The role of (5′R) and (5′S) 5′,8-cyclo-2′-deoxyadenosine in ds-DNA structure: A comparative QM/MM theoretical study

Reactions of a hydroxyl radical with nucleotides may lead to DNA damage formation. In this study the emphasis was placed on the double helix structure deformation, forced by 5′R and 5′S diastereomers of 5′,8-cyclo-2′-deoxyadenosine (cdA). It should be pointed out that (5′R)cdA and (5′S)cdA are formed in cells with different frequencies. Moreover both diastereomers showed different biological/biochemical behaviours. The results of theoretical QM/MM studies, presented in this article, show the slight influence of (5′S)cdA on the spatial geometry of ds-DNA opposite to (5′R)cdA. The structure of the double helix containing (5′R)cdA adopted the three dimensional shape similar to the 3D structure of ds-DNA containing cisplatin. Probably due to this fact, (5′R)cdA was found as a better substrate for NER system than (5′S)cdA. w3DNA analyses revealed that the 5′R diastereomer left the ds-DNA in natural B form instead of 5′S, which disrupted the internal parameters of the double helix in both directions. Probably, due to this, (5′R)cdA was not found as an inhibitor of polymerase-η activity opposite to (5′S)cdA, which was recognised as a stop point of the DNA elongation process. Therefore, the presented results are in good agreement with previous experimental data. Additionally, the strength of individual hydrogen bonds formed by 5′R and 5′S 5′,8-cyclo-2′-deoxyadenosines in ds-DNA structures, vertical electron affinity and vertical ionisation potential as well as stacking interaction were taken into consideration.