The role of (5′R) and (5′S) 5′,8-cyclo-2′-deoxyadenosine in ds-DNA structure

► QM/MM study of short ds-DNA containing (5′R)cdA::T, (5′R)cdA::T, dA::T. ► Stacking interaction was investigated for d[GXG]*[CTC] X: dA, (5′R)cdA, (5′S)cdA. ► HBs energies (kcal) were found: dA::T-18.8, (5′R)cdA::T-18.3, (5′S)cdA::T-14.3. ► (5′R)cdA changed the shape of double helix DNA much more visible than (5′S)cdA. ► (5′S)cdA demonstrated a higher influence on ds-DNA parameters.