Metal ions cause the isomerization of certain intramolecular triplexes - PubMed (original) (raw)
. 1992 Jan 15;267(2):1259-64.
Affiliations
- PMID: 1309767
Free article
Metal ions cause the isomerization of certain intramolecular triplexes
S M Kang et al. J Biol Chem. 1992.
Free article
Abstract
The influence of cations on the capacity of five oligopurine.oligopyrimidine mirror repeat sequences to adopt intramolecular triplexes (the usual H-y3 isomer and/or the rare H-y5 isomer) in recombinant plasmids was investigated. Unexpectedly, the presence of certain metal ions (magnesium, zinc, manganese, and calcium) stabilized the (GAA)4TTCGC(GAA)4 insert in the rare H-y5 when cloned into either of two different sequence backgrounds. Alternatively, either shortening or lengthening the sequence at the central interruption, which becomes the loop of the triplex, led to the formation of the canonical H-y3 under all conditions tested. Similarly, other oligopurine.oligopyrimidine mirror repeat sequences (i.e. (GAA)8 or (GGA)8) formed only the H-y3 under all experimental conditions. All triplexes were stabilized by negative supercoiling at pH 5.0; chemical probe and primer extension analyses served as critical structural tools. Hence, the nature of the central interruption sequence (the loop) of the mirror repeat is important for the stabilization of the H-y5. This region may be important for metal ion binding in the initial stages of triplex formation and thus may play a critical role in determining which isomer is formed. The possible biological role of a DNA sequence adopting three different conformations is discussed.
Similar articles
- The loop sequence plays crucial roles for isomerization of intramolecular DNA triplexes in supercoiled plasmids.
Shimizu M, Kubo K, Matsumoto U, Shindo H. Shimizu M, et al. J Mol Biol. 1994 Jan 7;235(1):185-97. doi: 10.1016/s0022-2836(05)80025-7. J Mol Biol. 1994. PMID: 8289240 - Multiple non-B-DNA conformations of polypurine.polypyrimidine sequences in plasmids.
Shimizu M, Hanvey JC, Wells RD. Shimizu M, et al. Biochemistry. 1990 May 15;29(19):4704-13. doi: 10.1021/bi00471a027. Biochemistry. 1990. PMID: 2372553 - The chemistry and biology of unusual DNA structures adopted by oligopurine.oligopyrimidine sequences.
Wells RD, Collier DA, Hanvey JC, Shimizu M, Wohlrab F. Wells RD, et al. FASEB J. 1988 Nov;2(14):2939-49. FASEB J. 1988. PMID: 3053307 Review. - Stabilities of double- and triple-strand helical nucleic acids.
Cheng YK, Pettitt BM. Cheng YK, et al. Prog Biophys Mol Biol. 1992;58(3):225-57. doi: 10.1016/0079-6107(92)90007-s. Prog Biophys Mol Biol. 1992. PMID: 1380719 Review.
Cited by
- The effect of zinc on the secondary structure of d(GA.TC)n DNA sequences of different length: a model for the formation *H-DNA.
Martínez-Balbás A, Azorín F. Martínez-Balbás A, et al. Nucleic Acids Res. 1993 Jun 11;21(11):2557-62. doi: 10.1093/nar/21.11.2557. Nucleic Acids Res. 1993. PMID: 8332452 Free PMC article. - Dynamics in the isomerization of intramolecular DNA triplexes in supercoiled plasmids.
Shindo H, Matsumoto N, Shimizu M. Shindo H, et al. Nucleic Acids Res. 1997 Dec 1;25(23):4786-91. doi: 10.1093/nar/25.23.4786. Nucleic Acids Res. 1997. PMID: 9365257 Free PMC article. - Alternative DNA structure formation in the mutagenic human c-MYC promoter.
Del Mundo IMA, Zewail-Foote M, Kerwin SM, Vasquez KM. Del Mundo IMA, et al. Nucleic Acids Res. 2017 May 5;45(8):4929-4943. doi: 10.1093/nar/gkx100. Nucleic Acids Res. 2017. PMID: 28334873 Free PMC article. - Trinucleotide repeats associated with human disease.
Mitas M. Mitas M. Nucleic Acids Res. 1997 Jun 15;25(12):2245-54. doi: 10.1093/nar/25.12.2245. Nucleic Acids Res. 1997. PMID: 9171073 Free PMC article. Review. - Triple-helix potential of the mouse genome.
Maekawa K, Yamada S, Sharma R, Chaudhuri J, Keeney S. Maekawa K, et al. Proc Natl Acad Sci U S A. 2022 May 10;119(19):e2203967119. doi: 10.1073/pnas.2203967119. Epub 2022 May 3. Proc Natl Acad Sci U S A. 2022. PMID: 35503911 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Research Materials
Miscellaneous