Segregation of partly melted DNA molecules

Nucleosides, Nucleotides and Nucleic Acids

Volumn 25, Issue 4-6, 2006, Pages 463-473

  Shiraishi, Masahiko ^a   Sekiya, Takao ^b  

^a INTERNATIONAL UNIVERSITY OF HEALTH AND WELFARE   (Japan)

^b MITSUBISHI KAGAKU INSTITUTE OF LIFE SCIENCES   (Japan)

Author keywords

dCpG islands; Denaturing gradient gel electrophoresis; Gene identification; Strand dissociation kinetics

Indexed keywords

DNA; DNA FRAGMENT;

ARTICLE; CPG ISLAND; DENATURING GRADIENT GEL ELECTROPHORESIS; DISSOCIATION; DNA DENATURATION; DNA SEQUENCE; DNA STRUCTURE; ELECTRIC FIELD; ELECTROPHORETIC MOBILITY; EPIGENETICS; GENE IDENTIFICATION;

BASE PAIRING; CPG ISLANDS; DNA; DNA METHYLATION; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HUMANS; NUCLEIC ACID DENATURATION;

EID: 33747614978     PISSN: 15257770     EISSN: 15322335     Source Type: Journal    
DOI: 10.1080/15257770600684159     Document Type: Article

References (38)

