ArticleNucleic acids research2006
DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force.
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 20 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
20 citing papers in PubMed, 33 citations in OpenAlex.
- LOOP-TAG: massively-parallel measurement of length-dependent protein-mediated DNA looping probabilities by tagmentationbioRxiv : the preprint server for biology · 2026Article
- HSV-1 origin binding protein UL9 forms intermolecular DNA tethers and intramolecular DNA loops.Nature communications · 2026Article
- Determining Trap Compliances, Microsphere Size Variations, and Response Linearities in Single DNA Molecule Elasticity Measurements with Optical Tweezers.Frontiers in molecular biosciences · 2021Article
- Determinants of cyclization-decyclization kinetics of short DNA with sticky ends.Nucleic acids research · 2020Article
- Novel parameter describing restriction endonucleases: Secondary-Cognate-Specificity and chemical stimulation of TsoI leading to substrate specificity change.Applied microbiology and biotechnology · 2019Article
- Single molecular investigation of DNA looping and aggregation by restriction endonuclease BspMI.Scientific reports · 2014Article
- Accurate measurement of force and displacement with optical tweezers using DNA molecules as metrology standards.Applied physics letters · 2014Article
- Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily.Nucleic acids research · 2012Article
- Single-molecule studies of viral DNA packaging.Advances in experimental medicine and biology · 2012Review
- DNA cleavage site selection by Type III restriction enzymes provides evidence for head-on protein collisions following 1D bidirectional motion.Nucleic acids research · 2011Article
- DNA modeling reveals an extended lac repressor conformation in classic in vitro binding assays.Biophysical journal · 2011Article
- 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
- Fused eco29kIR- and M genes coding for a fully functional hybrid polypeptide as a model of molecular evolution of restriction-modification systems.BMC evolutionary biology · 2011Article
- Creation of a type IIS restriction endonuclease with a long recognition sequence.Nucleic acids research · 2009Article
- Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA.Nucleic acids research · 2008Article
- Geometry of mediating protein affects the probability of loop formation in DNA.Biophysical journal · 2008Article
- Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping.PloS one · 2006Article
- Dynamics of single DNA looping and cleavage by Sau3AI and effect of tension applied to the DNA.Biophysical journal · 2006Article
- Tension-dependent DNA cleavage by restriction endonucleases: two-site enzymes are "switched off" at low force.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
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 at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Proteins interacting at multiple sites on DNA via looping play an important role in many fundamental biochemical processes. Restriction endonucleases that must bind at two recognition sites for efficient activity are a useful model system for studying such interactions. Here we used single DNA manipulation to study sixteen known or suspected two-site endonucleases. In eleven cases (BpmI, BsgI, BspMI, Cfr10I, Eco57I, EcoRII, FokI, HpaII, NarI, Sau3AI and SgrAI) we found that substitution of Ca2+ for Mg2+ blocked cleavage and enabled us to observe stable DNA looping. Forced disruption of these loops allowed us to measure the frequency of looping and probability distributions for loop size and unbinding force for each enzyme. In four cases we observed bimodal unbinding force distributions, indicating conformational heterogeneity and/or complex binding energy landscapes. Measured unlooping events ranged in size from 7 to 7500 bp and the most probable size ranged from less than 75 bp to nearly 500 bp, depending on the enzyme. In most cases the size distributions were in much closer agreement with theoretical models that postulate sharp DNA kinking than with classical models of DNA elasticity. Our findings indicate that DNA looping is highly variable depending on the specific protein and does not depend solely on the mechanical properties of 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.