Evidence map›Paper›PMID 40054730›Full record

ArticleJournal of molecular biology2025

Optimized Preparation of Segmentally Labeled RNAs for NMR Structure Determination.

Brian D Grossman, Bethel G Beyene, Bersabel Tekle, William Sakowicz, Xinjie Ji, Joshua Miguele Camacho, Nandini Vaishnav, Amina Ahmed, Naman Bhandari, Kush Desai and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of molecular biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Application of NMR to Large RNAs.Journal of molecular biology · 2025
    Review
  2. Article
  3. 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

14 authors.

Brian D GrossmanHoward Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Bethel G BeyeneHoward Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Bersabel TekleHoward Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
William SakowiczHoward Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Xinjie JiHoward Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Joshua Miguele CamachoHoward Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Nandini VaishnavHoward Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Amina AhmedHoward Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Naman BhandariHoward Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Kush DesaiHoward Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Josiah HardyHoward Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Nele M HollmanHoward Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Jan MarchantHoward Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Michael F SummersHoward Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA. Electronic address: summers@umbc.edu.

Funding

Center for Structural Biology of HIV RNAU54AI170660 · NIAID · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ALICE TELESNITSKY · 2022 to 2026
$32.1M
NMR Studies of Retroviral Nucleic Acid Binding ProteinsR01AI150498 · NIAID · UNIVERSITY OF MARYLAND BALTIMORE COUNTY · PI MICHAEL FINLEY SUMMERS · 2020 to 2026
$5.1M
Howard Hughes Medical InstituteNIAID NIH HHS R01 AI150498NIAID NIH HHS U54 AI170660
6 · The paper itself

Abstract

RNA structures are significantly underrepresented in public repositories (∼ 100-fold compared to proteins) despite their importance for mechanistic understanding and for development of structure prediction/validation tools. A substantial portion of deposited RNA structures have been determined by NMR (∼30%), but most comprise fewer than 60 nucleotides due to complications associated with NMR signal overlap. A promising approach for applying NMR to larger RNAs involves use of a mutated DNA polymerase (TGK) that can extend "primer" RNA strands generated independently by synthetic or enzymatic methods [Haslecker et al., Nature Commun. 2023]. In attempts to employ this technology, we uncovered sequence- and enzyme-dependent complications for most constructs examined that prohibited preparation of homogeneous samples. By using TGK extension efficiency and NMR as guides, we identified non-templated run-on by wild-type T7-RNA polymerase (RNAP

Indexed as

Nuclear Magnetic Resonance, BiomolecularRNADNA-Directed RNA PolymerasesMagnetic Resonance SpectroscopyNucleic Acid ConformationRNA-Directed DNA PolymeraseViral Proteinsbacteriophage T7 RNA polymeraseDNA-Directed RNA PolymerasesRNARNA-Directed DNA PolymeraseViral ProteinsNMRRNAsegmental labelingT7 RNA polymeraseThermophilus gorgonarius DNA polymerase

Identifiers

PMID40054730
PMCPMC11964825

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.