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BP: Fachverband Biologische Physik

BP 15: DNA/RNA and related enzymes

BP 15.3: Vortrag

Dienstag, 12. März 2013, 12:45–13:00, H43

A realistic potential for DNA-related biophysical processes — •Maria Fyta^1,2, Chia Wei Hsu², Greg Lakatos², Simone Melchionna^3,4, and Efthimios Kaxiras^2,4 — ¹Institut für Computerphysik, Universität Stuttgart, Germany — ²Department of Physics, Harvard University, Cambridge MA 02138, U.S.A — ³IPCF-CNR, Università La Sapienza, P.le A. Moro 2, 00185 Rome, Italy — ⁴School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, U.S.A.

Ab initio total-energy calculations based on density functional theory (DFT) are used to derive the coarse-grained interactions between DNA nucleotides. The interactions take into account base and sequence specificity, and are decomposed into physically distinct contributions that include hydrogen bonding, stacking interactions, backbone, and backbone-base interactions. The interaction energies of each contribution are calculated from DFT for a wide range of configurations. These interactions are then fitted by simple analytical expressions and can be used in a coarse-grained model for double-stranded DNA. Within this model each nucleotide is reduced into two sites, the base site and the sugar-phosphate site. Although this model is not derived from experimental data, it successfully reproduces the stable B-DNA structure and gives good predictions for the persistence length. It has already been used to model stretching experiments of B-DNA, as well as bubble formation within a thermalized DNA molecule. The potential may be used to realistically probe dynamics of DNA strands in various environments at the µs time scale and the µm length scale.