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 di erence equation algorithm This is the rst application of the method which approximates long time pathways to a nucleic acid system The free energy pro le is determined as a function of the pseudorotation phase angle from the data set of trajectories connecting the two dA conformations Analyses indicate that the south sugar pucker is favored over the north by 0.34 +(-) 0.2 kcal/mol and that the free energy barrier is about 2.2 +(-) 0.2 kcal/mol above the global minimum The transition occurs through the east pseudorotation energy barrier with signi cant decrease in the puckering amplitude of the furanose ring near the barrier region These results are consistent with prior studies on sugars in nucleic acids and indicate that the stochastic path approach has potential for large nucleic acid and nucleic acid protein systems.

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