Cited by 41DNA and Nucleic Acid ChemistryForce Microscopy Techniques and ApplicationsProtein Structure and Dynamics

Structural ensemble and microscopic elasticity of freely diffusing DNA by direct measurement of fluctuations

Open access
Shi, Xuesong, Herschlag, Daniel, Harbury, Pehr A. B.·2013·Proceedings of the National Academy of Sciences

Abstract

Significance: Deformation of the double helix is a ubiquitous feature of the protein–DNA interactions that regulate, replicate, repair, and pack DNA in cells. Understanding the energetics of DNA deformation is therefore of central importance. DNA is generally modeled as a linear elastic rod, but it has not been possible to test this directly by observing the nanometer-scale bending and twisting of the helix. Using an X-ray interferometry technique, we measured the structural fluctuations of a short B-form duplex. The results expose a potential nonlinearity of DNA elasticity and illustrate how to measure the structural ensemble of a freely diffusing macromolecule.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1073/pnas.1218830110

Cites

54 of 54 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 1

  1. Zhang Y, et al. (2010) Evidence against a genomic code for nucleosome positioning. Nat Struct Mol Biol 17(8):920-923.

Cited by

Sorted by citations

Authors
Shi, X., Herschlag, D., & Harbury, P. A. B.
Affiliations
  • Stanford University (US)
  • Department of Biochemistry, Stanford University, Stanford, CA 94305
Venue
Proceedings of the National Academy of Sciences
Published
2013-04
Volume
110
Issue
16
Pages
E1444-51
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
OpenAlex
W2126505866
Cited by
41
References
54
Citations by year
2024: 3 · 2023: 3 · 2022: 2 · 2021: 3 · 2020: 3 · 2019: 4 · 2018: 2 · 2017: 2 · 2016: 5 · 2015: 7 · 2014: 4 · 2013: 3
FWCI
2.84
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • National Institutes of Health (DP1OD000429, GM49243)
  • National Institute of General Medical Sciences (P01GM066275, R37GM049243, GM49243, R01GM068126, R01GM049243)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
  • Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Force Microscopy Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
B-DNA, DNA elasticity, torsional stiffness, X-ray interferometry, protein-DNA interactions, polymer mechanics, DNA stretching
MeSH terms
Diffusion, DNA, DNA-Binding Proteins, Interferometry, Models, Molecular, Nucleic Acid Conformation

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review