ArticleThe journal of physical chemistry. B2021
Synergy between Protein Positioning and DNA Elasticity: Energy Minimization of Protein-Decorated DNA Minicircles.
Article in The journal of physical chemistry. B, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 4 citations in OpenAlex.
- Physical genomics: Why gene regulation is tug of war between polymer physics and biochemistry.Current opinion in structural biology · 2026Review
- Contributions of Local Structural and Energetic Features of DNA to Large-scale Genomic Organization.Journal of molecular biology · 2026Review
- emDNA - A Tool for Modeling Protein-decorated DNA Loops and Minicircles at the Base-pair Step Level.Journal of molecular biology · 2022Article
- Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration.Life (Basel, Switzerland) · 2022Article
- Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF.Computational and structural biotechnology journal · 2022Article
- Designed architectural proteins that tune DNA looping in bacteria.Nucleic acids research · 2021Article
- Surprising Twists in Nucleosomal DNA with Implication for Higher-order Folding.Journal of molecular biology · 2021Article
- Insights into Genome Architecture Deduced from the Properties of Short Lac Repressor-mediated DNA Loops.Biophysical reviews · 2016Article
- Search by proteins for their DNA target site: 2. The effect of DNA conformation on the dynamics of multidomain proteins.Nucleic acids research · 2014Article
- What controls DNA looping?International journal of molecular sciences · 2014Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The binding of proteins onto DNA contributes to the shaping and packaging of the genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation of DNA involved in such processes, we developed a new method to minimize the elastic energy of DNA fragments at the mesoscale level. Our method makes it possible to obtain the optimal pathways of protein-decorated DNA molecules for which the terminal base pairs are spatially constrained. We focus in this work on the deformations induced by selected architectural proteins on circular DNA. We report the energy landscapes of DNA minicircles subjected to different levels of torsional stress and containing one or two proteins as functions of the chain length and spacing between the proteins. Our results reveal cooperation between the elasticity of the double helix and the structural distortions of DNA induced by bound proteins. We find that the imposed mechanical stress influences the placement of proteins on DNA and that the proteins, in turn, modulate the mechanical stress and thereby broadcast their presence along DNA.
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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.