ArticleNucleic acids research2002
The bulge region of HIV-1 TAR RNA binds metal ions in solution.
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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.
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.
Who cites it
29 citing papers in PubMed, 61 citations in OpenAlex.
- Structural elucidation of HIV-1 G-quadruplexes in a cellular environment and their ligand binding using responsiveChemical science · 2024Article
- Advances in RNA Labeling with Trifluoromethyl Groups.Chemistry (Weinheim an der Bergstrasse, Germany) · 2023Article
- Antimicrobial properties of a multi-component alloy.Scientific reports · 2022Article
- Incorporation and Utility of a Responsive Ribonucleoside Analogue in Probing the Conformation of a Viral RNA Motif by Fluorescence andChembiochem : a European journal of chemical biology · 2022Article
- 2'-Chemical science · 2020Article
- AromaticAngewandte Chemie (International ed. in English) · 2020Article
- The precious fluorine on the ring: fluorine NMR for biological systems.Journal of biomolecular NMR · 2020Article
- Exposing Hidden High-Affinity RNA Conformational States.Journal of the American Chemical Society · 2020Article
- Fluorescent peptide displacement as a general assay for screening small molecule libraries against RNA.Organic & biomolecular chemistry · 2019Article
- Applying Thymine Isostere 2,4-Difluoro-5-Methylbenzene as a NMR Assignment Tool and Probe of Homopyrimidine/Homopurine Tract Structural Dynamics.Methods in enzymology · 2016Article
- Expanding the Scope of 2'-SCF3 Modified RNA.Chemistry (Weinheim an der Bergstrasse, Germany) · 2015Article
- Surprising base pairing and structural properties of 2'-trifluoromethylthio-modified ribonucleic acids.Journal of the American Chemical Society · 2014Article
- From a structural average to the conformational ensemble of a DNA bulge.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Conformational heterogeneity of the protein-free human spliceosomal U2-U6 snRNA complex.RNA (New York, N.Y.) · 2013Article
- 2'-SCF3 uridine-a powerful label for probing structure and function of RNA by 19F NMR spectroscopy.Angewandte Chemie (International ed. in English) · 2012Article
- 5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy.Nucleic acids research · 2009Article
- A nonafluoro nucleoside as a sensitive 19f NMR probe of nucleic acid conformation.Organic letters · 2008Article
- Mechanism of T7 RNAP pausing and termination at the T7 concatemer junction: a local change in transcription bubble structure drives a large change in transcription complex architecture.Journal of molecular biology · 2008Article
- Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops.Biochemistry · 2007Article
- Efficient syntheses of 5'-deoxy-5'-fluoroguanosine and -inosine.The Journal of organic chemistry · 2007Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Binding of Mg2+, Ca2+ and Co(NH3)6(3+) ions to the HIV-1 TAR RNA in solution was analysed by 19F NMR spectroscopy, metal ion-induced RNA cleavages and Brownian dynamics (BD) simulations. Chemically synthesised 29mer oligoribonucleotides of the TAR sequence labelled with 5-fluorouridine (FU) were used for 19F NMR-monitored metal ion titration. The chemical shift changes of fluorine resonances FU-23, FU-25 and FU-40 upon titration with Mg2+ and Ca2+ ions indicated specific, although weak, binding at the bulge region with the dissociation constants (K(d)) of 0.9 +/- 0.6 and 2.7 +/- 1.7 mM, respectively. Argininamide, inducing largest (19)F chemical shifts changes at FU-23, was used as a reference ligand (K(d) = 0.3 +/- 0.1 mM). In the Pb2+-induced TAR RNA cleavage experiment, strong and selective cleavage of the C24-U25 phosphodiester bond was observed, while Mg2+ and Ca2+ induced cuts at all 3-nt residues of the bulge. The inhibition of Pb2+-specific TAR cleavage by di- and trivalent metal ions revealed a binding specificity [in the order Co(NH3)6(3+) > Mg2+ > Ca2+] at the bulge site. A BD simulation search of potential magnesium ion sites within the NMR structure of HIV-1 TAR RNA was conducted on a set of 20 conformers (PDB code 1ANR). For most cases, the bulge region was targeted by magnesium cations.
Indexed as
Identifiers
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.