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A QM/MM Study of Cisplatin–DNA Oligonucleotides: From Simple Models to Realistic Systems
Author(s) -
Robertazzi Arturo,
Platts James A.
Publication year - 2006
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.200501566
Subject(s) - stacking , guanine , chemistry , dna , oligonucleotide , molecule , crystallography , thymine , bifunctional , computational chemistry , hydrogen bond , binding energy , intermolecular force , stereochemistry , nucleotide , physics , atomic physics , biochemistry , organic chemistry , gene , catalysis
QM/MM calculations were employed to investigate the role of hydrogen bonding and π stacking in several single‐ and double‐stranded cisplatin–DNA structures. Computed geometrical parameters reproduce experimental structures of cisplatin and its complex with guanine–phosphate–guanine. Following QM/MM optimisation, single‐point DFT calculations allowed estimation of intermolecular forces through atoms in molecules (AIM) analysis. Binding energies of platinated single‐strand DNA qualitatively agree with myriad experimental and theoretical studies showing that complexes of guanine are stronger than those of adenine. The topology of all studied complexes confirms that platination strongly affects the stability of both single‐ and double‐stranded DNAs: PtNH⋅⋅⋅X (X = N or O) interactions are ubiquitous in these complexes and account for over 70 % of all H‐bonding interactions. The π stacking is greatly reduced by both mono‐ and bifunctional complexation: the former causes a loss of about 3–4 kcal mol −1 , whereas the latter leads to more drastic disruption. The effect of platination on Watson–Crick GC is similar to that found in previous studies: major redistribution of energy occurs, but the overall stability is barely affected. The BH&H/AMBER/AIM approach was also used to study platination of a double‐stranded DNA octamer d(CCTG*G*TCC)⋅d(GGACCAGG), for which an experimental structure is available. Comparison between theory and experiment is satisfactory, and also reproduces previous DFT‐based studies of analogous structures. The effect of platination is similar to that seen in model systems, although the effect on GC pairing was more pronounced. These calculations also reveal weaker, secondary interactions of the form Pt⋅⋅⋅O and Pt⋅⋅⋅N, detected in several single‐ and double‐stranded DNA.