1. Lerman, L.S.; Frisch, H.L. Why does the electrophoretic mobility of DNA in gels vary with the length of the molecule?, Biopolymers 1982, 21, 995-997.
2. Lumpkin, O.J.; Zimm, B.H. Mobility of DNA in gel electrophoresis. Biopolymers 1982, 21, 2315-2316.
3. Lumpkin, O.J.; Déjardin, P.; Zimm, B.H. Theory of gel electrophoresis of DNA. Biopolymers 1985, 24, 1573-1593.
4. Marini, J.C.; Levene, S.D.; Crothers, D.M.; Englund, P.T. Bent helical structure in kinetoplast DNA. Proceedings of the National Academy of Sciences USA 1982, 79, 7664-7668.
5. Wu, H.-M.; Crothers, D.M. The locus of sequence-directed and protein-induced DNA bending. Nature 1984, 308, 509-513.
6. Lerman, L.S.; Fischer, S.G.; Hurley, I.; Silverstein, K.; Lumelsky, N. Sequence-determined DNA separations. Annual Review of Biophysics & Bioengineering 1984, 13. 399-423.
7. Fischer, S.G.; Lerman, L.S. Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis. Cell 1979, 16, 191-200.
8. Fischer, S.G.; Lerman, L.S. Separation of random fragments of DNA according to properties of their sequences. Proceedings of the National Academy of Sciences USA 1980, 77, 4420-4424.
9. Fischer, S.G.; Lerman, L.S. DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proceedings of the National Academy of Sciences USA 1983, 80, 1579-1583.
10. Shiraishi, M.; Lerman, L.S.; Sekiya, T. Preferential isolation of DNA fragments associated with CpG islands. Proceedings of the National Academy of Sciences USA 1995, 92, 4229-4233.
11. Myers, R.M.; Maniatis, T.; Lerman, L.S. Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods in Enzymology 1987, 155, 501-527.
12. Abrams, E.S.; Stanton, Jr., V.P. Use of denaturing gradient gel electrophoresis to study conformational transitions in nucleic acids. Methods in Enzymology 1992, 212, 71-104.
13. Shiraishi, M. Denaturing gradient gel electrophoresis to detect methylation changes in DNA. In Methods in Mol. Biol. Vol. 287, Epigenetics Protocols, Tollefsbol, Ed. T.O. Humana Press, Tonowa 2004; 219-232.
14. Lerman, L.S.; Silverstein, K. Computational simulation of DNA melting and its application to denaturing gradient gel electrophoresis. Methods in Enzymology 1987, 155, 482-501.
15. Fixman, M.; Freire, J.J. Theory of DNA melting curves. Biopolymers 1977, 16, 2693-2704.
16. Poland, D. Recursion relation generation of probability profiles for specific sequence macromolecules with long-range correlations. Biopolymers 1974, 13, 1859-1871.
17. Myers, R.M.; Lumelsky, N.; Lerman, L.S.; Maniatis, T. Detection of single base substitutions in total genomic DNA. Nature 1985, 313, 495-498.
18. Myers, R.M.; Ellenson, L.H.; Hayashi, K. Detection of DNA variation. In: Genome Analysis Vol. 2, Detecting Genes; Eds. Birren, B. Green, E.D. Klapholz, S. Myers, R.M. Roskams, J. Cold Spring Harbor Laboratory Press: Plainview 1998; 287-384.
19. Myers, R.M.; Fischer, S.G.; Maniatis, T.; Lerman, L.S. Modification of the melting properties of duplex DNA by attachment of a GC-rich DNA sequence as determined by denaturing gradient gel electrophoresis. Nucleic Acids Research 1985, 13, 3111-3129.
20. Myers, R.M.; Fischer, S.G.; Lerman, L.S.; Maniatis, T. Nearly all single base substitution in DNA fragments jointed to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Research 1985, 13, 3131-3145.
21. Myers, R.M.; Lerman, L.S.; Maniatis, T. A general method for saturation mutagenesis of cloned DNA fragments. Science 1985, 229, 242-247.
22. Sheffield, V.; Cox, D.R.; Lerman, L.S.; Myers, R.M. Attachment of a 40-base-pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proceedings of the National Academy of Sciences USA 1989, 86, 232-236.
23. Abrams, E.S.; Murdaugh, S.E.; Lerman, L.S. Comprehensive detection of single base changes in human genomic DNA using denaturing gradient gel electrophoresis and a GC clamp. Genomics 1990, 7, 463-475.
24. Cross, S.H.; Bird, A.P. CpG islands and genes. Current Opinion in Genetic Development 1995, 5, 309-314.
25. Lindsay, S.; Bird, A.P. Use of restriction enzymes to detect potential gene sequences in mammalian DNA. Nature 1987, 327, 336-338.
26. Bickmore, W.A.; Bird, A.P. Use of restriction endonucleases to detect and isolate genes from mammalian cells. Methods in Enzymology 1992, 216, 224-244.
27. Shiraishi, M.; Oates, A.J.; Xu, L.; Hosoda, F.; Ohki, M.; Alitalo, T.; Lerman, L.S.; Sekiya, T. The isolation of CpG islands from human chromosomal regions 11q13 and Xp22 by segregation of partly melted molecules. Nucleic Acids Research 1998, 26, 5544-5550.
28. Duyk, G.M.; Kim, S.W.; Myers, R.M.; Cox, D.R. Exon trapping: a genetic screen to identify candidate transcribed sequences in cloned mammalian genomic DNA. Proceedings of the National Academy of Sciences USA 1990, 87, 8995-8999.
29. Buckler, A.J.; Chang, D.D.; Graw, S.L.; Brook, J.D.; Haber, D.A.; Sharp, P.A.; Housman, D.E. Exon amplification: a strategy to isolate mammalian genes based on RNA splicing. Proceedings of the National Academy of Sciences USA 1991, 88, 4005-4009.
30. Parimoo, S.; Patanjali, S.R.; Shukla, H.; Chaplin, D.D.; Weissman, S.M. cDNA selection: efficient PCR approach for the selection of cDNAs encoded in large chromosomal DNA fragments. Proceedings of the National Academy of Sciences USA 1991, 88, 9623-9627.
31. Lovett, M.; Kere, J.; Hinton, L.M. Direct selection: a method for the isolation of cDNAs encoded by large genomic regions. Proceedings of the National Academy of Sciences USA 1991, 88, 9628-9632.
32. Ventor, J.C.; Adams, M.D.; Myers, E.W.; Li, P.W.; Mural, R.J.; Sutton, G.G.; Smith, H.O.; Yandell, M.; Evans, C.A.; Holt, R.A. et al. The sequence of the human genome. Science 2001, 291, 1304-1351.
33. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 2001, 409, 860-921.
34. Baylin, S.B.; Herman, J.G.; Graff, J.R.; Vertino, P.M.; Issa, J.-P. Alterations in DNA methylation: a fundamental aspect of neoplasia. Advances in Cancer Research 1998, 72, 141-196.
35. Shiraishi, M.; Chuu, Y.H.; Sekiya, T. Isolation of DNA fragments associated with methylated CpG islands in human adenocarcinomas of the lung using a methylated DNA binding column and denaturing gradient del electrophoresis. Proceedings of the National Academy of Sciences USA 1999, 96, 2913-2918.
36. Shiraishi, M.; Sekiguchi, A.; Terry, M.J.; Oates, A.J.; Miyamoto, Y.; Chuu, Y.H.; Munakata, M.; Sekiya, T. A comprehensive catalog of CpG islands methylated in human lung adenocarcinomas for the identification of tumor suppressor genes. Oncogene 2002, 21, 3804-3813.
37. Cross, S.H.; Charlton, J.A.; Nan, X.; Bird, A.P. Purification of CpG island using a methylated DNA binding column. Nature Genetics 1994, 6, 236-244.
38. Shiraishi, M.; Oates, A.J.; Sekiya, T. An overview of the analysis of DNA methylation in mammalian genomes. Biological Chemistry 2002, 383, 893-906.