ArticleBiophysical journal2003
Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization.
Article in Biophysical journal, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
46 citing papers in PubMed.
- cgNA+min: computation of sequence-dependent dsDNA energy-minimizing minicircles.Nucleic acids research · 2026Article
- Building a better bridge between models and experimental data for DNA.Biophysical journal · 2025Article
- Laplace approximation of J factors for rigid base and rigid basepair models of DNA cyclization.Biophysical journal · 2025Article
- 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
- Surprising Twists in Nucleosomal DNA with Implication for Higher-order Folding.Journal of molecular biology · 2021Article
- Synergy between Protein Positioning and DNA Elasticity: Energy Minimization of Protein-Decorated DNA Minicircles.The journal of physical chemistry. B · 2021Article
- The complex architecture of p53 binding sites.Nucleic acids research · 2021Article
- Determinants of cyclization-decyclization kinetics of short DNA with sticky ends.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
- Quantifying the impact of simple DNA parameters on the cyclization J-factor for single-basepair-addition families.Scientific reports · 2018Article
- 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
- Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization.Scientific reports · 2017Article
- The role of structural parameters in DNA cyclization.BMC bioinformatics · 2016Article
- DNA cyclization and looping in the wormlike limit: Normal modes and the validity of the harmonic approximation.Biopolymers · 2015Article
- A statistical thermodynamic model for investigating the stability of DNA sequences from oligonucleotides to genomes.Biophysical journal · 2014Article
- DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation.Physical biology · 2013Article
- Article
- Measuring shape-dependent looping probability of DNA.Biophysical journal · 2013Article
- Bullied no more: when and how DNA shoves proteins around.Quarterly reviews of biophysics · 2012Review
- DNA modeling reveals an extended lac repressor conformation in classic in vitro binding assays.Biophysical journal · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
DNA cyclization is potentially the most powerful approach for systematic quantitation of sequence-dependent DNA bending and flexibility. We extend the statistical mechanics of the homogeneous DNA circle to a model that considers discrete basepairs, thus allowing for inhomogeneity, and apply the model to analysis of DNA cyclization. The theory starts from an iterative search for the minimum energy configuration of circular DNA. Thermodynamic quantities such as the J factor, which is essentially the ratio of the partition functions of circular and linear forms, are evaluated by integrating the thermal fluctuations around the configuration under harmonic approximation. Accurate analytic expressions are obtained for equilibrium configurations of homogeneous circular DNA with and without bending anisotropy. J factors for both homogeneous and inhomogeneous DNA are evaluated. Effects of curvature, helical repeat, and bending and torsional flexibility in DNA cyclization are analyzed in detail, revealing that DNA cyclization can detect as little as one degree of curvature and a few percent change in flexibility. J factors calculated by our new approach are well consistent with Monte Carlo simulations, whereas the new theory has much greater efficiency in computations. Simulation of experimental results has been demonstrated.
Indexed as
Identifiers
What OpenQuestion holds
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.