ArticleBiophysical journal2013
Obstacles may facilitate and direct DNA search by proteins.
Article in Biophysical journal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 63 citations in OpenAlex.
- Modeling Facilitated Diffusion of Proteins in Crowded Environment.Sub-cellular biochemistry · 2025Review
- Molecular basis of facilitated target search and sequence discrimination of TALE homeodomain transcription factor Meis1.Nature communications · 2024Article
- The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA.Nucleic acids research · 2020Article
- Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu.Biophysical journal · 2020Article
- Article
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
- Quantifying the two-state facilitated diffusion model of protein-DNA interactions.Nucleic acids research · 2019Article
- Facilitated Diffusion Mechanisms in DNA Base Excision Repair and Transcriptional Activation.Chemical reviews · 2018Review
- Mechanisms of Protein Search for Targets on DNA: Theoretical Insights.Molecules (Basel, Switzerland) · 2018Article
- Theory of Site-Specific DNA-Protein Interactions in the Presence of Nucleosome Roadblocks.Biophysical journal · 2018Article
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
- Optimal Length of Conformational Transition Region in Protein Search for Targets on DNA.The journal of physical chemistry letters · 2017Article
- Dynamic DNA binding licenses a repair factor to bypass roadblocks in search of DNA lesions.Nature communications · 2016Article
- Searching target sites on DNA by proteins: Role of DNA dynamics under confinement.Nucleic acids research · 2015Article
- Real sequence effects on the search dynamics of transcription factors on DNA.Scientific reports · 2015Article
- What matters for lac repressor search in vivo--sliding, hopping, intersegment transfer, crowding on DNA or recognition?Nucleic acids research · 2015Article
- Search by proteins for their DNA target site: 1. The effect of DNA conformation on protein sliding.Nucleic acids research · 2014Article
- Probing the rate-limiting step for intramolecular transfer of a transcription factor between specific sites on the same DNA molecule by (15)Nz-exchange NMR spectroscopy.Journal of the American Chemical Society · 2014Article
- Please, get in my way so that I can be more efficient!Biophysical journal · 2013Article
- The effects of transcription factor competition on gene regulation.Frontiers in genetics · 2013Article
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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 recognition by DNA-binding proteins (DBPs), which is a pivotal event in most gene regulatory processes, is often preceded by an extensive search for the correct site. A facilitated diffusion process in which a DBP combines three-dimensional diffusion in solution with one-dimensional sliding along DNA has been suggested to explain how proteins can locate their target sites on DNA much faster than predicted by three-dimensional diffusion alone. Although experimental and theoretical studies have recently advanced understanding of the biophysical principles underlying the search mechanism, the process under in vivo cellular conditions is poorly understood. In this study, we used various computational approaches to explore how the presence of obstacle proteins on the DNA influences search efficiency. At a low obstacle occupancy (i.e., when few obstacles occupy sites on the DNA), sliding by the searching DBP may be confined, which may impair search efficiency. The obstacles, however, can be bypassed during hopping events, and the number of bypasses is larger for higher obstacle occupancies. Dynamism on the part of the obstacles may even further facilitate search kinetics. Our study shows that the nature and efficiency of the search process may be governed not only by the intrinsic properties of the DBP and the salt concentration of the medium, but also by the in vivo association of DNA with other macromolecular obstacles, their location, and occupancy.
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