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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