ReviewBiophysical reviews2021
Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?
Review in Biophysical reviews, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed, 42 citations in OpenAlex.
- hexABC seeking the physical code of DNA.Nature communications · 2026Article
- cgNA+min: computation of sequence-dependent dsDNA energy-minimizing minicircles.Nucleic acids research · 2026Article
- Modular Scaffold Crystals for Programmable Installation and Structural Observation of DNA-Binding Proteins.bioRxiv : the preprint server for biology · 2026Article
- Computational Analysis of a Next-Generation Platinum-Based Chemotherapies that Induce DNA Double-Strand Breaks.Journal of chemical information and modeling · 2026Article
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- Predicting rare DNA conformations via dynamical graphical models: a case study of the B→A transition.Nucleic acids research · 2025Article
- Combining Cyclic Triimidazo Triazine Core With Ethynyl-N-Methyl-Pyridinium Groups for Targeting G-Quadruplex Structures.Archiv der Pharmazie · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- The need to implement FAIR principles in biomolecular simulations.Nature methods · 2025Article
- Computational identification of ultra-conserved elements in the human genome: a hypothesis on homologous DNA pairing.NAR genomics and bioinformatics · 2024Article
- CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes.Nucleic acids research · 2024Article
- Multiscale simulations of DNA from electrons to nucleosomes: 22 years of the Ascona B-DNA Consortium.Biophysical reviews · 2024Review
- Special issue: Multiscale simulations of DNA from electrons to nucleosomes.Biophysical reviews · 2024Article
- The nucleosome reference frame and standard geometries for octasomes.Biophysical reviews · 2024Review
- Temperature-dependent elasticity of DNA, RNA, and hybrid double helices.Biophysical journal · 2024Article
- How acidic amino acid residues facilitate DNA target site selection.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution.Nature structural & molecular biology · 2022Article
- Searching for Low Probability Opening Events in a DNA Sliding Clamp.Life (Basel, Switzerland) · 2022Article
- Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation.PLoS computational biology · 2022Article
Corrections and comments
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Authors and funding
26 authors at 12 institutions in 9 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational changes that lead to local and global changes in the helix geometry are mediated by a complex choreography of base and backbone rearrangements affecting the ability of the B-DNA to recognize ligands and consequently on its functionality. In this sense, the knowledge obtained from the sequence-dependent structural properties of B-DNA has always been thought crucial to rationalize how ligands and, most notably, proteins recognize B-DNA and modulate its activity, i.e. the structural basis of gene regulation. Honouring the anniversary of the first high-resolution X-ray structure of a B-DNA molecule, in this contribution, we present the most important discoveries of the last 40 years on the sequence-dependent structural and dynamical properties of B-DNA, from the early beginnings to the current frontiers in the field.
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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.