ArticleNucleic acids research2012
FRET studies of a landscape of Lac repressor-mediated DNA loops.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 24 citations in OpenAlex.
- Visualizing poloidal orientation in DNA minicircles.Biophysical journal · 2026Article
- Designed architectural proteins that tune DNA looping in bacteria.Nucleic acids research · 2021Article
- Base-Pair Mismatch Can Destabilize Small DNA Loops through Cooperative Kinking.Physical review letters · 2019Article
- Bacterial gene control by DNA looping using engineered dimeric transcription activator like effector (TALE) proteins.Nucleic acids research · 2018Article
- Optimized expression and purification of biophysical quantities of Lac repressor and Lac repressor regulatory domain.Protein expression and purification · 2016Article
- DNA topology confers sequence specificity to nonspecific architectural proteins.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Tethered particle motion reveals that LacI·DNA loops coexist with a competitor-resistant but apparently unlooped conformation.Biophysical journal · 2014Article
- Lac repressor mediated DNA looping: Monte Carlo simulation of constrained DNA molecules complemented with current experimental results.PloS one · 2014Article
- Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion.Nucleic acids research · 2014Article
- DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation.Physical biology · 2013Article
- Rationally designed coiled-coil DNA looping peptides control DNA topology.Nucleic acids research · 2013Article
- Structural insights into the role of architectural proteins in DNA looping deduced from computer simulations.Biochemical Society transactions · 2013Review
- Mechanism of promoter repression by Lac repressor-DNA loops.Nucleic acids research · 2013Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA looping mediated by the Lac repressor is an archetypal test case for modeling protein and DNA flexibility. Understanding looping is fundamental to quantitative descriptions of gene expression. Systematic analysis of LacI•DNA looping was carried out using a landscape of DNA constructs with lac operators bracketing an A-tract bend, produced by varying helical phasings between operators and the bend. Fluorophores positioned on either side of both operators allowed direct Förster resonance energy transfer (FRET) detection of parallel (P1) and antiparallel (A1, A2) DNA looping topologies anchored by V-shaped LacI. Combining fluorophore position variant landscapes allows calculation of the P1, A1 and A2 populations from FRET efficiencies and also reveals extended low-FRET loops proposed to form via LacI opening. The addition of isopropyl-β-D-thio-galactoside (IPTG) destabilizes but does not eliminate the loops, and IPTG does not redistribute loops among high-FRET topologies. In some cases, subsequent addition of excess LacI does not reduce FRET further, suggesting that IPTG stabilizes extended or other low-FRET loops. The data align well with rod mechanics models for the energetics of DNA looping topologies. At the peaks of the predicted energy landscape for V-shaped loops, the proposed extended loops are more stable and are observed instead, showing that future models must consider protein flexibility.
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