Related papers: DNA-Protein Binding Rates: Bending Fluctuation and…
We present a mean-field dynamical theory for single semiflexible polymers which can precisely capture, without fitting parameters, recent fluorescence correlation spectroscopy results on single monomer kinetics of DNA strands in solution.…
The model of facilitated diffusion describes how DNA-binding proteins, such as transcription factors (TFs), find their chromosomal targets by combining 3D diffusion through the cytoplasm and 1D sliding along nonspecific DNA sequences. The…
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…
We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the…
We theoretically study the molecular-weight dependence of DNA thermophoresis, which arises from mutual advection of the n repeat units of the molecular chain. As a main result we find that the dominant driving forces, i.e., the thermally…
Composites of flexible and rigid polymers are ubiquitous in biology and industry alike, yet the physical principles determining their mechanical properties are far from understood. Here, we couple force spectroscopy with large-scale…
The some dynamic properties of a random heteropolymer in the condensed state are studied in the mode coupling approximation. In agreement with recent report a dynamic friction increasing is predicted for the random heteropolymer with…
We present a statistical mechanical model of aggregation in colloidal systems with DNA mediated interactions. We obtain a general result for the two-particle binding energy in terms of the hybridization free energy $\Delta G$ of DNA and two…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
The paper deals with the two-state (opening-closing of base pairs) model used to describe the fluctuation dynamics of a single bubble formation. We present an exact solution for the discrete and finite size version of the model that…
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…
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…
A recent experiment [Sadoon AA, Wang Y. 2018 Phys. Rev. E 98, 042411] has revealed that nucleoid associated proteins (i.e., DNA-binding proteins) exhibit highly heterogeneous diffusion processes in bacteria where not only the diffusion…
DNA bending on length scales shorter than a persistence length plays an integral role in the translation of genetic information from DNA to cellular function. Quantitative experimental studies of these biological systems have led to a…
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that…
Plectonemes are intertwined helically looped domains which form when a DNA molecule is supercoiled, i.e. over- or under-wounded. They are ubiquitous in cellular DNA and their physical properties have attracted significant interest both from…
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…
We develop a simple but rigorous model of protein-protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding the native complex binding funnels. Guided…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters are estimated for this purpose for three different DNA…