Electrostatically induced undulations of lamellar DNA-lipid complexes

We consider DNA-cationic lipid complexes that form lamellar stacks of lipid bilayers with parallel DNA strands intercalated in between. We calculate the electrostatically induced elastic deformations of the lipid bilayers. It is found that the membranes undulate with a periodicity that is set by the DNA interaxial distance. As a consequence the lamellar repeat distance changes resulting in a swelling or compression of the lamellar stack. Such undulations may be responsible for the intermembrane coupling between DNA strands in different layers as it is observed experimentally.Comment: 7 pages, submitted to EPJ

Where the linearized Poisson-Boltzmann cell model fails: (II) the planar case as a prototype study

The classical problem of two uniformly charged infinite planes in electrochemical equilibrium with an infinite monovalent salt reservoir is solved exactly at the mean-field nonlinear Poisson-Boltzmann (PB) level, including an explicit expression of the associated nonlinear electrostatic contribution to the semi-grand-canonical potential. A linearization of the nonlinear functional is presented that leads to Debye-H\"uckel-like equations agreeing asymptotically with the nonlinear PB results in the weak-coupling (high-temperature) and counterionic ideal-gas limits. This linearization scheme yields artifacts in the low-temperature, large-separation or high-surface charge limits. In particular, the osmotic-pressure difference between the interplane region and the salt reservoir becomes negative in the above limits, in disagreement with the exact (at mean-field level) nonlinear PB solution. By using explicitly gauge-invariant forms of the electrostatic potential we show that these artifacts -- although thermodynamically consistent with quadratic expansions of the nonlinear functional -- can be traced back to the non-fulfillment of the underlying assumptions of the linearization. Explicit comparison between the analytical expressions of the exact nonlinear solution and the corresponding linearized equations allows us to show that the linearized results are asymptotically exact in the weak-coupling and counterionic ideal-gas limits, but always fail otherwise, predicting negative osmotic-pressure differences.Comment: 24 pages, 3 PostScript figures, submitted to J. Chem. Phy

Theory of Nucleosome Corkscrew Sliding in the Presence of Synthetic DNA Ligands

Histone octamers show a heat-induced mobility along DNA. Recent theoretical studies have established two mechanisms that are qualitatively and quantitatively compatible with in vitro experiments on nucleosome sliding: Octamer repositiong through one-basepair twist defects and through ten-basepair bulge defects. A recent experiment demonstrated that the repositioning is strongly suppressed in the presence of minor-groove binding DNA ligands. In the present study we give a quantitative theory for nucleosome repositioning in the presence of such ligands. We show that the experimentally observed octamer mobilities are consistent with the picture of bound ligands blocking the passage of twist defects through the nucleosome. This strongly supports the model of twist defects inducing a corkscrew motion of the nucleosome as the underlying mechanism of nucleosome sliding. We provide a theoretical estimate of the nucleosomal mobility without adjustable parameters, as a function of ligand concentration, binding affinity, binding site orientiation, temperature and DNA anisotropy. Having this mobility at hand we speculate about the interaction between a nucleosome and a transcribing RNA polymerase and suggest a novel mechanism that might account for polymerase induced nucleosome repositioning.Comment: 23 pages, 4 figures, submitted to J. Mol. Bio

Controlled DNA compaction within chromatin: the tail-bridging effect

We study the mechanism underlying the attraction between nucleosomes, the fundamental packaging units of DNA inside the chromatin complex. We introduce a simple model of the nucleosome, the eight-tail colloid, consisting of a charged sphere with eight oppositely charged, flexible, grafted chains that represent the terminal histone tails. We demonstrate that our complexes are attracted via the formation of chain bridges and that this attraction can be tuned by changing the fraction of charged monomers on the tails. This suggests a physical mechanism of chromatin compaction where the degree of DNA condensation can be controlled via biochemical means, namely the acetylation and deacetylation of lysines in the histone tails.Comment: 4 pages, 5 figures, submitte

Multi-plectoneme phase of double-stranded DNA under torsion

We use the worm-like chain model to study supercoiling of DNA under tension and torque. The model reproduces experimental data for a much broader range of forces, salt concentrations and contour lengths than previous approaches. Our theory shows, for the first time, how the behavior of the system is controlled by a multi-plectoneme phase in a wide range of parameters. This phase does not only affect turn-extension curves but also leads to a non-constant torque in the plectonemic phase. Shortcomings from previous models and inconsistencies between experimental data are resolved in our theory without the need of adjustable parameters.Comment: 4 pages, 6 figures, submitted, 2 typo's corrected, one reference adde

Biophysical Perspective: The Latest Twists in Chromatin Remodeling

International audienceIn its most restrictive interpretation, the notion of chromatin remodeling refers to the action of chromatin remodeling enzymes on nucleosomes with the aim to displace and remove them from the chromatin fiber (the effective polymer formed by a DNA molecule and proteins). This local modification of the fiber structure can have consequences for the initiation and repression of the transcription process and, when the remodeling processes spreads along the fiber, also results in long-range effects essential for fiber condensation. There are three regulatory levels of relevance that can be distinguished for this process: the first is the intrinsic sequence preference of the histone octamer which rules the positioning of the nucleosome along the DNA, notably in relation to the genetic information coded in DNA, the second is the recognition or selection of nucleosomal substrates by remodeling complexes, and the final one the motor action on the nucleosome exerted by the chromatin remodeler. On each of these three levels recent work has been able to provide crucial insights which add new twists to this exciting and unfinished story, which we highlight in this perspective

Chromatin remodelers as active Brownian dimers

International audienceChromatin remodelers are molecular motors which actively displace nucleosomes on chromatin. Recent results on the structural properties of these motors indicate that the displacement of nucleosomal DNA corresponds to an inchworm motion induced by the generation and propagation of twist defects. Here we show that this basic action mechanism can be described by a coarse-grained active Brownian dimer (ABD) model, thereby quantitatively rationalizing the notion of inchworm motion. The model allows for extensions to more microscopic as well towards more macroscopic descriptions of chromatin hydrodynamics

Nucleosome repositioning via loop formation

Active (catalysed) and passive (intrinsic) nucleosome repositioning is known to be a crucial event during the transcriptional activation of certain eucaryotic genes. Here we consider theoretically the intrinsic mechanism and study in detail the energetics and dynamics of DNA-loop-mediated nucleosome repositioning, as previously proposed by Schiessel et al. (H. Schiessel, J. Widom, R. F. Bruinsma, and W. M. Gelbart. 2001. {\it Phys. Rev. Lett.} 86:4414-4417). The surprising outcome of the present study is the inherent nonlocality of nucleosome motion within this model -- being a direct physical consequence of the loop mechanism. On long enough DNA templates the longer jumps dominate over the previously predicted local motion, a fact that contrasts simple diffusive mechanisms considered before. The possible experimental outcome resulting from the considered mechanism is predicted, discussed and compared to existing experimental findings

Electrostatic complexation of spheres and chains under elastic stress

We consider the complexation of highly charged semiflexible polyelectrolytes with oppositely charged macroions. On the basis of scaling arguments we discuss how the resulting complexes depend on the persistence length of the polyelectrolyte, the salt concentration, and the sizes and charges of the chain and the macroions. We study first the case of complexation with a single sphere and calculate the wrapping length of the chain. We then extend our considerations to complexes involving many wrapped spheres and study cooperative effects. The mechanical properties of such a complex under an external deformation are evaluated.Comment: 16 pages, submitted to J. Chem. Phy