Cisplatin GG-crosslinks within single-stranded DNA: Origin of the preference for left-handed helicity

Abstract

Molecular dynamics (MD) simulations of the single-stranded DNA trinucleotide TG*G*, with the G* guanines crosslinked by the antitumor drug cisplatin, were performed with explicit representation of the water as solvent. The purpose of the simulations was to explain previous NMR observations indicating that in single-stranded cisplatin-DNA adducts, the crosslinked guanines adopt a left-handed helical orientation, whereas in duplexes, the orientation is right-handed. The analysis of the MD trajectory of TG*G* has ascribed a crucial role to hydrogen-bonding (direct or through-water) interactions of the 5′-oriented NH3 ligand of platinum with acceptor groups at the 5′-side of the crosslink, namely the TpG* phosphate and the terminal 5′-OH group. These interactions bring about some strain into the trinucleotide which is slightly but significantly (1–1.5kcal.mol−1) higher for the right-handed orientation than for the left-handed one. During the unconstrained, 3ns long MD simulation, left-handed conformations were ~15 times more abundant than the right-handed ones. This sampling difference agrees roughly with the calculated energy difference in strain energy. Overall, these results show that the Pt-GG crosslink within single-stranded DNA is malleable and can access different conformations at a moderate energy cost. This malleability could be of importance in interactions between the platinated DNA and cellular proteins, in which the DNA is locally unwound.