Cited by 211RNA and protein synthesis mechanismsProtein Structure and DynamicsDNA and Nucleic Acid Chemistry

Molecular crowding stabilizes folded RNA structure by the excluded volume effect

Open access
Kilburn, Duncan, Roh, Joon Ho, Guo, Liang, Briber, Robert M., Woodson, Sarah A.·2010·Journal of the American Chemical Society

Abstract

Crowder molecules in solution alter the equilibrium between folded and unfolded states of biological macromolecules. It is therefore critical to account for the influence of these other molecules when describing the folding of RNA inside the cell. Small angle X-ray scattering experiments are reported on a 64 kDa bacterial group I ribozyme in the presence of polyethylene-glycol 1000 (PEG-1000), a molecular crowder with an average molecular weight of 1000 Da. In agreement with expected excluded volume effects, PEG favors more compact RNA structures. First, the transition from the unfolded to the folded (more compact) state occurs at lower MgCl(2) concentrations in PEG. Second, the radius of gyration of the unfolded RNA decreases from 76 to 64 A as the PEG concentration increases from 0 to 20% wt/vol. Changes to water and ion activities were measured experimentally, and theoretical models were used to evaluate the excluded volume. We conclude that the dominant influence of the PEG crowder on the folding process is the excluded volume effect.

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 · 10.1021/ja101500g

Cites

48 of 48 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?

  • Crowding effects contribute to the folding stability of ribozymes and reduce the effect of otherwise deleterious mutations.

    “since crowding effects contribute to the folding stability of ribozymes [144–148] and reduce the effect of otherwise deleterious mutations [149].”

    From The RNA world as a model system to study the origin of life (2015) · cites this paper as [146]

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: 3

  1. [27]Le Cour C Demé B Longeville S Phys Rev E 2009 79 031910 19391974
  2. [29]Tanner M Cech T RNA 1996 2 74 8846298 PMC1369352
  3. [41]Tanner MA Cech TR RNA 1996 2 74 8846298 PMC1369352

Cited by

Sorted by citations

Authors
Kilburn, D., Roh, J. H., Guo, L., Briber, R. M., & Woodson, S. A.
Affiliations
National Institute of Standards and Technology (US)
Corresponding author
  • Briber, Robert M.
  • Woodson, Sarah A.
Venue
Journal of the American Chemical Society
Published
2010-06-03
Volume
132
Issue
25
Pages
8690-8696
ISSN
  • 0002-7863 (ISSN-L)
  • 1520-5126
OpenAlex
W2069122773
Cited by
211
References
48
Citations by year
2026: 10 · 2025: 12 · 2024: 15 · 2023: 10 · 2022: 15 · 2021: 15 · 2020: 12 · 2019: 10 · 2018: 10 · 2017: 13 · 2016: 11 · 2015: 12 · 2014: 16 · 2013: 22 · 2012: 12
FWCI
6.51
Type
journal article
Language
en
Open access
Locations
  • Journal of the American Chemical Society (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • National Institute of General Medical Sciences (GM60819, R01GM060819)
  • National Center for Research Resources (P41RR008630, RR08630)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
Keywords
macromolecular crowding, RNA folding, excluded volume, group I ribozyme, polyethylene glycol, radius of gyration, magnesium ions, small-angle X-ray scattering
MeSH terms
Dose-Response Relationship, Drug, Nucleic Acid Conformation, Polyethylene Glycols, Water, X-Ray Diffraction, Magnesium Chloride, RNA, Catalytic, Azoarcus, RNA Stability, Scattering, Small Angle

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