ArticleNucleic acids research2006
Strong physical constraints on sequence-specific target location by proteins on DNA molecules.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed.
- Modeling Facilitated Diffusion of Proteins in Crowded Environment.Sub-cellular biochemistry · 2025Review
- Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu.Biophysical journal · 2020Article
- Optimal Length of Conformational Transition Region in Protein Search for Targets on DNA.The journal of physical chemistry letters · 2017Article
- 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
- Quantitative influence of macromolecular crowding on gene regulation kinetics.Nucleic acids research · 2014Article
- Obstacles may facilitate and direct DNA search by proteins.Biophysical journal · 2013Article
- The effects of transcription factor competition on gene regulation.Frontiers in genetics · 2013Article
- The influence of transcription factor competition on the relationship between occupancy and affinity.PloS one · 2013Article
- Computational models for large-scale simulations of facilitated diffusion.Molecular bioSystems · 2012Review
- System size reduction in stochastic simulations of the facilitated diffusion mechanism.BMC systems biology · 2012Article
- A comprehensive computational model of facilitated diffusion in prokaryotes.Bioinformatics (Oxford, England) · 2012Article
- Is photocleavage of DNA by YOYO-1 using a synchrotron radiation light source sequence dependent?European biophysics journal : EBJ · 2011Article
- Dancing on DNA: kinetic aspects of search processes on DNA.Chemphyschem : a European journal of chemical physics and physical chemistry · 2011Review
- DNA translocation by type III restriction enzymes: a comparison of current models of their operation derived from ensemble and single-molecule measurements.Nucleic acids research · 2011Review
- Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA.Nucleic acids research · 2008Article
- Spatial effects on the speed and reliability of protein-DNA search.Nucleic acids research · 2008Article
- Thermodynamic characterization of specific interactions between the human Lon protease and G-quartet DNA.Nucleic acids research · 2008Article
- General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage lambda.Nucleic acids research · 2007Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Sequence-specific binding to DNA in the presence of competing non-sequence-specific ligands is a problem faced by proteins in all organisms. It is akin to the problem of parking a truck at a loading bay by the side of a road in the presence of cars parked at random along the road. Cars even partially covering the loading bay prevent correct parking of the truck. Similarly on DNA, non-specific ligands interfere with the binding and function of sequence-specific proteins. We derive a formula for the probability that the loading bay is free from parked cars. The probability depends on the size of the loading bay and allows an estimation of the size of the footprint on the DNA of the sequence-specific protein by assaying protein binding or function in the presence of increasing concentrations of non-specific ligand. Assaying for function gives an 'activity footprint'; the minimum length of DNA required for function rather than the more commonly measured physical footprint. Assaying the complex type I restriction enzyme, EcoKI, gives an activity footprint of approximately 66 bp for ATP hydrolysis and 300 bp for the DNA cleavage function which is intimately linked with translocation of DNA by EcoKI. Furthermore, considering the coverage of chromosomal DNA by proteins in vivo, our theory shows that the search for a specific DNA sequence is very difficult; most sites are obscured by parked cars. This effectively rules out any significant role in target location for mechanisms invoking one-dimensional, linear diffusion along DNA.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.