Berlin 2005 – scientific programme

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AKB: Biologische Physik

AKB 100: Poster Session I

AKB 100.70: Poster

Saturday, March 5, 2005, 16:45–18:45, Poster TU D

Stacking interactions in a lattice model of DNA/RNA — •Christian Simm¹, Sanjay Kumar², and Ralf Everaers¹ — ¹Max-Planck-Institut für Physik komplexer Systeme, Nöthnitzer Straße 38, 01187 Dresden — ²Department of Physics, Banaras Hindu University, Varanasi 221 005, India

The binding strength of DNA/RNA strands is of crucial importance for many biological processes. Examples are the formation of DNA bubbles during transcription, RNA secondary stucture or hairpin formation in ssDNA and miRNA. Current lattice models of DNA only include of the effects of hydrogen bonding between complementary bases. We introduce an extension which accounts for base stacking interaction and the polarity of the DNA strand. We use Monte-Carlo simulations of the model to present results which show the effects of this extension and compare it to the simpler model.