Electrostatic interactions with histone tails may bend linker DNA in chromatin

Abstract

Is linker DNA bent in the 30-nm chromatin fiber at physiological conditions? We show here that electrostatic interactions between linker DNA and histone tails including salt condensation and release may bend linker DNA, thus affecting the higher order organization of chromatin.

Generalized electrostatic model of the wrapping of DNA around oppositely charged proteins

“…Following model 1 of our recent approach to DNA-protein interactions applied to linker DNA N-terminal histone H3 tail and DNA-octamer interactions in nucleosome 10 (paper I hereafter), let us model DNA as a negatively charged elastic cylinder of radius a (for DNA a ¼ 1 nm) and the protein as a positively charged sphere of radius R 0 and charge Z 0 . Describing a charged globular protein or protein complex as an uniformly charged sphere, physically defined by its radius and global charge is a drastic simplification suggested by the special electrostatic interaction of DNA, a highly charged cylindrical polyelectrolyte, with a highly charged countermacroion in concurrence with small counterions, in view of the particularly important role played by the condensation/release mechanism.…”

“…The first term F s (L À l) is calculated following directly the Manning procedure to derive the free energy of a straight DNA in condensation theory 10,12,18,19 : since the total charge of the straight DNA of length L À l is simply (L À l)/b, we have:…”

“…It is noteworthy that the approximations involved in these models require a salt concentration near physiological conditions. 2,10,12 The binding free energy of this DNA-sphere model is calculated as the difference of the free energy of the model with a length l of DNA wrapped on the sphere, to that of isolated straight DNA and sphere:…”

“…Here, we generalize an electrostatic model, recently proposed by us, 10 to describe the electrostatic interactions mediated by salt between DNA, strongly negatively charged, and oppositely charged spherical proteins or protein complexes, ultimately responsible of the wrapping of DNA around the surface of the protein. After improving several aspects of the electrostatic interactions mediated by salt, the model is used to explain the wrapping of DNA around the octamer in nucleosome, the action of chromatin remodeling factor CSB, and the condensation of chromosomes in archaea by the histonelike protein MC1.…”

Preparation and characterization of DNA aptamer based spin column for enrichment and separation of histones

“…It is generally accepted that DNA wraps with histones mainly through electrostatic interactions between the negatively charged phosphate groups of the DNA backbone and positively charged amino acids of the histone proteins in eukaryotic chromatin. 20,21 As shown in Fig. 1, almost all the histones can be captured by the aptamer-modified column in the loading process, which might be primarily due to the electrostatic interactions.…”