ArticlePloS one2006
Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping.
Article in PloS one, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology.Sensors (Basel, Switzerland) · 2020Review
- Characterization of Gene Repression by Designed Transcription Activator-like Effector Dimer Proteins.Biophysical journal · 2020Article
- Loop-closure kinetics reveal a stable, right-handed DNA intermediate in Cre recombination.Nucleic acids research · 2020Article
- Identifying Physical Causes of Apparent Enhanced Cyclization of Short DNA Molecules with a Coarse-Grained Model.Journal of chemical theory and computation · 2019Article
- Self-consistent theory of transcriptional control in complex regulatory architectures.PloS one · 2017Article
- DNA cyclization and looping in the wormlike limit: Normal modes and the validity of the harmonic approximation.Biopolymers · 2015Article
- Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics.Biophysical journal · 2015Article
- High-resolution mapping of architectural DNA binding protein facilitation of a DNA repression loop in Escherichia coli.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Plectoneme tip bubbles: coupled denaturation and writhing in supercoiled DNA.Scientific reports · 2015Article
- DNA topology confers sequence specificity to nonspecific architectural proteins.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins.Biochemistry · 2014Article
- What controls DNA looping?International journal of molecular sciences · 2014Article
- Design and analysis of LacI-repressed promoters and DNA-looping in a cyanobacterium.Journal of biological engineering · 2014Article
- Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and λ repressors.Proceedings of the National Academy of Sciences of the United States of America · 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
- Structural insights into the role of architectural proteins in DNA looping deduced from computer simulations.Biochemical Society transactions · 2013Review
- Spacing between core recognition motifs determines relative orientation of AraR monomers on bipartite operators.Nucleic acids research · 2013Article
- Mechanism of promoter repression by Lac repressor-DNA loops.Nucleic acids research · 2013Article
- Theoretical and experimental dissection of DNA loop-mediated repression.Physical review letters · 2013Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Interactions of E. coli lac repressor (LacR) with a pair of operator sites on the same DNA molecule can lead to the formation of looped nucleoprotein complexes both in vitro and in vivo. As a major paradigm for loop-mediated gene regulation, parameters such as operator affinity and spacing, repressor concentration, and DNA bending induced by specific or non-specific DNA-binding proteins (e.g., HU), have been examined extensively. However, a complete and rigorous model that integrates all of these aspects in a systematic and quantitative treatment of experimental data has not been available. Applying our recent statistical-mechanical theory for DNA looping, we calculated repression as a function of operator spacing (58-156 bp) from first principles and obtained excellent agreement with independent sets of in-vivo data. The results suggest that a linear extended, as opposed to a closed v-shaped, LacR conformation is the dominant form of the tetramer in vivo. Moreover, loop-mediated repression in wild-type E. coli strains is facilitated by decreased DNA rigidity and high levels of flexibility in the LacR tetramer. In contrast, repression data for strains lacking HU gave a near-normal value of the DNA persistence length. These findings underscore the importance of both protein conformation and elasticity in the formation of small DNA loops widely observed in vivo, and demonstrate the utility of quantitatively analyzing gene regulation based on the mechanics of nucleoprotein complexes.
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