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Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple biophysical model where interphase chromosomes are described in terms of the folding of chromatin sequences composed of alternating blocks of fibers with different thicknesses and flexibilities, and we use it to study the influence of sequence disorder on chromosome behaviors in space and time. By employing extensive computer simulations,we thus demonstrate that chromosomes undergo noticeable conformational changes only on length-scales smaller than $10^5$ basepairs and time-scales shorter than a few seconds, and we suggest there might exist effective upper bounds to the detection of chromosome reorganization in eukaryotes. We prove the relevance of our framework by modeling recent experimental FISH data on murine chromosomes., Comment: accepted for publication in PLOS Computational Biology

A class of nucleosome remodeling motors translocate nucleosomes, to which they are attached, toward the middle of DNA chain in the presence of ATP during in vitro experiments. Such a biological activity is likely based on a physical mechanism for detecting and comparing the lengths of the flanking polymer chains. Here we propose that a pivoting mode of DNA fluctuation near the surface of the nucleosome coupled with binding reaction with a DNA binding site of the motor provides a physical basis for length detection. Since the mean frequency of fluctuation is higher for a shorter chain than a longer one due to its lower drag coefficient, a shorter chain has a higher rate of receptor binding, which triggers the ATP-dependent activity of the remodeling motor. Dimerization of such units allows the motor to compare the length of the flanking DNA chains, enabling the translocation of the nucleosome toward the center of the DNA.

DNA unzipping, the separation of its double helix into single strands, is crucial in modulating a host of genetic processes. Although the large-scale separation of double-stranded DNA has been studied with a variety of theoretical and experimental techniques, the minute details of the very first steps of unzipping are still unclear. Here, we use atomistic molecular dynamics (MD) simulations, coarse-grained simulations and a statistical-mechanical model to study the initiation of DNA unzipping by an external force. The calculation of the potential of mean force profiles for the initial separation of the first few terminal base pairs in a DNA oligomer reveal that forces ranging between 130 and 230 pN are needed to disrupt the first base pair, values of an order of magnitude larger than those needed to disrupt base pairs in partially unzipped DNA. The force peak has an "echo," of approximately 50 pN, at the distance that unzips the second base pair. We show that the high peak needed to initiate unzipping derives from a free energy basin that is distinct from the basins of subsequent base pairs because of entropic contributions and we highlight the microscopic origin of the peak. Our results suggest a new window of exploration for single molecule experiments., Comment: 25 pages, 6 figures , Accepted for publication in Biophysical Journal

In this paper, we show that the coarse grain model for DNA, which has been proposed recently by Knotts, Rathore, Schwartz and de Pablo (J. Chem. Phys. 126, 084901 (2007)), can be adapted to describe the thermal and mechanical denaturation of long DNA sequences by adjusting slightly the base pairing contribution. The adjusted model leads to (i) critical temperatures for long homogeneous sequences that are in good agreement with both experimental ones and those obtained from statistical models, (ii) a realistic step-like denaturation behaviour for long inhomogeneous sequences, and (iii) critical forces at ambient temperature of the order of 10 pN, close to measured values. The adjusted model furthermore supports the conclusion that the thermal denaturation of long homogeneous sequences corresponds to a first-order phase transition and yields a critical exponent for the critical force equal to sigma=0.70. This model is both geometrically and energetically realistic, in the sense that the helical structure and the grooves, where most proteins bind, are satisfactorily reproduced, while the energy and force required to break a base pair lie in the expected range. It therefore represents a promising tool for studying the dynamics of DNA-protein specific interactions at an unprecedented detail level.

It has long been asserted that proteins like transcription factors may locate their target in DNA sequences at rates that surpass by several orders of magnitude the three-dimensional diffusion limit thank to facilitated diffusion, that is the combination of one-dimensional (sliding along the DNA) and three-dimensional diffusion. This claim has been supported along the years by several mass action kinetic models, while the dynamical model we proposed recently (J. Chem. Phys. 130, 015103 (2009)) suggests that acceleration of targeting due to facilitated diffusion cannot be large. In order to solve this apparent contradiction, we performed additional simulations to compare the results obtained with our model to those obtained with the kinetic model of Klenin et al (Phys. Rev. Letters 96, 018104 (2006)). We show in this paper that the two models actually support each other and agree in predicting a low efficiency for facilitated diffusion. Extrapolation of these results to real systems even indicates that facilitated diffusion necessarily slows down the targeting process compared to three-dimensional diffusion.

The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of single beads. In this paper, we first compare the results obtained with the updated model with those of the original one and then use it to investigate several aspects of the dynamics of DNA sampling, which could not be accounted for by the original model. These aspects include the effect on the speed of DNA sampling of the regularity and/or randomness of the protein charge distribution, the charge and location of the search site, and the shape and deformability of the protein. We also discuss the efficiency of facilitated diffusion, that is, the extent to which the combination of 1D sliding along the DNA and 3D diffusion in the cell can lead to faster sampling than pure 3D diffusion of the protein., Comment: accepted in JCP

2D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, according first to their size and then to their sequence composition. In this paper, we present an exhaustive study of the numerical issues associated with a model aimed at predicting the final absolute locations of DNA fragments in 2D display experiments. We show that simple expressions for the mobility of DNA fragments in both dimensions allow one to reproduce experimental final absolute locations to better than experimental uncertainties. On the other hand, our simulations also point out that the results of 2D display experiments are not sufficient to determine the best set of parameters for the modeling of fragments separation in the second dimension and that additional detailed measurements of the mobility of a few sequences are necessary to achieve this goal. We hope that this work will help in establishing simulations as a powerful tool to optimize experimental conditions without having to perform a large number of preliminary experiments and to estimate whether 2D DNA display is suited to identify a mutation or a genetic difference that is expected to exist between the genomes of closely related organisms., Comment: accepted in Electrophoresis

We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are varied to get predictions in better agreement with experimental results that were not addressed up to now, like mechanical unzipping, the evolution of the critical temperature with sequence length, and temperature resolution. We show that the model with the new parameters provides results that are in quantitative agreement with those obtained from statistical models. Investigation of the critical properties of the dynamical model suggests that DNA denaturation looks like a first-order phase transition in a broad temperature interval, but that there necessarily exists, very close to the critical temperature, a crossover to another regime. The exact nature of the melting dynamics in this second regime still has to be elucidated. We finally point out that the descriptions of the physics of the melting transition inferred from statistical and dynamical models are not completely identical and discuss the relevance of our model from the biological point of view.

We propose a dynamical model for non-specific DNA-protein interaction, which is based on the 'bead-spring' model previously developed by other groups, and investigate its properties using Brownian Dynamics simulations. We show that the model successfully reproduces some of the observed properties of real systems and predictions of kinetic models. For example, sampling of the DNA sequence by the protein proceeds via a succession of 3d motion in the solvent, 1d sliding along the sequence, short hops between neighboring sites, and intersegmental transfers. Moreover, facilitated diffusion takes place in a certain range of values of the protein effective charge, that is, the combination of 1d sliding and 3d motion leads to faster DNA sampling than pure 3d motion. At last, the number of base pairs visited during a sliding event is comparable to the values deduced from single-molecule experiments. We also point out and discuss some discrepancies between the predictions of this model and some recent experimental results as well as some hypotheses and predictions of kinetic models.