Related papers: Conformations of closed DNA
Effect of bending anisotropy on a planar DNA loop, using energy minimization and neglecting entropic effects, is studied. We show that the anisotropy results in polygonal shape of the loop and increasing the anisotropy makes the edges…
Recent experimental data indicate that the elastic wormlike rod model of DNA that works well on long length scales may break down on shorter scales relevant to biology. According to Noy and Golestanian (Phys. Rev. Lett. 109, 228101, 2012)…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages…
Protein-DNA complexes with loops play a fundamental role in a wide variety of cellular processes, ranging from the regulation of DNA transcription to telomere maintenance. As ubiquitous as they are, their precise in vivo properties and…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
We study the nonlinear dynamics of a deformed Deoxyribonucleic acid (DNA) molecular chain which is governed by a perturbed sine-Gordon equation coupled with a linear wave equation representing the lattice deformation. The DNA chain…
Parts of DNA sequences known as exons and introns play very different role in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations…
Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for…
Minuscule molecular forces can transform DNA into a structure that is elongated by more than half its original length. We demonstrate that this pronounced conformational transition is of relevance to ongoing experimental and theoretical…
The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…
We study RNA foldings and investigate their topology using a combination of knot theory and embedded rigid vertex graphs. Knot theory has been helpful in modeling biomolecules, but classical knots place emphasis on a biomolecule's…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
We show the existence of a high interrelation between the different loops that may appear in a DNA segment. Conformational changes in a chain segment caused by the formation of a particular loop may either promote or prevent the appearance…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
The strength of the spin-orbit interaction relevant to transport in a low dimensional structure depends critically on the relative geometrical arrangement of current carrying orbitals. Recent tight-binding orbital models for spin transport…
All known life forms are based upon a hierarchy of interwoven feedback loops, operating over a cascade of space, time and energy scales. Among the most basic loops are those connecting DNA and proteins. For example, in genetic networks, DNA…
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…