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. 1990 Nov 11;18(21):6413–6417. doi: 10.1093/nar/18.21.6413

A method for determining the relative effect of ligands on A-T and G-C base pairs in DNA: applications to metal ions, protons and two amino acids.

S G Haroutiunian 1, E B Dalian 1, V M Aslanian 1, Lando DYu 1, A A Akhrem 1
PMCID: PMC332524  PMID: 2173828

Abstract

A new method is described for the study of specific interactions of low-molecular ligands with the base pairs of DNA. This method is based on the comparative analysis of melting temperature changes in DNAs of different GC-content in the presence of low molecular weight ligands. In this paper, the method is applied to Mn2+, Ni2+, Co2+ ions, deprotonation, amino acids, beta-alanine and gamma-aminobutyric acid (gamma-ABA). Differences in Tm are affected not only by the changes of relative stability of AT- and GC-pairs, but also by other factors. A theoretical analysis of the sequence specificity of low-molecular ligands on the base pairs in DNA molecules characterized by a high degree of sequence heterogeneity is also presented.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Akhrem A. A., Arutiunian S. G., Aslanian V. M., Dalian E. B., Lando D. Iu. Perekhod spiral'-klubok DNK v shchelochnoi srede. Mol Biol (Mosk) 1989 Mar-Apr;23(2):518–525. [PubMed] [Google Scholar]
  2. Akhrem A. A., Lando D. Iu. Vliianie ligandov s izbiratel'nym kharakterom vzaimodeistviia na perekhod spiral'-klubok DNK. I. Model'. Teoriia. Mol Biol (Mosk) 1979 Sep-Oct;13(5):1098–1109. [PubMed] [Google Scholar]
  3. Akhrem A. A., Lando D. Iu. Vliianie ligandov s izbiratel'nym kharakterom vzaimodeistviia na perekhod spiral'-klubok DNK. III. Raschet krivykh plavleniia komplekosov DNK s ligandami. Mol Biol (Mosk) 1981 Sep-Oct;15(5):1083–1092. [PubMed] [Google Scholar]
  4. Aslanian V. M., Arutiunian S. G., Lando D. Iu, Dalian E. B., Shpokovskii A. G. Izbiratel'noe vliianie ligandov na AT- i GTs-pary osnovanii DNK. Biofizika. 1988 May-Jun;33(3):430–436. [PubMed] [Google Scholar]
  5. Berestetskaya I. V., Frank-Kamenetskii M. D., Lazurkin Y. S. Effect of ionic conditions on DNA melting curve parameters. Biopolymers. 1974 Jan;13(1):193–205. doi: 10.1002/bip.1974.360130113. [DOI] [PubMed] [Google Scholar]
  6. Förster W., Bauer E., Schütz H., Berg H., Akimenko M., Minchenkova L. E., Evdokimov YuM, Varshavsky Ia M. Thermodynamics and kinetics of the interaction of copper (II) ions with native DNA. Biopolymers. 1979 Mar;18(3):625–661. doi: 10.1002/bip.1979.360180311. [DOI] [PubMed] [Google Scholar]
  7. GEIDUSCHEK E. P., HERSKOVITS T. T. Nonaqueous solutions of DNA. Reversible and irreversible denaturation in methanol. Arch Biochem Biophys. 1961 Oct;95:114–129. doi: 10.1016/0003-9861(61)90116-3. [DOI] [PubMed] [Google Scholar]
  8. HERSKOVITS T. T., SINGER S. J., GEIDUSCHEK E. P. Nonaqueous solutions of DNA. Denaturation in methanol and ethanol. Arch Biochem Biophys. 1961 Jul;94:99–114. doi: 10.1016/0003-9861(61)90016-9. [DOI] [PubMed] [Google Scholar]
  9. Luck G., Zimmer C. Conformational aspects and reactivity of DNA. Effects of manganese and magnesium ions on interaction with DNA. Eur J Biochem. 1972 Sep 25;29(3):528–536. doi: 10.1111/j.1432-1033.1972.tb02018.x. [DOI] [PubMed] [Google Scholar]
  10. Melchior W. B., Jr, Von Hippel P. H. Alteration of the relative stability of dA-dT and dG-dC base pairs in DNA. Proc Natl Acad Sci U S A. 1973 Feb;70(2):298–302. doi: 10.1073/pnas.70.2.298. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Ott G. S., Bastia D., Bauer W. A spectroscopic and electron microscopic examination of the highly condensed DNA structures formed by denaturation in Mg(ClO4)2. Biochim Biophys Acta. 1978 Apr 27;518(2):216–232. doi: 10.1016/0005-2787(78)90179-x. [DOI] [PubMed] [Google Scholar]
  12. Shin Y. A. Interaction of metal ions with polynucleotides and related compounds. XXII. Effect of divalent metal ions on the conformational changes of polyribonucleotides. Biopolymers. 1973 Nov;12(11):2459–2475. doi: 10.1002/bip.1973.360121103. [DOI] [PubMed] [Google Scholar]

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