ArticleNucleic acids research2015
Searching target sites on DNA by proteins: Role of DNA dynamics under confinement.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 50 citations in OpenAlex.
- Retroviral intasome architecture shapes the dynamics of target DNA search and integration.PLoS pathogens · 2026Article
- Multiphasic Organization and Differential Dynamics of Proteins within Protein-DNA Biomolecular Condensates.The journal of physical chemistry. B · 2025Article
- Memory effects of transcription regulator-DNA interactions in bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- Interdomain dynamics in human Replication Protein A regulates kinetics and thermodynamics of its binding to ssDNA.PloS one · 2023Article
- Nucleosome breathing facilitates cooperative binding of pluripotency factors Sox2 and Oct4 to DNA.Biophysical journal · 2022Article
- Probing Amyloid-DNA Interaction with Nanofluidics.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Understanding protein diffusion on force-induced stretched DNA conformation.Frontiers in molecular biosciences · 2022Article
- Kinetic origin of nucleosome invasion by pioneer transcription factors.Biophysical journal · 2021Article
- Nonspecific interactions between SpCas9 and dsDNA sites located downstream of the PAM mediate facilitated diffusion to accelerate target search.Chemical science · 2021Article
- The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition.The journal of physical chemistry. B · 2021Article
- One-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by chemical ratchet mechanism.Scientific reports · 2021Article
- Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu.Biophysical journal · 2020Article
- Single-particle trajectories reveal two-state diffusion-kinetics of hOGG1 proteins on DNA.Nucleic acids research · 2018Article
- Role of Macromolecular Crowding on the Intracellular Diffusion of DNA Binding Proteins.Scientific reports · 2018Article
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
- DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid.Biophysical journal · 2017Article
- How motif environment influences transcription factor search dynamics: Finding a needle in a haystack.BioEssays : news and reviews in molecular, cellular and developmental biology · 2016Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA-binding proteins (DBPs) rapidly search and specifically bind to their target sites on genomic DNA in order to trigger many cellular regulatory processes. It has been suggested that the facilitation of search dynamics is achieved by combining 3D diffusion with one-dimensional sliding and hopping dynamics of interacting proteins. Although, recent studies have advanced the knowledge of molecular determinants that affect one-dimensional search efficiency, the role of DNA molecule is poorly understood. In this study, by using coarse-grained simulations, we propose that dynamics of DNA molecule and its degree of confinement due to cellular crowding concertedly regulate its groove geometry and modulate the inter-communication with DBPs. Under weak confinement, DNA dynamics promotes many short, rotation-decoupled sliding events interspersed by hopping dynamics. While this results in faster 1D diffusion, associated probability of missing targets by jumping over them increases. In contrast, strong confinement favours rotation-coupled sliding to locate targets but lacks structural flexibility to achieve desired specificity. By testing under physiological crowding, our study provides a plausible mechanism on how DNA molecule may help in maintaining an optimal balance between fast hopping and rotation-coupled sliding dynamics, to locate target sites rapidly and form specific complexes precisely.
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