Studies of the B-Z transition of DNA: The temperature dependence of the free-energy difference, the composition of the counterion sheath in mixed salt, and the preparation of a sample of the 5'-d[T-(m(5) C-G)12 -T] duplex in pure B-DNA or Z-DNA form

Biopolymers
M GuéronM Filoche

Abstract

It is often envisioned that cations might coordinate at specific sites of nucleic acids and play an important structural role, for instance in the transition between B-DNA and Z-DNA. However, nucleic acid models explicitly devoid of specific sites may also exhibit features previously considered as evidence for specific binding. Such is the case of the "composite cylinder" (or CC) model which spreads out localized features of DNA structure and charge by cylindrical averaging, while sustaining the main difference between the B and Z structures, namely the better immersion of the B-DNA phosphodiester charges in the solution. Here, we analyze the non-electrostatic component of the free-energy difference between B-DNA and Z-DNA. We also compute the composition of the counterion sheath in a wide range of mixed-salt solutions and of temperatures: in contrast with the large difference of composition between the B-DNA and Z-DNA forms, the temperature dependence of sheath composition, previously unknown, is very weak. In order to validate the model, the mixed-salt predictions should be compared to experiment. We design a procedure for future measurements of the sheath composition based on Anomalous Small-Angle X-ray Scattering and comple...Continue Reading

References

Jul 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·M Guéron, J P Demaret
Aug 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·J B Chaires, J M Sturtevant
Aug 1, 1985·Journal of Biomolecular Structure & Dynamics·M D Frank-KamenetskiiV V Anshelevich
Mar 1, 1981·Proceedings of the National Academy of Sciences of the United States of America·M Behe, G Felsenfeld
Jan 1, 1983·Cold Spring Harbor Symposia on Quantitative Biology·F M Pohl
Oct 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·L J Peck, J C Wang
Aug 1, 1984·Proceedings of the National Academy of Sciences of the United States of America·D M Soumpasis
Aug 30, 1983·Biochemical and Biophysical Research Communications·K B Roy, H T Miles
Mar 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·D J PatelA Rich
Apr 3, 2002·Chemistry & Biology·Martin Egli
Feb 9, 2005·Physical Review Letters·K AndresenL Pollack
Feb 11, 2005·Journal of Biomolecular Structure & Dynamics·Christine RauchErwin Mayer
Nov 5, 2010·Journal of the American Chemical Society·Suzette A PabitLois Pollack
Dec 20, 2011·Nucleic Acids Research·Tatsuya MaehigashiLoren Dean Williams
Nov 29, 2014·The Journal of Chemical Physics·Duc NguyenMartin Gruebele

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