Mesoscopic Model for Free Energy Landscape Analysis of DNA sequences

Abstract

A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores the sequence interacting more importantly with open base pairs of the DNA chain. We apply the model to promoter sequences of different organisms. The free energy landscape obtained for these promoters shows a complex structure that is strongly connected to their biological behavior. The analysis method used is able to quantify free energy differences of sites within genome sequences.

arXiv comment7 pages, 5 figures, 1 table

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Cited by in corpus (5)

• Heterogeneity and chaos in the Peyrard-Bishop-Dauxois DNA model
• Distributions of Bubble Lifetimes and Bubble Lengths in DNA
• Bubble lifetimes in DNA gene promoters and their mutations affecting transcription
• Base pair fluctuations in helical models for nucleic acids
• Thermal activation at moderate-to-high and high damping: finite barrier effects and force spectroscopy