# Kinetics of Protein-DNA Interactions: First-Passage Analysis

Source: [Kinetics of Protein-DNA Interactions: First-Passage Analysis](<https://www.sota2.com/research/paper/68fa5eda1e209131ce9e5b2a>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-25T19:01:51.543Z

Authors: Maria P. Kochugaeva, Alexey A. Shvets, Anatoly B. Kolomeisky

Published: 2018-04-26T15:34:57.000Z

## Abstract

All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of investigating dynamics of protein-DNA interactions, which govern all major biological processes. It is based on a first-passage analysis of biochemical and biophysical transitions, and it provides a fully analytic description of the processes. Our approach is explained for the case of a single protein searching for a specific binding site on DNA. In addition, the application of the method to investigations of the effect of DNA sequence heterogeneity, and the role multiple targets and traps in the protein search dynamics are discussed.

## Recorded benchmark results

A research result applies to its stated dataset, split, metric and evaluation configuration. Compare like-for-like settings, preserve the metric's unit and direction, and distinguish paper-reported results from independent reproduction. The best result recorded here is not a claim of exhaustive, current global coverage.

## Original sources and implementation

[Original paper](<https://arxiv.org/abs/1804.10114>)

[PDF](<https://arxiv.org/pdf/1804.10114.pdf>)