Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations

From: Biophysical Journal | Date: August 1, 2003| Author: Nakatani, Bradley J; Pande, Vijay S; Rhee, Young Min; Sorin, Eric J | Copyright information

ABSTRACT The helical hairpin is one of the most ubiquitous and elementary secondary structural motifs in nucleic acids, capable of serving functional roles and participating in long-range tertiary contacts. Yet the self-assembly of these structures has not been well-characterized at the atomic level. With this in mind, the dynamics of nucleic acid hairpin formation and disruption have been studied using a novel computational tool: large-scale, parallel, atomistic molecular dynamics simulation...

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