Diffusion and Search Dynamics

Defining reversible binding rates in 1D systems dependent on diffusion, density, and excluded volume

This paper develops a framework to model 1D reaction-diffusion dynamics with excluded volume, showing when single-rate continuum models accurately describe reversible binding kinetics.

Recognition in Confinement: The Dynamics of Homologous Gene Pairing

This study extends Helical Coherence Theory to model homologous DNA pairing under confinement, showing that optimal confinement accelerates pairing while avoiding tangling and metastable states.

A Dynamic Search Mechanism Enables APE1 to Identify AP-Sites in DNA

This study reveals how APE1 uses a dynamic search mechanism combining 1D and 3D diffusion to efficiently locate and repair AP-sites in DNA.

Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization

This paper shows how protein dimerization can enhance or impair DNA target selectivity by redistributing protein populations across the genome, using kinetic models and ChIP-seq data.

Electrostatic properties of disordered regions control transcription factor search and pioneer activity

This study shows that the electrostatic properties of disordered regions in transcription factors influence their search efficiency and pioneer activity on chromatin.

HU searches and binds specific DNA via a multi-step process combining weak electrostatic binding, protein reorientation and DNA flexibility

This study uses atomic simulations to show that HU binds DNA through a multi-step process involving weak electrostatic interactions, protein reorientation, and DNA flexibility, ensuring specific binding at target sites.

Fluctuations in first passage times and utility of resetting protocol in biochemical systems with two-state toggling

The paper analyzes first passage time fluctuations and resetting protocols in three biochemical systems with two-state toggling, showing non-monotonic behavior and re-entrant transitions in resetting efficacy.

Design principles of transcription factors with intrinsically disordered regions

This study identifies design principles of transcription factor intrinsically disordered regions that enhance binding affinity and search time for target DNA.

Mechanistic insights into direct DNA and RNA strand transfer and dynamic protein exchange of SSB and RPA

This study investigates the mechanisms of DNA and RNA strand transfer and protein exchange between SSB and RPA using smFRET, revealing dynamic interactions and length-dependent behavior.

Protein target search diffusion-association/dissociation free energy landscape around DNA binding site with flanking sequences

The paper models protein diffusional search along DNA, showing how sequence-dependent sliding and free energy landscapes are influenced by interfacial hydrogen bonds and flanking DNA sequences.

Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells

The paper reveals that pioneer transcription factors use mesoscale chromatin confinement to efficiently search for and bind to closed chromatin regions in live cells.

Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors

The paper investigates how HIF-1 and HIF-2 subunits exhibit distinct binding dynamics and gene regulation despite sharing the same DNA binding specificity, revealing the role of intrinsically disordered regions in chromatin binding and target selectivity.

Mitotic chromosome binding predicts transcription factor properties in interphase

The paper shows that mitotic chromosome binding of transcription factors correlates with their interphase properties and impact on chromatin accessibility.