Evidence map›Paper›PMID 41261770›Full record

ArticleBiophysical journal2026

NMR and molecular dynamics demonstrate the RNA internal loop GAGU is dynamic and adjacent basepairs determine conformational preference.

Olayinka Akinyemi, Scott D Kennedy, James P McSally, David H Mathews

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Biophysical journal, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Reparameterization of the Amber RNA Force Field Non-Bonded Terms.bioRxiv : the preprint server for biology · 2026
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Olayinka AkinyemiCenter for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
Scott D KennedyCenter for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
James P McSallyCenter for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
David H MathewsCenter for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York; Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York. Electronic address: david_mathews@urmc.rochester.edu.

Funding

RNA Structure Modeling Using Physics and Sequence ComparisonR35GM145283 · NIGMS · UNIVERSITY OF ROCHESTER · PI DAVID H. MATHEWS · 2022 to 2026
$2.7M
NIGMS NIH HHS R35 GM145283
6 · The paper itself

Abstract

The conformational variability of RNA duplexes with internal loop 5'GAGU/3'UGAG was investigated by nuclear magnetic resonance (NMR) spectroscopy and all-atom molecular dynamics (MD) simulations. It was previously found that the CG-flanked internal loop in 5'GACGAGUGUCA/3'ACUGUGAGCAG existed in a major conformation (I) characterized by U7 and U7

Indexed as

Base PairingMolecular Dynamics SimulationNucleic Acid ConformationRNAHydrogen BondingMagnetic Resonance SpectroscopyRNA

Identifiers

PMID41261770
PMCPMC12821006

What OpenQuestion holds

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Registered trials

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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.