Effect of PCR conditions on the formation of heteroduplex and single-stranded DNA products in the amplification of bacterial ribosomal DNA spacer regions

Genome Research

Volumn 3, Issue 3, 1993, Pages 186-194

  Jensen, Mark A ^a   Straus, Neil ^b  

^a DUPONT COMPANY   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; DNA POLYMERASE; DOUBLE STRANDED DNA; HETERODUPLEX; RIBOSOME DNA; SINGLE STRANDED DNA; SPACER DNA;

ARTICLE; BACTERIUM; DNA HYBRIDIZATION; DNA SEQUENCE; DNA STRUCTURE; DNA TEMPLATE; ENZYME ACTIVITY; GENE AMPLIFICATION; MOLECULAR WEIGHT; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

BASE SEQUENCE; DNA PRIMERS; DNA, BACTERIAL; DNA, RIBOSOMAL; DNA, SINGLE-STRANDED; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ENDONUCLEASES; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HETERODUPLEXES; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S;

EID: 0027745825     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.3.3.186     Document Type: Article

References (16)

1. Jensen, M.A., J.A. Webster, and N. Straus. 1993. Rapid identification of bacteria based on polymerase chain-reaction amplified ribosomal DNA spacer polymorphisms. Appl. Environ. Microbiol. 59: 945-952 (patent pending).
2. Williams, J.G.K., A.R. Kubelik, K.J. Livak, J.A. Rafalski, and S.V. Tingey. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18: 6531-6535.
3. Welsh, J. and M. McClelland. 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 18: 7213-7218.
4. Welsh, J., C. Petersen, and M. McClelland. 1990. Polymorphisms generated by arbitrarily primed PCR in the mouse: Application to strain identification and genetic mapping. Nucleic Acids Res. 19: 303-306.
5. Goodwin, P.H. and S.L. Annis. 1991. Rapid identification of genetic variation and pathotype of Leptosphaeria maculans by Random Amplified Polymorphic DNA assay. Appl. Environ. Microbiol. 57: 2482-2486.
6. Brosius, J., T.J. Dull, D.D. Sleeter, and H.F. Noller. 1981. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148: 107-127.
7. Grimont, F. and P.A.D. Grimont. 1986. Ribosomal ribonucleic acid gene restriction patterns as potential taxonomic tools. Annu. Inst. Pasteur/Microbiol. 137B: 165-175.
8. Webster, J.A. January 1988. U.S. patent 4,717,653.
9. Dams, E., L. Hendriks, Y. Van de Peer, J. Neefs, G. Smits, I. Vandenbempt, and R. De Wachter, 1988. Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. (Suppl.) 16: r87-r171.
10. Gutell, R.R. and G.E. Fox. 1988. A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Res. (Suppl.) 16: r175-r201.
11. Morgan, E.A., T. Ikemura, L.E. Post, and M. Nomura. 1979. tRNA genes in ribosomal RNA operons of Escherichia coli. In Transfer RNA: Biological aspects (ed. D. Soll, J. Abelson, and P. Schimmel), pp. 259-266. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
12. Young, R.A., R. Macklis, and J.A. Steitz. 1979. Sequence of the 16S-23S spacer region in two ribosomal RNA operons of Escherichia coli. J. Biol. Chem. 254: 3264-3271.
13. Becker-André, M. and K. Hahlbrock. 1989. Absolute mRNA quantification using the polymerase chain reaction (PCR). A novel approach by a PCR aided transcript titration assay. Nucleic Acids Res. 17: 9437-9446.
14. Hsieh, C.-H. and J.D. Griffith. 1989. Deletions of bases in one strand of duplex DNA, in contrast to single-base mismatches, produce highly kinked molecules: Possible relevance to the folding of single-stranded nucleic acids. Proc. Natl. Acad. Sci. 86: 4833-4837.
15. Ruano, G. and K.K. Kidd. 1992. Modeling of heteroduplex formation during PCR from mixtures of DNA templates. PCR Methods Applic. 2: 112-116.
16. Orita, M., H. Iwahana, H. Kanazawa, K. Hayashi, and T. Sekiya. 1989. Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc. Natl. Acad. Sci. 86: 2766-2770.