Evaluation of DNA intramolecular interactions for nucleosome positioning in yeast.

Abstract

We calculated intramolecular interaction energies of DNA by threading DNA sequences around crystal structures of nucleosomes. The strength of the intramolecular energy oscillations at frequency approximately 10 bps for dinucleotides was in agreement with previous nucleosome models. The intramolecular energy calculated along yeast genome positively correlated with nucleosome positioning experimentally measured.