Journal:JBSD:17

DNA Conformation and Energy in Nucleosome Core: A Theoretical Approach

Davood Norouzi and Farshid Mohammad-Rafiee ^[1]

Molecular Tour
DNA in eukaryotes is packaged into nucleosomes by wrapping around positively charged histone proteins. Each histone octamer is associated with 147 base pairs (bps) of DNA, in which the DNA is wrapped in about 1.65 turns around the core particle of histone proteins. The complex of DNA and histone proteins is ubiquitous in eukaryotic nuclei and has a major role in many essential life processes. Recent experiments revealed a lot of information about the structure and positioning of nucleosomes along the genome.

DNA conformation in complex with proteins is far from its canonical B-form. The affinity of complex formation and structure of DNA depend on its attachment configuration and sequence. In this article, we develop a mechanical model to address the problem of DNA structure and energy under deformation. The structure and energy of nucleosomal DNA is calculated based on its sequence and positioning state. The inferred structure has remarkable similarity with X-ray data. Although there is no sequence-specific interaction of bases and the histone core, we found considerable sequence dependency for the nucleosomal DNA positioning. We argue that structural energy determines the natural state of nucleosomal DNA and is the main reason for affinity differences in vitro. This theory can be utilized for the DNA structure and energy determination in protein-DNA complexes in general.