ArticleBiophysical journal2005
Single-molecule spectroscopic determination of lac repressor-DNA loop conformation.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 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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Who cites it
26 citing papers in PubMed, 59 citations in OpenAlex.
- Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor.Nature communications · 2023Article
- Factors Impacting Invader-Mediated Recognition of Double-Stranded DNA.Molecules (Basel, Switzerland) · 2022Article
- Serine-γPNA, Invader probes, and chimeras thereof: three probe chemistries that enable sequence-unrestricted recognition of double-stranded DNA.Organic & biomolecular chemistry · 2022Article
- Impact of non-nucleotidic bulges on recognition of mixed-sequence dsDNA by pyrene-functionalized Invader probes.Organic & biomolecular chemistry · 2020Article
- Direct Single-Molecule Observation of Sequential DNA Bending Transitions by the Sox2 HMG Box.International journal of molecular sciences · 2018Article
- Tethered particle motion reveals that LacI·DNA loops coexist with a competitor-resistant but apparently unlooped conformation.Biophysical journal · 2014Article
- Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion.Nucleic acids research · 2014Article
- Article
- Variational Bayes analysis of a photon-based hidden Markov model for single-molecule FRET trajectories.Biophysical journal · 2012Article
- Sequence dependence of transcription factor-mediated DNA looping.Nucleic acids research · 2012Article
- FRET studies of a landscape of Lac repressor-mediated DNA loops.Nucleic acids research · 2012Article
- Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging.Annual review of physical chemistry · 2012Review
- A photoprotection strategy for microsecond-resolution single-molecule fluorescence spectroscopy.Nature methods · 2011Article
- Wrapped-around models for the lac operon complex.Biophysical journal · 2010Article
- DNA curvature and flexibility in vitro and in vivo.Quarterly reviews of biophysics · 2010Review
- Tetramer opening in LacI-mediated DNA looping.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- First-principles calculation of DNA looping in tethered particle experiments.Physical biology · 2009Article
- Monitoring Simultaneous Distance and Orientation Changes in Discrete Dimers of DNA Linked Gold Nanoparticles.The journal of physical chemistry. C, Nanomaterials and interfaces · 2009Article
- Article
- Computational analysis of looping of a large family of highly bent DNA by LacI.Biophysical journal · 2008Article
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
No grant is acknowledged in the PubMed record.
Abstract
The Escherichia coli lactose repressor protein (LacI) provides a classic model for understanding protein-induced DNA looping. LacI has a C-terminal four-helix bundle tetramerization domain that may act as a flexible hinge. In previous work, several DNA constructs, each containing two lac operators bracketing a sequence-induced bend, were designed to stabilize different possible looping geometries. The resulting hyperstable LacI-DNA loops exist as both a compact "closed" form with a V-shaped repressor and also a more "open" form with an extended hinge. The "9C14" construct was of particular interest because footprinting, electrophoretic mobility shift, and ring closure experiments suggested that it forms both geometries. Previous fluorescence resonance energy transfer (FRET) measurements gave an efficiency of energy transfer (ET) of 70%, confirming the existence of a closed form. These measurements could not determine whether open form or intermediate geometries are populated or the timescale of interconversion. We have now applied single-molecule FRET to Cy3, Cy5 double-labeled LacI-DNA loops diffusing freely in solution. By using multiple excitation wavelengths and by carefully examining the behavior of the zero-ET peak during titration with LacI, we show that the LacI-9C14 loop exists exclusively in a single closed form exhibiting essentially 100% ET.
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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.