Discover Community Create You

Loading publication...

Noodle always counts identifier-free feature events for service operation. With your permission, Google Analytics can also estimate audience and engagement. Search text, publication identifiers, cookies, IP addresses and browser fingerprints are never included in Noodle's first-party event counters.

Privacy details

Article

Revealing hidden protonated conformational states in RNA dynamic ensembles.

Nucleic acids research - 26 Nov 2025

Geng Ainan, Roy Rohit, Ganser Laura, Li Linshu, Al-Hashimi Hashim M

Abstract excerpt

Identifying protonated states within RNA ensembles, quantifying their pKas, and elucidating the kinetic mechanisms by which they form is essential for understanding protonation-coupled biochemical reactions and how RNAs sense and adapt to pH fluctuations. However, detecting protonated states is challenging when they are short-lived and lowly populated. Here, using pH-dependent NMR chemical exchange, kinetic...

Read the complete abstract on PubMed

Topics

Share this publication in a Topic to start or enrich a Post.

Share to Base Pair Mismatch
Share to Base Pairing
Share to HIV-1

Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

Share to HIV Long Terminal Repeat

Share to Hydrogen-Ion Concentration

Share to Nuclear Magnetic Resonance, Biomolecular

Share to Nucleic Acid Conformation

Share to Protons

Source

Open in PubMed Open full text

Identifiers

PMID: 41414670
DOI: 10.1093/nar/gkaf1366
PMCID: PMC12714568

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 7 Sept 2026.

Related research

Semantic proximity does not establish scientific evidence.

Research trail→

Click a neighbor to travelStep 1 · 12 closest

Revealing hidden protonated conformational states in RNA dynamic ensembles.PMID 41414670Read ↗

Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes.Semantic proximity Read ↗

Visualizing a protonated RNA state that modulates microRNA-21 maturation.Semantic proximity Read ↗

Activation of the influenza B M2 proton channel (BM2)Semantic proximity Read ↗

Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch.Semantic proximity Read ↗

High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states.Semantic proximity Read ↗

Activation of the Influenza B M2 Proton Channel (BM2).Semantic proximity Read ↗

Trapped water molecules are essential to structural dynamics and function of a ribozyme.Semantic proximity Read ↗

Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme.Semantic proximity Read ↗

Chemical shift prediction of RNA imino groups: application toward characterizing RNA excited states.Semantic proximity Read ↗

Structural dynamics as a contributor to error-prone replication by an RNA-dependent RNA polymerase.Semantic proximity Read ↗

Constant-pH MD simulations of the protonation-triggered conformational switching in diphtheria toxin translocation domain.Semantic proximity Read ↗

The A2453-C2499 wobble base pair in Escherichia coli 23S ribosomal RNA is responsible for pH sensitivity of the peptidyltransferase active site conformation.Semantic proximity Read ↗

⌁Select a neighboring publication to make it the new centre.