Genome profiling: A realistic solution for genotype-based identification of species

Journal of Biochemistry

Volumn 128, Issue 1, 2000, Pages 107-112

  Nishigaki, Koichi ^b   Naimuddin, Mohammed ^b   Hamano, Keiichi ^a,b  

^a KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^b SAITAMA UNIVERSITY   (Japan)

Author keywords

Genome Profiling; Random PCR; Species identification and information amount; TGGE

Indexed keywords

ARTICLE; GENETIC ANALYSIS; GENOME; GENOTYPE; NONHUMAN; POLYMERASE CHAIN REACTION; SPECIES DIFFERENTIATION;

EID: 0033914245     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.jbchem.a022719     Document Type: Article

References (17)

1. Caetano-Anolles, G. (1996) Scanning of nucleic acids by in vitro amplification: new developments and applications. Nat. Biotechnol. 14, 1668-1674
2. Tsipouras, P. (1987) Restriction fragment length polymorphisms. Methods Enzymol. 145, 205-213
3. Nishigaki, K., Amano, N., and Takasawa, T. (1991) DNA profiling-An approach of systemic characterization, classification and comparison of genomic DNAs. Chem. Lett. 1991, 1097-1100
4. Hamano, K., Takasawa, T., Kurazono, T., Okuyama, Y., and Nishigaki, K. (1996) Genome profiling - Establishment and practical evaluation of its methodology. Nikkashi 1996, 54-61
5. Wang, H., Qin, M., and Cutler, A.J. (1993) A simple method of preparing plant samples for PCR. Nucleic Acids Res. 21, 4153-4154
6. Sakuma, Y. and Nishigaki, K. (1994) Computer prediction of general PCR products based on dynamical solution structures of DNA. J. Biochem. 116, 736-741
7. Rosenzweig, M.L. (1995) Species Diversity in Space and Time, Cambridge University Press, Cambridge
8. Cavalier-Smith, T. (1985) The Evolution of Genome Size, Wiley, New York
9. Nishigaki, K., Husimi, Y., Masuda, M., Kaneko, K., and Tanaka, T. (1984) Strand dissociation and cooperative melting of double-stranded DNAs detected by denaturant gradient gel electrophoresis. J. Biochem. 95, 627-635
10. Nishigaki, K., Tsubota, M., Miura, T., Chonan, Y., and Husimi, Y. (1992) Structural analysis of nucleic acids by precise denaturing gradient gel electrophoresis: II. Applications to the analysis of subtle and drastic mobility changes of oligo-and polynucleotides. J. Biochem. 111, 151-156
11. Nishigaki, K., Saito, A., Hasegawa, T., and Naimuddin, M., (2000) Whole genome sequence-enabled prediction of sequences performed for random PCR products of Escherichia coli. Nucleic Acids Res. 28, 1879-1884
12. Fischer, S.G. and Lerman, L.S. (1983) DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc. Natl. Acad. Sci. USA 80, 1579-1583
13. Steger, G. (1994) Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction. Nucleic Acids Res. 22, 2760-2768
14. Abrams, E.S. and Stanton, V.P., Jr. (1992) Use of denaturing gradient gel electrophoresis to study conformational transitions in nucleic acids. Methods Enzymol. 212, 71-104
15. Papadopoulos, D., Schneider, D., Meier-Eiss, J., Arber, W., Lenski, R.E., and Blot, M. (1999) Genomic evolution during a 10,000-generation experiment with bacteria. Proc. Natl. Acad. Sci. USA 96, 3807-3812
16. Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A., and Tingey, S.V. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18, 6531-6535
17. Welsh, J. and McClelland, M. (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 18, 7213-7218