ArticleRNA (New York, N.Y.)2009
Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA.
Article in RNA (New York, N.Y.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
What it found
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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.
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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.
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Who cites it
59 citing papers in PubMed, 84 citations in OpenAlex.
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- Limits of experimental evidence in RNA secondary structure prediction.Frontiers in bioinformatics · 2024Article
- Structural analysis of MALAT1 long noncoding RNA in cells and in evolution.RNA (New York, N.Y.) · 2023Article
- Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication.Microbiology and molecular biology reviews : MMBR · 2022Review
- Acylation probing of "generic" RNA libraries reveals critical influence of loop constraints on reactivity.Cell chemical biology · 2022Article
- Conjugation of RNAChemical communications (Cambridge, England) · 2022Article
- Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site.RNA biology · 2022Article
- Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures.Nucleic acids research · 2021Article
- High-throughput determination of RNA structures.Nature reviews. Genetics · 2018Review
- New windows into retroviral RNA structures.Retrovirology · 2018Review
- Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility.The journal of physical chemistry letters · 2018Article
- SHAPE analysis of theRNA (New York, N.Y.) · 2017Article
- Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism.RNA (New York, N.Y.) · 2017Article
- Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo.Biophysical journal · 2017Article
- Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle.Nucleic acids research · 2017Article
- Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution.Wiley interdisciplinary reviews. RNA · 2017Review
- Rational engineering of the Neurospora VS ribozyme to allow substrate recognition via different kissing-loop interactions.Nucleic acids research · 2016Article
- Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis.Nature protocols · 2015Article
- Multiple conformations are a conserved and regulatory feature of the RB1 5' UTR.RNA (New York, N.Y.) · 2015Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Hydroxyl-selective electrophiles, including N-methylisatoic anhydride (NMIA) and 1-methyl-7-nitroisatoic anhydride (1M7), are broadly useful for RNA structure analysis because they react preferentially with the ribose 2'-OH group at conformationally unconstrained or flexible nucleotides. Each nucleotide in an RNA has the potential to form an adduct with these reagents to yield a comprehensive, nucleotide-resolution, view of RNA structure. However, it is possible that factors other than local structure modulate reactivity. To evaluate the influence of base identity on the intrinsic reactivity of each nucleotide, we analyze NMIA and 1M7 reactivity using four distinct RNAs, under both native and denaturing conditions. We show that guanosine and adenosine residues have identical intrinsic 2'-hydroxyl reactivities at pH 8.0 and are 1.4 and 1.7 times more reactive than uridine and cytidine, respectively. These subtle, but statistically significant, differences do not impact the ability of selective 2'-hydroxyl acylation analyzed by primer extension-based (SHAPE) methods to establish an RNA secondary structure or monitor RNA folding in solution because base-specific influences are much smaller than the reactivity differences between paired and unpaired nucleotides.
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What OpenQuestion holds
Registered trials
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.