Exceptional thermodynamic stability of DNA duplexes modified by nonpolar base analogues is due to increased stacking interactions and favorable solvation: Correlated ab initio calculations and molecular dynamics simulations

Chemistry : a European Journal
David RehaPavel Hobza

Abstract

The geometries of DNA hexamer (5'-GGAACC-3') and DNA 13-mer (5'-GCGTACACATGCG-3') have been determined by molecular dynamics (MD) simulations using an empirical force field. The central canonical base pair was replaced by a pair of nonpolar base analogues, 2,2'-bipyridyl and 3-methylisocarbostyril. The stabilization energy of the model system (model A) consisting of a central base pair (base-analogue pair) and two neighboring base pairs was determined by the RI-MP2 method using an extended aug-cc-pVDZ basis set. The geometry of the model was averaged from structures determined by MD simulations. The role of the solvent was covered by the COSMO continuum solvent model and calculations were performed for a larger model system (model B) which also contained a sugar-phosphate backbone. The total stabilization energies of the unperturbed system and the system perturbed by a base-analogue pair (model A) were comparable to the stability of both duplexes experimentally determined. This is due to large stacking interaction energy of the base-analogue self-pair which compensates for the missing hydrogen-bonding energy of the replaced adenine...thymine base pair. The selectivity of the base-analogue pair was reproduced (model B) when thei...Continue Reading

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Citations

Aug 10, 2007·Journal of the American Chemical Society·Shigeo MatsudaFloyd E Romesberg
Oct 5, 2007·Physical Chemistry Chemical Physics : PCCP·Jirí Cerný, Pavel Hobza
May 6, 2009·Angewandte Chemie·Hans-Jörg Schneider
Jul 2, 2009·Chemistry : a European Journal·Lucie ZendlováPavel Hobza
Dec 22, 2009·Physical Chemistry Chemical Physics : PCCP·Filippo LippariniBenedetta Mennucci
Aug 26, 2015·Angewandte Chemie·Denis A Malyshev, Floyd E Romesberg
Jan 25, 2012·Physical Chemistry Chemical Physics : PCCP·Lesley R Rutledge, Stacey D Wetmore
Apr 18, 2008·The Journal of Organic Chemistry·Jan BártaMichal Hocek
Sep 19, 2009·Chemical Reviews·Jan StambaskýPavel Kocovský
Aug 2, 2007·The Journal of Organic Chemistry·Nicolas JoubertMichal Hocek
Sep 26, 2013·ACS Chemical Biology·Jason G HarrisonDean J Tantillo
Apr 22, 2015·The Journal of Physical Chemistry. B·Sk Jahiruddin, Ayan Datta
May 18, 2011·The Journal of Physical Chemistry. B·Michal KolářPavel Hobza
Aug 8, 2018·The Journal of Physical Chemistry. B·Zahedeh Bashardanesh, David van der Spoel
Sep 9, 2006·The Journal of Organic Chemistry·Milan UrbanMichal Hocek

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