Solvent effects on ionization potentials of guanine runs and chemically modified guanine in duplex DNA: effect of electrostatic interaction and its reduction due to solvent.

The Journal of Physical Chemistry. B
Satoshi YokojimaAkira Okada

Abstract

We examined the ionization potential (IP) corresponding to the free energy of a hole on duplex DNA by semiempirical molecular orbital theory with a continuum solvent model. As for the contiguous guanines (a guanine run), we found that the IP in the gas phase significantly decreases with the increasing number of nucleotide pairs of the guanine run, whereas the IP in water (OP, oxidation potential) only slightly does. The latter result is consistent with the experimental result for DNA oligomers in water. This decrease in the IP is mainly due to the attractive electrostatic interaction between the hole and a nucleotide pair in the duplex DNA. This interaction is reduced in water, which results in the small decrease in the IP in water. This mechanism explains the discrepancy between the experimental result and the previous computational results obtained by neglecting the solvent. As for the chemically modified guanine, the previous work showed that the removal of some solvent (water) molecules due to the attachment of a neutral functional group to a guanine in a duplex DNA stabilizes the hole on the guanine. One might naively have expected the opposite case, since a polar solvent usually stabilizes ions. This mechanism also explai...Continue Reading

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Citations

Apr 25, 2012·Physical Chemistry Chemical Physics : PCCP·Yang LiuVladimir Shafirovich
Oct 3, 2013·PLoS Genetics·Albino BacollaKaren M Vasquez
Jun 10, 2011·Chembiochem : a European Journal of Chemical Biology·Young-Ae LeeVladimir Shafirovich
Apr 22, 2015·Nucleic Acids Research·Albino BacollaKaren M Vasquez
Jan 10, 2020·The Journal of Chemical Physics·Bo PengSriram Krishnamoorthy
Sep 15, 2020·Journal of Chemical Theory and Computation·Polydefkis DiamantisUrsula Rothlisberger

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Methods Mentioned

BETA
X-ray

Software Mentioned

COSMO
MOPAC2002
MOZYME
3DNA

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