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The Effects of a Guanine Hole on the Structure and Dynamics of DNA Duplexes. Consequences for Theoretical Estimation of Charge Transfer Parameters

Anna Sadowska 1Cezary Czaplewski 1Janusz Rak 1Alexander A. Voityuk 2

1. University of Gdańsk, Chemistry, Sobieskiego 18, Gdańsk 80-952, Poland
2. Universitat de Girona (UDG), Campus de Montilivi, Girona 17071, Spain

Abstract

Control over charge transfer in DNA attracts a great attention since it opens a route to the common usage of the biopolymer in nanoelectronics and might be relevant for understanding its oxidative damage and mutations. Today a consensus exists that guanine radical cation (G+) is a key intermediate in a hole transfer mediated by DNA. A hole, initially created on a guanine, hopes through the DNA stack using other guanine bases as resting states. This mechanism may be described as G-hopping, a series of tunneling steps between G sites separated by AT pairs. The rate of the tunneling charge transfer is proportional to the square of the electronic coupling, Vda, between the donor and acceptor sites. Therefore, the Vda matrix element is a major factor which controls the efficiency of charge transfer in DNA.Thermal fluctuations are known to affect considerably the structure and properties of biomolecules. Recently it was recognized that conformational changes in DNA can produce significant variations in π-stacking of base pairs and thereby modulate the efficiency of charge transfer. However, in theoretical studies on hole transfer one usually uses the geometries of a neutral π-stack neglecting thus any structural effects of a positive charge localized on the one of guanines. Thus, in the present study we estimate the effects of a hole on the structure of DNA duplex (including counter-ions and water molecules) and the corresponding consequences of its structural changes on charge transfer parameters.We employ a combination of molecular dynamics and quantum chemical calculations to compare the propensity to hole transfer for the neutral and positively charged Watson-Crick base pair dimers (WCPs) incorporated into the B-DNA π-stack. Namely, we carried out five nanoseconds MD simulations for two B-DNA double-stranded octamers of the 5'-A1A2G3A4A5G6A7A8-3' sequence. These systems differed with the charge localized to the third guanine that was neutral or positively charged. The MD trajectories were analyzed in terms of effects that the positive charge exerts on the DNA dynamics and, in consequence, on electronic coupling. In particular, the analyzed WCP dimer conformational parameters for the neutral and charged species were compared. Moreover these geometrical characteristics were correlated with the variations of electronic coupling along the MD trajectories.Our main finding indicates that in order to predict reliable values of Vda one cannot neglect the effects of electron hole on the DNA structure. It turned out that accounting for these effects may essentially (by a factor of 2) change the magnitude of computed electronic couplings.Acknowledgements. This work was supported by the: Polish Ministry of Education and Science, grants Nos. Dec.127/02/E-335/S2006 (J.R.) and DS-8372-4-0138-5 (C.C.), (ii) Spanish Ministerio de Educación y Ciencia, Project No. CTQ2005-04563 (A.V.).

 

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Presentation: poster at 18th Conference on Physical Organic Chemistry, Posters, by Anna Sadowska
See On-line Journal of 18th Conference on Physical Organic Chemistry

Submitted: 2006-05-27 17:10
Revised:   2009-06-07 00:44