ArticleProceedings of the National Academy of Sciences of the United States of America2003
High-throughput approach for detection of DNA bending and flexibility based on cyclization.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Special issue: Multiscale simulations of DNA from electrons to nucleosomes.Biophysical reviews · 2024Article
- A molecular mechanism for the "digital" response of p53 to stress.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- DNA strand breaks and gaps target retroviral intasome binding and integration.Nature communications · 2023Article
- The complex architecture of p53 binding sites.Nucleic acids research · 2021Article
- Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology.Sensors (Basel, Switzerland) · 2020Review
- Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules.Sensors (Basel, Switzerland) · 2020Article
- Identifying Physical Causes of Apparent Enhanced Cyclization of Short DNA Molecules with a Coarse-Grained Model.Journal of chemical theory and computation · 2019Article
- Diverse p53/DNA binding modes expand the repertoire of p53 response elements.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Orientation-dependent FRET system reveals differences in structures and flexibilities of nicked and gapped DNA duplexes.Nucleic acids research · 2017Article
- Production of DNA minicircles less than 250 base pairs through a novel concentrated DNA circularization assay enabling minicircle design with NF-κB inhibition activity.Nucleic acids research · 2017Article
- Simulation of DNA Supercoil Relaxation.Biophysical journal · 2016Article
- DNA cyclization and looping in the wormlike limit: Normal modes and the validity of the harmonic approximation.Biopolymers · 2015Article
- Key determinants of target DNA recognition by retroviral intasomes.Retrovirology · 2015Article
- Article
- Measurements of DNA-loop formation via Cre-mediated recombination.Nucleic acids research · 2012Article
- DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics.Nucleic acids research · 2012Article
- Sequence-dependent cooperative binding of p53 to DNA targets and its relationship to the structural properties of the DNA targets.Nucleic acids research · 2011Article
- Quantitative methods for measuring DNA flexibility in vitro and in vivo.Methods in enzymology · 2011Article
- Gel mobilities of linking-number topoisomers and their dependence on DNA helical repeat and elasticity.Biophysical chemistry · 2010Article
- DNA curvature and flexibility in vitro and in vivo.Quarterly reviews of biophysics · 2010Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
We have developed a high-throughput approach to the labor-intensive problems of DNA cyclization, which we use to characterize DNA curvature and mechanical properties. The method includes a combinatorial approach to make the DNA constructs needed and automated real-time measurement of the kinetics using fluorescence. We validated the approach and investigated the flexibility of two kinds of nicked DNA and AT dinucleotide repeats. We found that, although the nicks hardly alter the bending flexibility, they significantly increase the torsional flexibility, and that the AT repeat has 28% (+/-12%) lower bending rigidity than a generic DNA sequence.
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