Molecular dynamics simulations for the detection of unfolding pathways and stable conformations of DNA G-quadruplexes (C08*)

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We study the unfolding pathways and stable conformations of DNA G-quadruplexes via atomistic molecular dynamics simulations. G-quadruplexes are a specific class of non-Watson-Crick-like DNA structures which consist of repetitive sequences of guanine. It is planned to force the unfolding of these structures in terms of biased Metadynamics simulations which also allows us to study stable conformations with regard to the calculated free energy landscapes. Further analysis includes the usage of umbrella integration which will give detailed insights into the unfolding mechanism. In addition, the influence of osmolytes on the stability of the structures will be investigated.