Related papers: Constraints, Histones, and the 30 Nanometer Spiral
A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm…
We present an elastic model of B-form DNA as a stack of thin, rigid plates or base pairs that are not permitted to deform. The symmetry of DNA and the constraint of plate rigidity limit the number of bulk elastic constants contributing to a…
Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $\mu$m…
Found in all eukaryotic cells, linker histones H1 are known to bind to and rearrange nucleosomal linker DNA. In vitro, the fundamental nature of H1/DNA interactions has attracted wide interest among research communities - for biologists…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
The scaling properties of DNA knots of different complexities were studied by atomic force microscope. Following two different protocols DNA knots are adsorbed onto a mica surface in regimes of (i) strong binding, that induces a kinetic…
In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for numerous covalent epigenetic tags. While nucleosome positions in vitro are…
A theory is presented of DNA hairpins enclosed in a nanochannel. A hairpin becomes constrained as it approaches the wall of a channel which leads to an entropic force causing the hairpin to tighten. The free energy of the hairpin computed…
Packing problems, which ask how to arrange a collection of objects in space to meet certain criteria, are important in a great many physical and biological systems, where geometrical arrangements at small scales control behaviour at larger…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
In vivo configurations of dsDNA of bacteriophage viruses in a capsid are known to form hexagonal chromonic liquid crystal phases. This article studies the liquid crystal ordering of viral dsDNA in an icosahedral capsid, combining the…
A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…
We present a theoretical analysis of the structural and mechanical properties of the 30-nm chromatin fiber. Our study is based on the two-angle model introduced by Woodcock et al. (Woodcock, C. L., S. A. Grigoryev, R. A. Horowitz, and N.…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
Apart from being the gateway for all access to the eukaryotic genome, chromatin has in recent years been identified as carrying an epigenetic code regulating transcriptional activity. The detailed knowledge of this code contrasts the…
Faithful segregation of genetic material during cell division requires alignment of chromosomes between two spindle poles and attachment of their kinetochores to each of the poles. Failure of these complex dynamical processes leads to…
Interplay between structure and function in atomically thin crystalline nanoribbons is sensitive to their conformations yet the ability to prescribe them is a formidable challenge. Here, we report a novel paradigm for controlled nucleation…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of…