., Cwirla, S., Lanier, L.L., Davis, M.M., 1989. Polymerase chain reaction with single-sided specificity: analysis of T cell receptor delta chain. Science 243, 217-220.
13. Malo, M.S., Srivastava, K., Andresen, J.M., Chen, X.N., Korenberg, J.R., Ingram, V.M., 1994. Targeted gene walking by low stringency polymerase chain reaction: assignment of a putative human brain sodium channel gene (SCN3A) to chromosome 2q24-31. Proc. Natl. Acad. Sci. USA 91, 2975-2979.
14. Marra, M., Weinstock, L.A., Mardis, E.R., 1996. End sequence determination from large insert clones using energy transfer fluorescent primers. Genome Res. 6, 1118-1122.
15. Ochman, H., Gerber, A.S., Hartl, D.L., 1988. Genetic applications of an inverse polymerase chain reaction. Genetics 120, 621-623.
16. Olsson, M.O., Isaksson, L.A., 1979. Analysis of rpsD mutations in Escherichia coli. I. Comparison of mutants with various alterations in ribosomal protein S4. Mol. Gen. Genet. 169, 251-257.
17. Parker, J.D., Rabinovitch, P.S., Burmer, G.C., 1991. Targeted gene walking polymerase chain reaction. Nucleic Acids Res. 19, 3055-3060.
18. Riley, J., Butler, R., Ogilvie, D., Finniear, R., Jenner, D., Powell, S., Anand, R., Smith, J.C., Markham, A.F., 1990. A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosome (YAC) clones. Nucleic Acids Res. 18, 2887-2890.
19. Rosenthal, A., Jones, D.S., 1990. Genomic walking and sequencing by oligo-cassette mediated polymerase chain reaction. Nucleic Acids Res. 18, 3095-3096.
20. Rosenthal, A., Platzer, M., Charnock-Jones, S., 1994. Capture PCR: an efficient method for walking along chromosomal DNA and cDNA. In: Mullis, K.B., Ferré, F., Gibbs, R.A. (Eds.), The Polymerase Chain Reaction. Birkhauser, Boston, pp. 222-229.
21. Roux, K.H., Dhanarajan, P., 1990. A strategy for single site PCR amplification of dsDNA: priming digested cloned or genomic DNA from an anchor-modified restriction site and a short internal sequence [published erratum appears in Biotechniques 1990, 8(3): 265]. Biotechniques 8, 48-57.
22. Sambrook, J., Fritsch, E.F., Maniatis, T., 1989. Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
23. Sarkar, G., Turner, R.T., Bolander, M.E., 1993. Restriction-site PCR: a direct method of unknown sequence retrieval adjacent to a known locus by using universal primers. PCR Methods Appl. 2, 318-322.
24. Shyamala, V., Ames, G.F., 1989. Genome walking by single-specific-primer polymerase chain reaction: SSP-PCR. Genetics 84, 1-8.
25. Sørensen, A.B., Duch, M., Jorgensen, P., Pedersen, F.S., 1993. Amplification and sequence analysis of DNA flanking integrated proviruses by a simple two-step polymerase chain reaction method. J. Virol. 67, 7118-7124.
26. Triglia, T., Peterson, M.G., Kemp, D.J., 1988. A procedure for in vitro amplification of DNA segments that lie outside the boundaries of known sequences. Nucleic Acids Res. 16, 81-86.
27. Törmänen, V.T., Swiderski, P.M., Kaplan, B.E., Pfeifer, G.P., Riggs, A.D., 1992. Extension product capture improves genomic sequencing and DNase I footprinting by ligation-mediated PCR. Nucleic Acids Res. 20, 5487-5488.
28. Verhasselt, P., Voet, M., Volckaert, G., 1992. DNA sequencing by a subcloning-walking strategy using a specific and semi-random primer in the polymerase chain reaction. DNA Seq. 2, 281-287.