TCBG Seminar

Coarse Grained DNA Models and how they can be used to Predict DNA Function

Professor Zoi Rapti
Department of Mathematics
University of Illinois at Urbana-Champaign
Urbana, Illinois

Monday, April 19, 2010
3:00 pm (CT)
3269 Beckman Institute


We will present two DNA models that have been used to predict DNA function such as the location of transcription start sites and core promoter elements. Instrumental in our analysis is the study of bubble formation, that is, the study of temporary and localized openings along the double strand. Both models take into account only the major contributions to DNA stability, such as base-stacking and hydrogen bonding. One of the models is discrete, in the sense that the hydrogen bond can be in one of two states (open and closed), while in the other, the displacement of the complementary bases from equilibrium is described by a continuous variable. We will review old results based on a statistical mechanics formulation of the problem, and we will finish with findings based on a continuous model that considers stacking interactions with base pairs several bases away.

2:30 pm: Coffee hour Theoretical and Computational Biophysics Group area, 3rd Floor Beckman

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