ArticleProceedings of the National Academy of Sciences of the United States of America2010
Sequence dependence of DNA bending rigidity.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
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Who cites it
100 citing papers in PubMed.
- Visualizing poloidal orientation in DNA minicircles.Biophysical journal · 2026Article
- Crowding-induced collapse and adsorption of polymers with nonuniform bending stiffness.Soft matter · 2026Article
- Ring-Electrode AC Plasmonic Nanopore Sensing for DNA Load Characterization of Single Adeno-Associated Viruses.Sensors (Basel, Switzerland) · 2026Article
- Searching for sequence features that control DNA cyclizability.PNAS nexus · 2026Article
- DNA Cut-Ligation Cyclization Surpasses Jacobson-Stockmayer J-Factor Expectations by over Threefold.Biomolecules · 2026Article
- Physics-based nucleosome-resolution modeling of epigenetic-driven chromatin domain dynamics.Nucleic acids research · 2026Article
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.Journal of chemical theory and computation · 2026Article
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.bioRxiv : the preprint server for biology · 2025Article
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- Crowding-induced collapse and adsorption of polymers with nonuniform bending stiffness.bioRxiv : the preprint server for biology · 2025Article
- Deep learning guided programmable design of Escherichia coli core promoters from sequence architecture to strength control.Nucleic acids research · 2025Article
- DNAcycP2: improved estimation of intrinsic DNA cyclizability through data augmentation.Nucleic acids research · 2025Article
- Influence of Media Disorder on DNA Melting: A Monte Carlo Study.Journal of chemical theory and computation · 2025Article
- Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells.Discover nano · 2025Article
- Molecular basis for the transcriptional regulation of an epoxide-based virulence circuit in Pseudomonas aeruginosa.Nucleic acids research · 2024Article
- Molecular mechanism of parental H3/H4 recycling at a replication fork.Nature communications · 2024Article
- PeculiarGenes · 2024Article
- Depletion of CpG dinucleotides in bacterial genomes may represent an adaptation to high temperatures.NAR genomics and bioinformatics · 2024Article
- Nucleosomal DNA has topological memory.Nature communications · 2024Article
- Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2024Article
40 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
For many aspects of DNA-protein interaction, it is vital to know how DNA bending rigidity (or persistence length, a) depends on its sequence. We addressed this problem using the method based on cyclization of short DNA fragments, which allows very accurate determination of a. Our approach was based on assigning specific values of a to each of 10 distinct dinucleotide steps. We prepared DNA fragments, each about 200 bp in length, with various quasi-periodic sequences, measured their cyclization efficiencies (j factors), and fitted the data by the theoretical equation to obtain the values of a for each fragment. From these data, we obtained a set of a for the dinucleotide steps. To test this set, we used it to design DNA sequences that should correspond to very low and very high values of a, prepared the corresponding fragments, and determined their values of a experimentally. The measured and calculated values of a were very close to one another, confirming that we have found the correct solution to this long-standing problem. The same experimental data also allowed us to determine the sequence dependence of DNA helical repeat.
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