Conformation and dynamics of ethylated DNA

Abstract

N-nitroso compounds are known to modify normal DNA bases chemically and result in mutations which are either corrected by repair proteins or lead to misreading of the code and possibly carcinogenesis. In order to model the conformation of these modified sequences, we have used molecular dynamics simulations which are commonly applied to the study of normal oligonucleotide sequences. As part of this study, we have extended the AMBER force field to allow for the modified base O⁶-ethylguanine (O⁶-EtG) in the self-complementary d(CGCG*AGCTCGCG) duplex. Our results show that the AMBER force field produces stable oligonucleotide double helices over 2400 ps. The modified sequence with ethylguanine: cytosine base pairs leads to local disruption of the base pair because of the chemical modification of the guanine base but all other base pairs retain their normal conformation. The modified base pair has only two hydrogen bonds and adopts the so-called wobble conformation. In principle, there are two likely alkyl group conformations which can exist in the duplex, namely the trans,trans-ethylguanine (t,t-EtG) and the cis,trans-ethylguanine (c,t-EtG). The t,t-EtG sequence has a very similar equilibrium structure to the normal sequence whereas the c,t-EtG helix unwinds resulting in a helix which is one and a half times its original length. This change in conformation, together with other thermodynamic and energetic properties, indicates that c,t-EtG is less stable than t,t-EtG when paired with cytosine. The resulting structural changes are therefore factors that could be used in the recognition process prior to the repair.