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Base flipping in DNA using potential energy landscapes

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First Year PhD Report

Energy landscape theory is a fundamental framework that is used to explore the structure, thermodynamics and kinetics associated with a chemical process. Here, we have explored the process of base flipping in a deoxyribonucleic acid (DNA) duplex with the sequence 5’-GAGAGAGAGAGA-3’ from the energy landscape perspective. Experimentally, NMR imino-proton exchange and fluorescence correlation studies have been used to obtain lifetimes of bases in paired and extra helical states. However, the difference of almost four orders of magnitude in lifetimes obtained by the two methods implies that they are exploring different pathways, and possibly different open states. In our work, flipping pathways for four central bases: adenine, guanine, cytosine, and thymine were investigated in a DNA duplex modelled using the AMBER force field with an implicit solvent model. The pathway between closed and open states is visualised using disconnectivity graphs. Our results support the previous suggestion that minor groove opening may be favoured by bending, and reveal links between sequence effects and the direction of opening, i.e., whether the base flips towards the major or the minor groove side. The calculated rate constants are compared with previous experimental and computational studies, and a rationale for differences is provided in terms of mechanism, sequence effects, and the experimental or computational framework in question.

This talk is part of the Theory - Chemistry Research Interest Group series.

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