Predicting the configuration and energy of DNA in a nucleosome by coarse-grain modelling
Rasa Giniūnaitė, Daiva Petkevičiūtė-Gerlach
Abstract
model, which is a coarse-grained model of DNA bases and phosphates, to compute the free energy of a given DNA configuration for a given sequence. Minimising the free energy subject to the aforementioned structural constraints results in a preferred configuration for a given DNA sequence on a nucleosome. The energetic cost of forming a nucleosome with a particular DNA sequence can then be computed. We use this framework to compare the energetic costs with the persistence length of the same DNA sequence to verify whether less rigid (lower persistence length) sequences require less energy to wrap into nucleosomes.
Topics & Concepts
NucleosomeDNAEnergy (signal processing)Statistical physicsComputational biologyBiological systemChemical physicsBiologyMaterials scienceBiophysicsPhysicsHistoneGeneticsQuantum mechanicsGenomics and Chromatin DynamicsRNA and protein synthesis mechanismsBacteriophages and microbial interactions