Charged rosettes at high and low ionic strengths

The complexation between a semiflexible polyelectrolyte and an oppositely charged macroion leads to a multitude of structures ranging from tight complexes with the chain wrapped around the macroion to open multileafed rosette-like complexes. Rosette structures, expected to occur for short-ranged attractions between the macroion and the chain, have now also been seen in recent Monte Carlo simulations with long-range (unscreened) interactions [Akinchina and Linse Macromolecules 2002, 35, 5183]. The current study provides scaling theories for both cases and shows that rosette structures are indeed quite robust against changes in the ionic strength. However, the transition from the wrapped to the rosette configuration has a dramatically different characteristics: The short-range case leads to a strongly discontinuous transition into a rosette with large leaves whereas the long-range case occurs in a continuous fashion. We provide the complete diagram of states for both cases.Comment: 9 pages, 3 figures, submitted to Macromolecule

Histone mark recognition controls nucleosome translocation via a kinetic proofreading mechanism: Confronting theory and high-throughput experiments

International audienceChromatin remodelers are multi-domain enzymatic motor complexes that displace nucleosomes along DNA and hence 'remodel chromatin structure', i.e., they dynamically reorganize nucleosome positions in both gene activation and gene repression. Recently, experimental insights from structural biology methods and remodeling assays have substantially advanced the understanding of these key chromatin components. Here we confront the kinetic proofreading scenario of chromatin remodeling, which proposes a mechanical link between histone residue modifications and the ATP-dependent action of remodelers, with recent experiments. We show that recent high-throughput data on nucleosome libraries assayed with remodelers from the ISWI family are in accord with our earlier predictions of the kinetic proofreading scenario. We make suggestions for new experimentally verifiable predictions of the kinetic proofreading scenarios for remodelers from other families

Unwinding Dynamics of a Helically Wrapped Polymer

We study the rotational dynamics of a flexible polymer initially wrapped around a rigid rod and unwinding from it. This dynamics is of interest in several problems in biology and constitutes a fundamental instance of polymer relaxation from a state of minimal entropy. We investigate the dynamics of several quantities such as the total and local winding angles and metric quantities. The results of simulations performed in two and three dimensions, with and without self-avoidance, are explained by a theory based on scaling arguments and on a balance between frictional and entropic forces. The early stage of the dynamics is particularly rich, being characterized by three coexisting phases.Comment: 9 pages, 9 figure

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

Active Nucleosome Displacement: A Theoretical Approach

AbstractThree-quarters of eukaryotic DNA are wrapped around protein cylinders forming so-called nucleosomes that block the access to the genetic information. Nucleosomes need therefore to be repositioned, either passively (by thermal fluctuations) or actively (by molecular motors). Here we introduce a theoretical model that allows us to study the interplay between a motor protein that moves along DNA (e.g., an RNA polymerase) and a nucleosome that it encounters on its way. We aim at describing the displacement mechanisms of the nucleosome and the motor protein on a microscopic level to understand better the intricate interplay between the active step of the motor and the nucleosome-repositioning step. Different motor types (Brownian ratchet versus power-stroke mechanism) that perform very similarly under a constant load are shown to have very different nucleosome repositioning capacities

Sequence Dependent Plectoneme Dynamics

Theoretical Physic

Equation of State of Looped DNA

We derive the equation of state of DNA under tension that features a loop. Such loops occur transiently during DNA condensation in the presence of multivalent ions or permanently through sliding protein linkers such as condensin. The force-extension relation of such looped-DNA modeled as a wormlike chain is calculated via path integration in the semiclassical limit. This allows us to rigorously determine the high stretching asymptotics. Notably the functional form of the force-extension curve resembles that of straight DNA, yet with a strongly renormalized apparent persistence length. We also present analogous results for DNA under tension with several protein-induced kinks and/or loops. That means that the experimentally extracted single-molecule elasticity does not necessarily only reflect the bare DNA stiffness, but can also contain additional contributions that depend on the overall chain conformation and length

Analisis Willingness to Pay (Wtp) Dan Kebutuhan Air Di Kecamatan Merawang

The population growth and diversity of activities in the community in various fields occasion requirement of water have an important issue. Especially, supply of clean water. However, the availability of water in the Merawang Subdistrict had occurs dryness cause by drought in the 2015. Finally, many people using services from the Water Supply Company (PDAM) Tirta Bangka, Merawang Subdistrict. This indicated that there is a high ability and willingness of people to pay for services of PDAM. Therefore, in this research aims to examine the relationship between Willingness to Pay (WTP) of clean water in PDAM with the urgent water needs. Type of research is quantitative research, which is located in four villages in the Merawang Subdistrict. Such as Baturusa village, Riding Panjang village, Dwi Makmur (Sunghin) village, and Merawang village. In this case, we use Contingent Valuation Method (CVM) which using questionnaires and interviews to respondents in the village. The results of research showed that the rates paid by people who are willing to be in the range of Rp.50000.00/month until Rp.99000.00/month, average Rp.73378.00/month. Based on the results, tariff of WTP is Rp.2197.00/m3. In addition, from the analysis obtained the PDAM Tirta Bangka in Merawang was installed capacity of 10 l/s and water needs in the four villages, which is constitute the PDAM service area of less than 10 l/s. This suggests that the capacity of Water Supply Company (PDAM) Tirta Bangka has enough supplies for 10 years in Merawang Subdistrict

The role of DNA sequence in nucleosome breathing

Roughly 3/4 of human genomes are sequestered by nucleosomes, DNA spools with a protein core, dictating a broad range of biological processes, ranging from gene regulation, recombination, and replication, to chromosome condensation. Nucleosomes are dynamical structures and temporarily expose wrapped DNA through spontaneous unspooling from either end, a process called site exposure or nucleosome breathing. Here we ask how this process is influenced by the mechanical properties of the wrapped DNA, which is known to depend on the underlying base pair sequence. Using a coarse-grained nucleosome model we calculate the accessibility profiles for site exposure. We find that the process is very sensitive to sequence effects, so that evolution could potentially tune the accessibility of nucleosomal DNA and would only need a small number of mutations to do so