ArticleNucleic acids research2006
Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI.
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 34 papers.
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Who cites it
34 citing papers in PubMed, 60 citations in OpenAlex.
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- Enhanced tethered-particle motion analysis reveals viscous effects.Biophysical journal · 2014Article
- Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion.Nucleic acids research · 2014Article
- Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level.International journal of molecular sciences · 2013Article
- The effect of nonspecific binding of lambda repressor on DNA looping dynamics.Biophysical journal · 2012Article
- DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations.Nucleic acids research · 2012Article
- DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics.Nucleic acids research · 2012Article
- DNA modeling reveals an extended lac repressor conformation in classic in vitro binding assays.Biophysical journal · 2011Article
- Probing DNA topology using tethered particle motion.Methods in molecular biology (Clifton, N.J.) · 2011Article
- DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme.Nucleic acids research · 2010Article
- Quantitative analysis of DNA-looping kinetics from tethered particle motion experiments.Methods in enzymology · 2010Article
- Dissecting protein-induced DNA looping dynamics in real time.Nucleic acids research · 2009Article
- Differences between Ca2+ and Mg2+ in DNA binding and release by the SfiI restriction endonuclease: implications for DNA looping.Nucleic acids research · 2009Article
- Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes.Physical review letters · 2009Article
- First-principles calculation of DNA looping in tethered particle experiments.Physical biology · 2009Article
- Article
- Type III restriction enzymes communicate in 1D without looping between their target sites.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many restriction enzymes require binding of two copies of a recognition sequence for DNA cleavage, thereby introducing a loop in the DNA. We investigated looping dynamics of Type IIE restriction enzymes NaeI and NarI by tracking the Brownian motion of single tethered DNA molecules. DNA containing two endonuclease recognition sites spaced a few 100 bp apart connect small polystyrene beads to a glass surface. The position of a bead is tracked through video microscopy. Protein-mediated looping and unlooping is then observed as a sudden specific change in Brownian motion of the bead. With this method we are able to directly follow DNA looping kinetics of single protein-DNA complexes to obtain loop stability and loop formation times. We show that, in the absence of divalent cations, NaeI induces DNA loops of specific size. In contrast, under these conditions NarI mainly creates non-specific loops, resulting in effective DNA compaction for higher enzyme concentrations. Addition of Ca2+ increases the NaeI-DNA loop lifetime by two orders of magnitude and stimulates specific binding by NarI. Finally, for both enzymes we observe exponentially distributed loop formation times, indicating that looping is dominated by (re)binding the second recognition site.
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