Fluctuation-facilitated charge migration along DNA

We propose a model Hamiltonian for charge transfer along the DNA double helix with temperature-driven fluctuations in the base pair positions acting as the rate limiting factor for charge transfer between neighboring base pairs. We compare the predictions of the model with the recent work of Barton and Zewail on the unusual two-stage charge transfer of DNA.

RecA force generation by hydrolysis waves

We present a simple theory of the dynamics of force generation by RecA during homologous strand exchange and a continuous, deterministic mathematical model of the proposed process. Calculations show that force generation is possible in this model for certain reasonable values of the parameters. We predict the shape of the force-velocity curve for the Holliday junction, which exhibits a distinctive kink at large retarding force, and suggest experiments which should distinguish between the proposed model and other models in the literature.

Adhesive switching of membranes: experiment and theory

We report on a study of a model bioadhesion system: giant vesicles in contact with a supported lipid bilayer. Embedded in both membranes are very low concentrations of homophilic recognition molecules (contact site A receptors) competing with higher concentrations of repeller molecules: polyethylene glycol (PEG) lipids. These repellers mimic the inhibiting effect of the cell glycocalyx on adhesion. The effective adhesive interaction between the two membranes is probed by interferometric analysis of thermal fluctuations. We find two competing states of adhesion: initial weak adhesion is followed by slower aggregation of the adhesion molecules into small, tightly bound clusters that coexist with the regions of weak adhesion. We interpret our results in terms of a double-well intermembrane potential, and we present a theoretical analysis of the intermembrane interaction in the presence of mobile repeller molecules at a fixed chemical potential that shows that the interaction potential indeed should have just such a double-well shape. At a fixed repeller concentration we recover a conventional purely repulsive potential. We discuss the implications of our findings in terms of a general amplification mechanism of the action of sparse adhesion molecules by a nonspecific double-well potential. We also discuss the important role of the Helfrich undulation force for the proposed scenario.

DNA-protein cooperative binding through variable-range elastic coupling

Cooperativity plays an important role in the action of proteins bound to DNA. A simple mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations, is proposed. These proteins are not in direct physical contact. DNA segments intercalating bound proteins are modeled as a worm-like chain, which is free to deform in two dimensions. The tension-controlled protein-protein interaction is the consequence of two effects produced by the protein binding. The first is the introduction of a bend in the host DNA and the second is the modification of the bending modulus of the DNA in the immediate vicinity of the bound protein. The interaction between two bound proteins may be either attractive or repulsive, depending on their relative orientation on the DNA. Applied tension controls both the strength and the range of protein-protein interactions in this model. Properties of the cooperative interaction are discussed, along with experimental implications.

Motion of RNA polymerase along DNA: a stochastic model

RNA polymerase is a key transcription enzyme that moves along a DNA double helix to polymerize an RNA transcript. Recent progress in micromechanical experiments permits quantitative studies of forces and motion generated by the enzyme. We present in this paper a chemical kinetics description of RNA polymerase motion. The model is based on a classical chemical kinetics description of polymerization reactions driven by a free energy gain that depends on forces applied externally at the catalytic site. The RNA polymerase controlled activation barrier of the reaction is assumed to be strongly dependent on inhibitory internal strains of the RNA polymerase molecule. The sequence sensitivity of RNA polymerase is described by a linear coupling between the height of the activation barrier and the local DNA sequence. Our model can simulate optical trap experiments and allows us to study the dynamics of chemically halted complexes that are important for footprinting studies. We find that the effective stall force is a sequence-dependent, statistical quantity, whose distribution depends on the observation time. The results are consistent with the experimental observations to date.

Elasticity theory of the B-DNA to S-DNA transition

We propose in this note a simple model--the two-state Worm Like Chain--to describe the elasticity of the recently discovered stress-induced transformation from B-DNA to S-DNA. The model reduces for low tractions to the well-known Worm Like chain theory, which is used to describe the elastic properties of B-DNA, while in the limit of high chain-bending moduli it reduces to the two-state Ising model proposed by Cluzel et al. for the B-S transition [Cluzel, P., A. Lebrun, C. Heller, R. Lavery, J-L. Viovy, D. Chatenay, and F. Caron. 1996. DNA: an extensible molecule. Science. 271:792-794]. Our model can be treated analytically to produce an explicit form of the force-extension relationship which agrees reasonably with the observations. We use the model to show that conformational fluctuations of the chain play a role also for the B to S transformation.

Self-assembly of membrane junctions

We present a mechanism for the aggregation of mobile intermembrane junctions, such as the connexon dyad of gap junctions. The model demonstrates that intermembrane repulsion provides a powerful self-assembly pressure. If the membrane repulsion is strong enough to prevent membrane adhesion, then the self-assembly pressure is of effective infinite range.