Related papers: Orientational correlations in confined DNA
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…
The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional…
Ionic currents accompanying DNA translocation strongly depend on molarity of the electrolyte solution and the shape and surface charge of the nanopore. By means of the Poisson-Nernst-Planck equations it is shown how conductance is modulated…
We studied the correlation between the molecular structure and the formation of helical nanofilaments (HNFs) of bent-core dimeric molecules with varying linkage lengths. To obtain precise structural data, a single domain of HNFs was…
We introduce a method to estimate continuum percolation thresholds and illustrate its usefulness by investigating geometric percolation of non-interacting line segments and disks in two spatial dimensions. These examples serve as models for…
A number of recent experiments have provided detailed observations of the configurations of long DNA strands under nano-to-micrometer sized confinement. We therefore revisit the problem of an excluded volume polymer chain confined between…
The influence of tension on DNA looping has been studied both experimentally and theoretically in the past. However, different theoretical models have yielded different predictions, leaving uncertainty about their validity. We briefly…
Standard DNA melting curves record the separation of the two strands versus temperature, but they do not provide any information on the location of the opening. We introduce an experimental method which adds a new dimension to the melting…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
We demonstrate simultaneous measurements of DNA translocation into glass nanopores using ionic current detection and fluorescent imaging. We verify the correspondence between the passage of a single DNA molecule through the nanopore and the…
With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
The force-extension relation for a semi-flexible polymer such as DNA confined in a nanoslit is investigated and it is found that both the effective persistence length and the form of the force-extension relation change as the chain goes…
Lasers based on biological materials are attracting an increasing interest in view of their use in integrated and transient photonics. DNA as optical biopolymer in combination with highly-emissive dyes has been reported to have excellent…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
The realization of single-molecule electronic devices, in which a nanometer-scale molecule is connected to macroscopic leads, requires the reproducible production of highly ordered nanoscale gaps in which a molecule of interest is…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
The effect of confinement on the orientational structure of a nematic liquid crystal model has been investigated by using a version of density-functional theory (DFT). We have focused on the case of a nematic confined by opposing flat…