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Influence of solvating water molecules on the attacking mechanisms of OH-radical to DNA base pairs: DFT calculations in explicit waters

Content Provider	Springer Nature Link
Author	Shimamura, Kanako Okutsu, Naoko Shimizu, Eisuke Shulga, Sergiy Blume, Yaroslav B. Danilov, Victor I. Kurita, riyuki
Copyright Year	2016
Abstract	To elucidate the influence of solvating water molecules on the attacking mechanism of OH-radical to DNA base pairs (G–C and A–T), we investigated the reaction mechanism in water, by the use of the density functional theory (DFT) calculations by considering water molecules explicitly. The results reveal that OH-radical is stabilized near the NH$_{2}$ group of cytosine of G–C by the water molecules hydrogen bonded to the OH-radical and that 2.5 kcal/mol activation free energy is needed for extracting the hydrogen atom from the NH$_{2}$ group. On the other hand, OH-radical prefers to extract the hydrogen atom from the NH$_{2}$ group of adenine in the solvated A–T. As for the tautomeric reaction of the base pair attacked by OH-radical, we found the transition state for the reaction from A to T to its tautomeric form A–T, although the activation free energy is rather large (25 kcal/mol). By contrast, in the G–C attacked by OH-radical, one central proton can move freely from G to C, resulting in the tautomeric form G–C. Therefore, our DFT calculations in explicit water molecules elucidate the possibility that the attacking of OH-radical to G–C causes its tautomeric form G–C, while A–T attacked by OH-radical cannot transform into its A–T form in a normal condition. This finding will be useful for predicting the effect of OH-radical on the genetic information recorded in DNA base sequences.
Starting Page	1793
Ending Page	1806
Page Count	14
File Format	PDF
ISSN	10400400
Journal	Structural Chemistry
Volume Number	27
Issue Number	6
e-ISSN	15729001
Language	English
Publisher	Springer US
Publisher Date	2016-07-18
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	DFT DNA base pair Tautomeric reaction Transition state Radical Attacking mechanism Computer Applications in Chemistry Physical Chemistry Theoretical and Computational Chemistry
Content Type	Text
Resource Type	Article
Subject	Physical and Theoretical Chemistry Condensed Matter Physics

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