Related papers: DNA-Protein Cooperative Binding through Long-Range…
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…
RNA binding proteins play a crucial role in post-transcriptional gene regulation by controlling the transport, processing, and translation of their target RNAs. Post-transcriptional gene regulation leads to the differential expression of…
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
The function of proteins arises from cooperative interactions and rearrangements of their amino acids, which exhibit large-scale dynamical modes. Long-range correlations have also been revealed in protein sequences, and this has motivated…
Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these…
In the present paper we address the general problem of selective electrodynamic interactions between DNA and protein, which is motivated by decades of theoretical study and our very recent experimental findings (M. Lechelon et al,…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
Allosteric interactions between molecules bound to DNA at distant locations have been known for a long time. The phenomenon has been studied via experiments and numerical simulations, but a comprehensive understanding grounded in a theory…
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…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…