ArticleBiophysical journal2000
Multimerization-cyclization of DNA fragments as a method of conformational analysis.
Article in Biophysical journal, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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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, 53 citations in OpenAlex.
- Article
- A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results.Frontiers in molecular biosciences · 2021Review
- Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules.Sensors (Basel, Switzerland) · 2020Article
- Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes.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
- Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning.Nucleic acids research · 2014Article
- Bullied no more: when and how DNA shoves proteins around.Quarterly reviews of biophysics · 2012Review
- Impact of methylation on the physical properties of DNA.Biophysical journal · 2012Article
- Quantitative methods for measuring DNA flexibility in vitro and in vivo.Methods in enzymology · 2011Article
- Sequence dependence of DNA bending rigidity.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- DNA curvature and flexibility in vitro and in vivo.Quarterly reviews of biophysics · 2010Review
- Simulation of DNA catenanes.Physical chemistry chemical physics : PCCP · 2009Review
- First-principles calculation of DNA looping in tethered particle experiments.Physical biology · 2009Article
- Poly(dA:dT) tracts: major determinants of nucleosome organization.Current opinion in structural biology · 2009Review
- Computational analysis of looping of a large family of highly bent DNA by LacI.Biophysical journal · 2008Article
- Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations.Journal of molecular biology · 2008Article
- CRANKITE: A fast polypeptide backbone conformation sampler.Source code for biology and medicine · 2008Article
- Protein-induced local DNA bends regulate global topology of recombination products.Journal of molecular biology · 2007Article
- Gapped DNA and cyclization of short DNA fragments.Biophysical journal · 2005Article
- Cyclization of short DNA fragments and bending fluctuations of the double helix.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Ligation of short DNA fragments results in the formation of linear and circular multimers of various lengths. The distribution of products in such a reaction is often used to evaluate fragment bending caused by specific chemical modification, by bound ligands or by the presence of irregular structural elements. We have developed a more rigorous quantitative approach to the analysis of such experimental data based on determination of j-factors for different multimers from the distribution of the reaction products. j-Factors define the effective concentration of one end of a linear chain in the vicinity of the other end. To extract j-factors we assumed that kinetics of the reaction is described by a system of differential equations where j-factors appear as coefficients. The assumption was confirmed by comparison with experimental data obtained here for DNA fragments containing A-tracts. At the second step of the analysis j-factors are used to determine conformational parameters of DNA fragments: the equilibrium bend angle, the bending rigidity of the fragment axis, and the total twist of the fragments. This procedure is based on empirical equations that connect the conformational parameters with the set of j-factors. To obtain the equations, we computed j-factors for a large array of conformational parameters that describe model fragments. The approach was tested on both simulated and actual experimental data for DNA fragments containing A-tracts. A-tract DNA bend angle determined here is in good agreement with previously published data. We have established a set of experimental conditions necessary for the data analysis to be successful.
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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.