ABSTRACT
Chromatin remodeling factors are enzymes being able to alter locally chromatin structure at the nucleosomal level and they actively participate in the regulation of gene expression. Using simple rules for individual nucleosome motion induced by a remodeling factor, we designed simulations of the remodeling of oligomeric chromatin, in order to address quantitatively collective effects in DNA accessibility upon nucleosome mobilization. Our results suggest that accessibility profiles are inhomogeneous thanks to borders effects like protein binding. Remarkably, we show that the accessibility lifetime of DNA sequence is roughly doubled in the vicinity of borders as compared to its value in bulk regions far from the borders. These results are quantitatively interpreted as resulting from the confined diffusion of a large nucleosome depleted region.
ABSTRACT
We present in this work in vitro measurements of the force ejecting DNA from two distinct bacteriophages (T5 and lambda using the osmotic-suppression technique. Our data are analyzed by revisiting the current theories of DNA packaging in spherical capsids. In particular we show that a simplified analytical model based on bending considerations only is able to account quantitatively for the experimental findings. Physical and biological consequences are discussed.
Subject(s)
Bacteriophages/genetics , DNA/chemistry , Osmosis , Bacteriophages/metabolism , Capsid/chemistry , Chemistry Techniques, Analytical/methods , Chemistry, Physical/methods , Deoxyribonuclease I/metabolism , Genome, Viral , Models, Statistical , Models, Theoretical , Polymers/chemistry , Pressure , RNA/chemistry , Spectrophotometry, Ultraviolet/methods , Static Electricity , ThermodynamicsABSTRACT
We consider the problem of inserting a stiff chain into a colloidal suspension of particles that interact with it through excluded volume forces. The free energy of insertion is associated with the work of creating a cavity devoid of colloid and sufficiently large to accommodate the chain. The corresponding work per unit length is the force that resists the entry of the chain into the colloidal suspension. In the case of a hard sphere fluid, this work can be calculated straightforwardly within the scaled particle theory; for solutions of flexible polymers, on the other hand, we employ simple scaling arguments. The forces computed in these ways are shown, for nanometer chain and colloid diameters, to be of the order of tens of pN for solution volume fractions of a few tenths. These magnitudes are argued to be important for biophysical processes such as the ejection of DNA from viral capsids into the cell cytoplasm.
