CONFORMATION AND DYNAMICS OF ETHYLATED DNA

N-nitroso compounds are known to modify normal DNA bases chemically an d 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 mo lecular dynamics simulations which are commonly applied to the study o f normal oligonucleotide sequences. As part of this study, we have ext ended the AMBER force field to allow for the modified base O-6-ethylgu anine (O-6-EtG) in the self-complementary d(CGCGAGCTCGCG) duplex. Our results show that the AMBER force field produces stable oligonucleoti de double helices over 2400 ps. The modified sequence with ethylguanin e: cytosine base pairs leads to local disruption of the base pair beca use of the chemical modification of the guanine base but all other bas e pairs retain their normal conformation. The modified base pair has o nly two hydrogen bonds and adopts the so-called wobble conformation. I n 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 i ts original length. This change in conformation, together with other t hermodynamic and energetic properties, indicates that c,t-EtG is less stable than t,t-EtG when paired with cytosine. The resulting structura l changes are therefore factors that could be used in the recognition process prior to the repair.