ArticleBiophysical journal2007
Probability of the site juxtaposition determines the rate of protein-mediated DNA looping.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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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.
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Who cites it
21 citing papers in PubMed, 35 citations in OpenAlex.
- Coarse-grained modeling reveals the impact of supercoiling and loop length in DNA looping kinetics.Biophysical journal · 2022Article
- Two-phase dynamics of DNA supercoiling based on DNA polymer physics.Biophysical journal · 2022Article
- Single-molecule insights into torsion and roadblocks in bacterial transcript elongation.Transcription · 2021Article
- Novel insights into chromosomal conformations in cancer.Molecular cancer · 2017Review
- Towards quantitative analysis of gene regulation by enhancers.Epigenomics · 2017Review
- Nucleosome-free DNA regions differentially affect distant communication in chromatin.Nucleic acids research · 2017Article
- DNA cyclization and looping in the wormlike limit: Normal modes and the validity of the harmonic approximation.Biopolymers · 2015Article
- Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling.Nucleic acids research · 2015Article
- Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping.The Journal of chemical physics · 2014Article
- Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Effect of supercoiling on the λ switch.Bacteriophage · 2014Article
- DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Distant activation of transcription: mechanisms of enhancer action.Molecular and cellular biology · 2012Review
- The importance of being supercoiled: how DNA mechanics regulate dynamic processes.Biochimica et biophysica acta · 2012Review
- Internucleosomal interactions mediated by histone tails allow distant communication in chromatin.The Journal of biological chemistry · 2012Article
- Unlinking of supercoiled DNA catenanes by type IIA topoisomerases.Biophysical journal · 2011Article
- Action at hooked or twisted-hooked DNA juxtapositions rationalizes unlinking preference of type-2 topoisomerases.Journal of molecular biology · 2010Article
- Simulation of DNA catenanes.Physical chemistry chemical physics : PCCP · 2009Review
- The why and how of DNA unlinking.Nucleic acids research · 2009Review
- Analysis of distant communication on defined chromatin templates in vitro.Methods in molecular biology (Clifton, N.J.) · 2009Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
Numerous biological processes are regulated by DNA elements that communicate with their targets over a distance via formation of protein-bridged DNA loops. One of the first questions arising in studies of DNA looping is whether the rate of loop formation is limited by diffusion of the DNA sites. We addressed this question by comparing the in vitro measured rates of transcription initiation in the NtrC-glnAp2 enhancer-dependent transcription initiation system with predictions of two different theoretical models. The promoter and enhancer were in a 7.6-kb plasmid and separated by 2.5 kb. The measurements were performed for different values of the plasmid superhelix density, from 0 to -0.07. Earlier theoretical analysis, based on the Monte Carlo simulation of DNA conformations, showed that if the rate of loop formation is determined by the equilibrium probability of juxtaposition of the DNA sites, the rate should be approximately 100 times higher in supercoiled than in relaxed DNA. On the other hand, Brownian dynamics simulation showed that if the rate of loop formation is limited by the site diffusion, it should be nearly independent of DNA supercoiling. We found that efficiency of the transcription initiation increases by nearly two orders of magnitude as a result of the corresponding increase of the template supercoiling. This clearly shows that the rate of bridging in the enhancer-promoter system is not limited by diffusion of the DNA sites to one another. We argue that this conclusion derived for the specific system is likely to be valid for the great majority of biological processes involving protein-mediated DNA looping.
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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.