Binding of molecules to DNA and other semiflexible polymers

Abstract

A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers (e.g., DNA) represent an intermediate case between flexible polymers and stiff, rod-like ones, whose association with small molecules was previously studied. The chains are not flexible enough to actively participate in the self-assembly, yet their fluctuations induce long-range attractive interactions between bound molecules. In cases where the binding significantly affects the local chain stiffness, those interactions lead to a very sharp, cooperative association. This scenario is of relevance to the association of DNA with surfactants and compact proteins such as RecA. External tension exerted on the chain is found to significantly modify the binding by suppressing the fluctuation-induced interaction.61.25.Hq,87.15.Nn,87.14.Gg

Similarities between polyelectrolyte gels and biopolymer solutions

“…It is known that stiff polymer chains in solutions can undergo a sharp collapse from a spatially extended conformation to a compact one. 37 For example, enhanced rigidity of double-stranded DNA compared to the single strand leads to sharp, controllable conformational transitions. Of course, other factors besides chain rigidity (e.g., electrostatic interactions, charge density, ion binding, solvent quality) also contribute to the osmotic modulus, and these Figure 5.…”

An exact theory of histone-DNA adsorption and wrapping

“…One-dimensional theories in statistical mechanics have been successfully applied to numerous biophysical systems, including DNA denaturation [1], particle transport across biological channels [2,3], adsorption on 1D substrates [4,5], and transport [6] along microtubules. In this Letter, we study protein-DNA binding and wrapping by solving a new 1D theory of interacting particles with dynamically varying particle sizes.…”

Elastically Driven Linker Aggregation between Two Semiflexible Polyelectrolytes

“…In this paper, we will study the intermediate case of semi-flexible chains, appropriate to biologically important polymers such as DNA. It has been shown theoretically that counterion correlations can modify the bending rigidity of a single semi-flexible chain [10][11][12] and can even render the chain unstable to collapse [11]. Here, we consider two semiflexible chains from a different point of view: instead of studying how counterions modify the effective interactions between monomers on chains, we examine how chain flexibility modifies the effective interaction between generalized linkers, which could be simple polyvalent counterions [6] or weakly-binding (crosslinking or bundling) proteins [4].…”

“…The chain persistence length l p characterizes the decay of correlations in the chain orientation. Any dependence of bending rigidity on the composition of the surrounding solution [10][11][12]21] is implicit in l p . The total free energy per linker f (l; h) = E el + E bend can be calculated numerically and minimized with respect to h [22].…”