A TDDFT-based study on the proton-DNA collision

Journal Of Physical Chemistry B 121 (30), 7276 - 7283 (2017)

A TDDFT-based study on the proton-DNA collision

R.Seraide,M.A.Bernal,G.Brunetto,U.De Giovannini, A.Rubio

The interaction of heavy charged particles with DNA is of interest for several areas,from hadrontherapy to aero-space industry. In this paper, a TD-DFT study on the interaction of a 4 keV proton with an isolated DNA base pair was carried out. Ehrensfest dynamics was used to study the evolution of the system during and after the proton impact up to about 193 fs. This time was long enough to observe the dissociation of the target, which occurs between 80-100 fs. The effect of base pair linking to the DNA double helix was emulated by fixing the four O3’ atoms responsible for the attachment.The base pair tends to dissociate into its main components, namely the phosphate groups, sugars and nitrogenous bases. A central impact with energy transfer of 17.9 eV only produces base damage while keeping the backbone intact. An impact on a phosphate group with energy transfer of about 60 eV leads to backbone break at that site togehter with base damage, while the opposite backbone site integrity is kept is this situation. As the whole system is perturbed during such a collision, no atom remains passive. These results suggest that base damage accompanies all backbone breaks since hydrogen bonds that keep bases together are much weaker that those between the other components of the DNA.

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http://dx.doi.org/10.1021/acs.jpcb.7b04934
Notes
M.B. thanks the Conselho Nacional para o Desenvolvimento Científico e Tecnológico (CNPq), Brazil, for financing his research activities through the project 306775/2015-8. A.R. and U.D.G. acknowledge financial support from the European Research Council(ERC-2015-AdG-694097), Grupos Consolidados (IT578-13), H2020-NMP-2014 project MOSTOPHOS (GA no. 646259), European Union's H2020 programme under GA no.676580 (NOMAD) and COST Action MP1306 (EUSpec). The images of this work were made with VMD software support. VMD is developed with NIH support by the Theoretical and Computational Biophysics group at the Beckman Institute, University of Illinois at Urbana-Champaign.

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