ArticleProceedings of the National Academy of Sciences of the United States of America2013
Structural ensemble and microscopic elasticity of freely diffusing DNA by direct measurement of fluctuations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 43 citations in OpenAlex.
- Determination of absolute intramolecular distances in proteins using anomalous X-ray scattering interferometry.Nanoscale · 2025Article
- Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2024Article
- Mapping the Morphology of DNA on Carbon Nanotubes in Solution Using X-ray Scattering Interferometry.Journal of the American Chemical Society · 2024Article
- Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2022Article
- Monitoring Nuclease Activity by X-Ray Scattering Interferometry Using Gold Nanoparticle-Conjugated DNA.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The structural ensemble of a Holliday junction determined by X-ray scattering interference.Nucleic acids research · 2020Article
- Halogen bonding and host-guest chemistry betweenBeilstein journal of organic chemistry · 2019Article
- Recording and Analyzing Nucleic Acid Distance Distributions with X-Ray Scattering Interferometry (XSI).Current protocols in nucleic acid chemistry · 2018Article
- Gold nanocrystal labels provide a sequence-to-3D structure map in SAXS reconstructions.Science advances · 2018Article
- Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry.Nucleic acids research · 2017Article
- Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell.Chemical reviews · 2016Review
- Sequence Affects the Cyclization of DNA Minicircles.The journal of physical chemistry letters · 2016Article
- The solution structural ensembles of RNA kink-turn motifs and their protein complexes.Nature chemical biology · 2016Article
- Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.Journal of the American Chemical Society · 2015Article
- Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs.The journal of physical chemistry. B · 2015Article
- From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function.Current opinion in structural biology · 2015Review
- Blind predictions of DNA and RNA tweezers experiments with force and torque.PLoS computational biology · 2014Article
- From a structural average to the conformational ensemble of a DNA bulge.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Advances in the determination of nucleic acid conformational ensembles.Annual review of physical chemistry · 2014Review
- Probing the elastic limit of DNA bending.Nucleic acids research · 2014Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Precisely measuring the ensemble of conformers that a macromolecule populates in solution is highly challenging. Thus, it has been difficult to confirm or falsify the predictions of nanometer-scale dynamical modeling. Here, we apply an X-ray interferometry technique to probe the solution structure and fluctuations of B-form DNA on a length scale comparable to a protein-binding site. We determine an extensive set of intrahelix distance distributions between pairs of probes placed at distinct points on the surface of the DNA duplex. The distributions of measured distances reveal the nature and extent of the thermally driven mechanical deformations of the helix. We describe these deformations in terms of elastic constants, as is common for DNA and other polymers. The average solution structure and microscopic elasticity measured by X-ray interferometry are in striking agreement with values derived from DNA-protein crystal structures and measured by force spectroscopy, with one exception. The observed microscopic torsional rigidity of DNA is much lower than is measured by single-molecule twisting experiments, suggesting that torsional rigidity increases when DNA is stretched. Looking forward, molecular-level interferometry can provide a general tool for characterizing solution-phase structural ensembles.
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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.