Deoxyadenosine sugar puckering pathway simulated by the stochastic difference equation algorithm

The conformational transition pathway of sugar puckering between the C2′-endo and C3′-endo conformations of deoxyadenosine (dA) is reported using the stochastic difference equation (SDE) algorithm, which approximates long-time pathways. The south pucker is favored over the north by 0.34 ± 0.2 kcal/mol, and the free energy barrier is about 2.2 ± 0.2 kcal/mol above the global minimum. The transition occurs through the east barrier, with significant decrease in puckering amplitude near the barrier. These results are consistent with prior studies on sugars in nucleic acids and indicate that the SDE has potential for large nucleic acid and nucleic acid/protein systems.