Evidence map›Paper›PMID 40215227›Full record

ArticleAngewandte Chemie (International ed. in English)2025

An A-T Hoogsteen Base Pair in a Naked DNA Hairpin Motif: A Protein-Recognized Conformation.

Serafima Guseva, Or Szekely, Ainan Geng, Kai Smith, Supriya Pratihar, Yeongjoon Lee, Linshu Li, Sophie M Korn, Stephanie Gu, Hashim M Al-Hashimi

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Angewandte Chemie (International ed. in English), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Nature communications · 2026
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Serafima Guseva *Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
Or Szekely *Department of Biology, Duke University, Durham, NC, 27710, USA.
Ainan GengDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
Kai SmithDepartment of Biomedical Engineering, University of Arizona, Tuscon, AZ, 85721, USA.
Supriya PratiharDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
Yeongjoon LeeDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
Linshu LiDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
Sophie M KornDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
Stephanie GuDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
Hashim M Al-HashimiDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.

Funding

The Center for HIV RNA Studies (CRNA)P50GM103297 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI AL-HASHIMI, HASHIM M · 2012 to 2016
$21.7M
RM1 Center on Macromolecular Dynamics by NMR Spectroscopy at the New York Structural Biology Center (CoMD/NMR)- Equipment Supplement RequestRM1GM145397 · NIGMS · NEW YORK STRUCTURAL BIOLOGY CENTER · PI ARTHUR G PALMER · 2022 to 2026
$8.3M
Role of DNA structural dynamics in mutagenesis and oncogenesisR01GM089846 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Hashim M Al-Hashimi · 2010 to 2026
$5.2M
900 MHz NMR Spectrometer for Structural BiologyP41GM066354 · NIGMS · NEW YORK STRUCTURAL BIOLOGY CENTER · PI COWBURN, DAVID · 2002 to 2006
$4.7M
Acquisition of a 900 MHz NMR Spectrometer Console and ProbesS10OD030373 · OD · NEW YORK STRUCTURAL BIOLOGY CENTER · PI PALMER, ARTHUR G · 2021 to 2021
$1.7M
Acquisition of an 800 MHz TXO CryoProbeS10OD028577 · OD · NEW YORK STRUCTURAL BIOLOGY CENTER · PI PALMER, ARTHUR G · 2020 to 2020
$299k
American Cancer Society PF-24-1250040-01-DMCNIGMS NIH HHS P41 GM066354NIGMS NIH HHS P50 GM103297NIGMS NIH HHS R01 GM089846NIGMS NIH HHS RM1 GM145397NIH HHS S10 OD028577NIH HHS S10 OD030373NIH HHS S10OD030373NIH National Institute of General Medical Sciences RM1GM145397the NIH National Institute of General Medical Sciences P41GM066354the NIH National Institute of General Medical Sciences R01GM089846
6 · The paper itself

Abstract

In duplex DNA, A-T and G-C form Watson-Crick base pairs, and Hoogsteen pairing only dominates upon protein binding or DNA damage. Using NMR, we show that an A-T Hoogsteen base pair previously observed in crystal structures of transposon DNA hairpins bound to TnpA protein forms in solution even in the absence of TnpA. This Hoogsteen base pair, located adjacent to a dinucleotide apical loop, exists in dynamic equilibrium with a minor Watson-Crick conformation (population ∼11% and lifetime ∼55 µs). Extending the apical loop to three residues inverted the equilibrium, making Watson-Crick the dominant state and the Hoogsteen conformation recognized by TnpA a minor state (population ∼14% and lifetime ∼28 µs). The propensity for Hoogsteen pairing depended on apical loop residues, which form contacts directly or indirectly stabilizing the Hoogsteen conformation. A structure survey did not reveal Hoogsteen pairing near RNA apical loops making them unique to DNA. Our results demonstrate that Hoogsteen can be the dominant state even in naked unmodified duplex DNA and identify 5'-CTT(T/C)AG-3' as a DNA-specific apical loop motif stabilized by Hoogsteen pairing. Hoogsteen base pairs may be prevalent in DNA hairpins forming during replication and transcription, with broad implications for the genomic landscape.

Indexed as

DNABase PairingNucleic Acid ConformationDNADNA dynamicsDNA shapeNMRProtein‐DNA recognitionRelaxation dispersionTransposable elements

Identifiers

PMID40215227
PMCPMC12173782

What OpenQuestion holds

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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.