Binding of molecules to DNA and other semiflexible polymers

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.Comment: 15 pages, 7 figures, RevTex, the published versio

Charge transport in poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers

We investigate the charge transport in synthetic DNA polymers built up from single types of base pairs. In the context of a polaron-like model, for which an electronic tight-binding system and bond vibrations of the double helix are coupled, we present estimates for the electron-vibration coupling strengths utilizing a quantum-chemical procedure. Subsequent studies concerning the mobility of polaron solutions, representing the state of a localized charge in unison with its associated helix deformation, show that the system for poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers, respectively possess quantitatively distinct transport properties. While the former supports unidirectionally moving electron breathers attributed to highly efficient long-range conductivity the breather mobility in the latter case is comparatively restrained inhibiting charge transport. Our results are in agreement with recent experimental results demonstrating that poly(dG)-poly(dC) DNA molecules acts as a semiconducting nanowire and exhibits better conductance than poly(dA)-poly(dT) ones.Comment: 11 pages, 5 figure

Molecular recognition by van der Waals interaction between polymers with sequence-specific polarizabilities

We analyze van der Waals interactions between two rigid polymers with sequence-specific, anisotropic polarizabilities along the polymer backbones, so that the dipole moments fluctuate parallel to the polymer backbones. Assuming that each polymer has a quenched-in polarizability sequence which reflects, for example, the polynucleotide sequence of a double-stranded DNA molecule, we study the van der Waals interaction energy between a pair of such polymers with rod-like structure for the cases where their respective polarizability sequences are (i) distinct and (ii) identical, with both zero and non-zero correlation length of the polarizability correlator along the polymer backbones in the latter case. For identical polymers, we find a novel $r^{-5}$ scaling behavior of the van der Waals interaction energy for small inter-polymer separation $r$, in contradistinction to the $r^{-4}$ scaling behavior of distinct polymers, with furthermore a pronounced angular dependence favoring attraction between sufficiently aligned identical polymers. Such behavior can assist the molecular recognition between polymers.Comment: 16 pages, 5 figure

Pulling Pinned Polymers and Unzipping DNA

We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random DNA sequences with short-ranged correlations, we obtain exact results for the number of monomers liberated and the specific heat, including the critical behavior at the transition. Related systems include a random heteropolymer pulled away from an adsorbing surface and a vortex line in a type II superconductor tilted away from a fragmented columnar defect.Comment: 4 pages, 1 EPS figure; revised references and very brief discussion of order of the transition added; to appear in Phys. Rev. Let

From the double-stranded helix to the chiral nematic phase of B-DNA: a molecular model

B-DNA solutions of suitable concentration form left-handed chiral nematic phases (cholesterics). Such phases have also been observed in solutions of other stiff or semiflexible chiral polymers; magnitude and handedness of the cholesteric pitch are uniquely related to the molecular features. In this work we present a theoretical method and a numerical procedure which, starting from the structure of polyelectrolytes, lead to the prediction of the cholesteric pitch. Molecular expressions for the free energy of the system are obtained on the basis of steric and electrostatic interactions between polymers; the former are described in terms of excluded volume, while a mean field approximation is used for the latter. Calculations have been performed for 130 bp fragments of B-DNA. The theoretical predictions provide an explanation for the experimental behavior, by showing the counteracting role played by shape and charge chirality of the molecule.Comment: 42 pages, 6 figure

Radial distribution function of semiflexible polymers

We calculate the distribution function of the end--to--end distance of a semiflexible polymer with large bending rigidity. This quantity is directly observable in experiments on single semiflexible polymers (e.g., DNA, actin) and relevant to their interpretation. It is also an important starting point for analyzing the behavior of more complex systems such as networks and solutions of semiflexible polymers. To estimate the validity of the obtained analytical expressions, we also determine the distribution function numerically using Monte Carlo simulation and find good quantitative agreement.Comment: RevTeX, 4 pages, 1 figure. Also available at http://www.cip.physik.tu-muenchen.de/tumphy/d/T34/Mitarbeiter/frey.htm

Colloids dragged through a polymer solution: experiment, theory and simulation

We present micro-rheological measurments of the drag force on colloids pulled through a solution of lambda-DNA (used here as a monodisperse model polymer) with an optical tweezer. The experiments show a violation of the Stokes-Einstein relation based on the independently measured viscosity of the DNA solution: the drag force is larger than expected. We attribute this to the accumulation of DNA infront of the colloid and the reduced DNA density behind the colloid. This hypothesis is corroborated by a simple drift-diffusion model for the DNA molecules, which reproduces the experimental data surprisingly well, as well as by corresponding Brownian dynamics simulations.Comment: 9 pages, 13 figures, 3 table