Thermodynamic analysis of 3 -> 2 transition in oligonucleotide triple-helix complexes dAn-2dTm

  • Yu.P. Blagoi B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine
  • V.N. Zozulya B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine
  • S.A. Egupov B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine
  • O.A. Ryazanova B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine
  • A.S. Shcherbakova B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine
Keywords: oligonucleotide triplexes, helix-coil transition, stabilization of triplexes by dye

Abstract

The work considers a possibility for thermodynamically describing the transition in oligomeric complexes dA15-2dT10 and dA19-2dT19 from the triplex form to the duplex+single strand (3—»2 transition), using the "Staggering Zipper" model and assuming the transition to be bimolecular reaction A 2B<=>AB+B. It was shown that upon physically grounded values of the transition thermodynamic parameters (ΔH23, ΔS:23, nucleation parameter β23, and others) the model describes adequately the experimental melting curves for triplexes with various lengths of oligonucleotide chains and different ionic conditions. As well, the work considers the effects of the dye covalently attached to dT10, intercalating between   A·T pairs of the duplex on the transition parameters. Possible causes of great dispersion of the experimental data obtained for ΔH32 by different methods (DSC, ITC, van't Hoff analysis, and so on) are analyzed. It is shown that the disordering of the triplex and duplex ends (the so-called "end fraying") has a significant influence on the form of melting curves and on thermodynamic transition parameters.

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Author Biographies

Yu.P. Blagoi, B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine

47 Lenin Ave., 61103, Kharkov, Ukraine

V.N. Zozulya, B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine

47 Lenin Ave., 61103, Kharkov, Ukraine

S.A. Egupov, B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine

47 Lenin Ave., 61103, Kharkov, Ukraine

O.A. Ryazanova, B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine

47 Lenin Ave., 61103, Kharkov, Ukraine

A.S. Shcherbakova, B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine

47 Lenin Ave., 61103, Kharkov, Ukraine

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Published
2002-06-05
Cited
How to Cite
Blagoi, Y., Zozulya, V., Egupov, S., Ryazanova, O., & Shcherbakova, A. (2002). Thermodynamic analysis of 3 -&gt; 2 transition in oligonucleotide triple-helix complexes dAn-2dTm . Biophysical Bulletin, 1(10), 5-11. Retrieved from https://periodicals.karazin.ua/biophysvisnyk/article/view/18373
Issue
Vol. 1 No. 10 (2002): Біофізичний вісник
Section
Molecular biophysics
Copyright (c) 2002 Biophysical visnik

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