Mesoscopic Model for Free Energy Landscape Analysis of DNA sequences
arXiv:1208.3950 · doi:10.1103/PhysRevE.86.021908
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.
7 pages, 5 figures, 1 table
References in corpus (7)
- Maps of random walks on complex networks reveal community structure
- Entropy Rate of Diffusion Processes on Complex Networks
- Exploring the Free Energy Landscape: From Dynamics to Networks and Back
- Spatial effects on the speed and reliability of protein-DNA search
- Structurally specific thermal fluctuations identify functional sites for DNA transcription
- Importance of Metastable States in the Free Energy Landscapes of Polypeptide Chains
- Thermal and mechanical properties of a DNA model with solvation barrier