ArticleBMC bioinformatics2016
The role of structural parameters in DNA cyclization.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Laplace approximation of J factors for rigid base and rigid basepair models of DNA cyclization.Biophysical journal · 2025Article
- DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors.Nucleic acids research · 2024Article
- Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention.bioRxiv : the preprint server for biology · 2024Article
- Article
- Examining DNA breathing with pyDNA-EPBD.Bioinformatics (Oxford, England) · 2023Article
- Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology.Sensors (Basel, Switzerland) · 2020Review
- Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization.Scientific reports · 2017Article
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Authors and funding
4 authors.
Funding
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Abstract
backgroundThe intrinsic bendability of DNA plays an important role with relevance for myriad of essential cellular mechanisms. The flexibility of a DNA fragment can be experimentally and computationally examined by its propensity for cyclization, quantified by the Jacobson-Stockmayer J factor. In this study, we use a well-established coarse-grained three-dimensional model of DNA and seven distinct sets of experimentally and computationally derived conformational parameters of the double helix to evaluate the role of structural parameters in calculating DNA cyclization.
resultsWe calculate the cyclization rates of 86 DNA sequences with previously measured J factors and lengths between 57 and 325 bp as well as of 20,000 randomly generated DNA sequences with lengths between 350 and 4000 bp. Our comparison with experimental data is complemented with analysis of simulated data.
conclusionsOur data demonstrate that all sets of parameters yield very similar results for longer DNA fragments, regardless of the nucleotide sequence, which are in agreement with experimental measurements. However, for DNA fragments shorter than 100 bp, all sets of parameters performed poorly yielding results with several orders of magnitude difference from the experimental measurements. Our data show that DNA cyclization rates calculated using conformational parameters based on nucleosome packaging data are most similar to the experimental measurements. Overall, our study provides a comprehensive large-scale assessment of the role of structural parameters in calculating DNA cyclization rates.
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