Related papers: Protein-DNA electrostatics: toward a new paradigm …
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
DNA shape readout is an important mechanism of target site recognition by transcription factors, in addition to the sequence readout. Several models of transcription factor-DNA binding which consider DNA shape have been developed in recent…
The mechanism of threshold elongation (overstretching) of DNA macromolecules under the action of external force is studied within the framework of phenomenological approach. When considering the task it is taken into account that…
Transcription factors (TFs) are macromolecules that bind to \textit{cis}-regulatory specific sub-regions of DNA promoters and initiate transcription. Finding the exact location of these binding sites (aka motifs) is important in a variety…
We studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip…
Efficient capture and detection of minute amount of deoxyribonucleic acid (DNA) molecules are pivotal for an array of modern gene technologies which are widely utilized in medical, forensic and defense applications, including DNA…
The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…
Protein motifs are conserved fragments occurred frequently in protein sequences. They have significant functions, such as active site of an enzyme. Search and clustering protein sequence motifs are computational intensive. Most existing…
The response of a semiflexible polyelectrolyte chain to stretching in the regimes of moderate and weak screening is studied theoretically, with a special focus on DNA experiments. By using the nonlinear Poisson--Boltzmann description of…
Cells deploy robust mechanisms to repair DNA damage, safeguarding genomic stability and cellular health, but the physical principles underlying these processes remain incompletely understood. Experiments show \emph{in vitro} that upon a DNA…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
The problem of detecting a binding site -- a substring of DNA where transcription factors attach -- on a long DNA sequence requires the recognition of a small pattern in a large background. For short binding sites, the matching probability…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc.), the rate of which can be regulated by small non-coding microRNAs through multiple…
Speciation is of fundamental importance to understanding the huge diversity of life on Earth. In contrast to current phenomenological models, we develop a biophysically motivated approach to study speciation involving the co-evolution of…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…