Berlin 2015 – scientific programme

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BP: Fachverband Biologische Physik

BP 25: Posters: DNA/RNA and related enzymes

BP 25.9: Poster

Tuesday, March 17, 2015, 14:00–16:00, Poster A

Effects of Collectivity in Homology Recognition: a density functional theory based approach. — •Sergio Cruz¹, Claudia Danilowicz², Chantal Prevost³, Mara Prentiss², and Maria Fyta¹ — ¹Institute for Computational Physics, University of Stuttgart, Germany — ²Physics Department, Harvard University, Cambride, MA, USA — ³LBT - CNRS and Univ Paris Diderot, Sorbonne Paris Cite, Paris, France

RecA is a family of proteins for performing homology recognition while trying to repair DNA. The atomistic mechanism by which this process occurs is not still fully understood. Crystallographic evidence shows that RecA separates a strand in sequences of three bases (triplet), and then searches for the homologous partner. However, 'recognition in duplets' is suggested as a possible mechanism by recent experiments. In our current investigation, the importance of collectivity in recognition is explored by means of quantum mechanical calculations at the level of dispersion corrected density functional theory. We compare the average binding energy for singlets, duplets, and triplets for canonical Watson-Crick and mismatched base pairs. There is a clear distinction between recognition in singlets, and recognition in duplets or triplets. We calculate the energy for duplets and triplets containing mismatches and compare this with the energetics of the respective singlets. Analysis on the energy difference will shed light to a better understanding of this homology recognition process.