ArticleBiophysical journal2012
The effect of nonspecific binding of lambda repressor on DNA looping dynamics.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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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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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.
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Who cites it
22 citing papers in PubMed, 26 citations in OpenAlex.
- Insights on the effect of macromolecular crowding on transcription and its regulation.QRB discovery · 2025Article
- Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time.Nucleic acids research · 2021Article
- Single-molecule insights into torsion and roadblocks in bacterial transcript elongation.Transcription · 2021Article
- Non-monotonic auto-regulation in single gene circuits.PloS one · 2019Article
- Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Article
- Measurement of gene regulation in individual cells reveals rapid switching between promoter states.Science (New York, N.Y.) · 2016Article
- Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.PLoS computational biology · 2015Article
- Single-molecule analysis of RAG-mediated V(D)J DNA cleavage.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- DNA supercoiling: a regulatory signal for the λ repressor.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Tethered particle analysis of supercoiled circular DNA using peptide nucleic acid handles.Nature protocols · 2014Article
- Studying DNA looping by single-molecule FRET.Journal of visualized experiments : JoVE · 2014Article
- Probing transient protein-mediated DNA linkages using nanoconfinement.Biomicrofluidics · 2014Article
- Tethered particle motion reveals that LacI·DNA loops coexist with a competitor-resistant but apparently unlooped conformation.Biophysical journal · 2014Article
- Probing the elastic limit of DNA bending.Nucleic acids research · 2014Article
- Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion.Nucleic acids research · 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
- Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites.Biophysical journal · 2013Article
- Measuring shape-dependent looping probability of DNA.Biophysical journal · 2013Article
- Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level.International journal of molecular sciences · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The λ repressor (CI) protein-induced DNA loop maintains stable lysogeny, yet allows efficient switching to lysis. Herein, the kinetics of loop formation and breakdown has been characterized at various concentrations of protein using tethered particle microscopy and a novel, to our knowledge, method of analysis. Our results show that a broad distribution of rate constants and complex kinetics underlie loop formation and breakdown. In addition, comparison of the kinetics of looping in wild-type DNA and DNA with mutated o3 operators showed that these sites may trigger nucleation of nonspecific binding at the closure of the loop. The average activation energy calculated from the rate constant distribution is consistent with a model in which nonspecific binding of CI between the operators shortens their effective separation, thereby lowering the energy barrier for loop formation and broadening the rate constant distribution for looping. Similarly, nonspecific binding affects the kinetics of loop breakdown by increasing the number of loop-securing protein interactions, and broadens the rate constant distribution for this reaction. Therefore, simultaneous increase of the rate constant for loop formation and reduction of that for loop breakdown stabilizes lysogeny. Given these simultaneous changes, the frequency of transitions between the looped and the unlooped state remains nearly constant. Although the loop becomes more stable thermodynamically with increasing CI concentration, it still opens periodically, conferring sensitivity to environmental changes, which may require switching to lytic conditions.
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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.