Evidence map›Paper›PMID 42182257›Full record

ArticlebioRxiv : the preprint server for biology2026

Nearest Neighbor Parameters for Estimating the Folding Stability of RNA Including Pseudouridine.

Thandolwethu S Shabangu, Elzbieta Kierzek, Sebastian Arteaga, Gregory S Orf, Julia Stone, Olivia M Hiltke, Megan Miaro, Elizabeth A Jolley, Marta Soszyńska-Jóźwiak, Marta Szabat and 5 more

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PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

15 authors.

Thandolwethu S ShabanguDepartment of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14526, USA.
Elzbieta KierzekInstitute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Sebastian ArteagaDepartment of Chemistry, Saint Louis University, Saint Louis, Missouri 63103, USA.
Gregory S OrfDepartment of Chemistry, Saint Louis University, Saint Louis, Missouri 63103, USA.
Julia StoneDepartment of Chemistry, Saint Louis University, Saint Louis, Missouri 63103, USA.
Olivia M HiltkeDepartment of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14526, USA.
Megan MiaroDepartment of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14526, USA.
Elizabeth A JolleyDepartment of Chemistry and Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
Marta Soszyńska-JóźwiakInstitute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Marta SzabatInstitute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Sharon AviranBiomedical Engineering Department and Genome Center, University of California Davis, Davis, California 95616, USA.ORCID 0000-0003-1872-9820
Philip C BevilacquaDepartment of Chemistry and Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA.ORCID 0000-0001-8074-3434
Brent M ZnoskoDepartment of Chemistry, Saint Louis University, Saint Louis, Missouri 63103, USA.
Ryszard KierzekInstitute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
David H MathewsDepartment of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14526, USA.ORCID 0000-0002-2907-6557

Funding

RNA folding and catalysis at the interface of biophysics and genomicsR35GM127064 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI PHILIP C BEVILACQUA · 2018 to 2026
$3.4M
Training in Wellness and Resiliency at the University of Rochester Medical Center and College of Arts, Sciences & EngineeringT32GM135134 · NIGMS · UNIVERSITY OF ROCHESTER · PI Jeffrey J Hayes, Lynne E Maquat · 2020 to 2026
$2.9M
RNA Structure Modeling Using Physics and Sequence ComparisonR35GM145283 · NIGMS · UNIVERSITY OF ROCHESTER · PI DAVID H. MATHEWS · 2022 to 2026
$2.7M
Understanding the Thermodynamics and Structure of RNA Secondary Structure MotifsR15GM085699 · NIGMS · SAINT LOUIS UNIVERSITY · PI ZNOSKO, BRENT · 2009 to 2025
$2.0M
Prediction of nearest neighbor parameters for folding RNAs with modified nucleotidesR21GM148835 · NIGMS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI AVIRAN, SHARON · 2023 to 2024
$369k
NIGMS NIH HHS R15 GM085699NIGMS NIH HHS R21 GM148835NIGMS NIH HHS R35 GM127064NIGMS NIH HHS R35 GM145283NIGMS NIH HHS T32 GM135134
6 · The paper itself

Abstract

Nearest neighbor parameters are widely used in software for estimating the conformational stability of an RNA sequence folding into a specific structure. Folding stability for RNA with canonical nucleotides A, C, G, and U has been widely studied, but the same is not true for most modified nucleotides. In this work, we present a comprehensive set of nearest neighbor parameters for estimating the folding stability of RNA including pseudouridine in helical or loop contexts. These parameters are derived from 210 optical melting experiments involving helices with pseudouridine-A and pseudouridine-G pairs and with pseudouridine in loop motifs. The experiments include sequences with pseudouridine and U in the same strand, including U-A and U-G pairs, allowing us to consider the folding stability of sequences with both U and pseudouridine. On average, pseudouridine stabilizes RNA folding compared to U in an analogous motif, although this effect is sequence-context dependent. These parameters improve the modeling of folding stability for RNA secondary structures containing pseudouridine. We demonstrate that these parameters successfully model the secondary structure change for

Identifiers

PMID42182257
PMCPMC13192807

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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.