CRC TRR 61 C02 - Understanding the properties of tetrameric structures via computer simulations

Basic data for this project

Type of project: Subproject in DFG-joint project hosted at University of Münster
Duration: 06/06/2008 - 31/05/2012 | 1st Funding period

Description

The folding of specific DNA sequences into tetrameric structures rather than the standard Watson-Crick double helix gives rise to many interesting applications. In the planned Transregio this is exploited by D.Liu (C3) to construct a proton driven DNA motor based on the i-motif structure and by S. Wang (C5) for bio-recognition based on the G-quadruplex structure. The goal of the present project is to obtain deeper insight into the nature of tetrameric structures as well as their unfolding/folding properties via computer simulations. So far, a microscopic understanding of the unfolding/folding properties is still lacking. This endeavour requires the use of extensive molecular dynamics simulations as well as specific techniques to efficiently explore the DNA configuration space. In collaboration with D. Liu and S. Wang these results may be used to explain some of their observations in previous or planned work such as the dependence of the folding rate on the presence of electric fields for the i-motif structure.

Keywords: tetrameric structures; computer simulation; unfolding/folding properties; molecular dynamics simulations; DNA configuration space; DNA