ArticleRNA (New York, N.Y.)2004
Evidence for a base triple in the free HIV-1 TAR RNA.
Article in RNA (New York, N.Y.), 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 27 citations in OpenAlex.
- Three-dimensional structure of the palbociclib-HIV TAR complex.Nucleic acids research · 2026Article
- The kinase inhibitor palbociclib binds to HIV TAR RNA with very low nanomolar affinity and exquisite specificity.Nucleic acids research · 2026Article
- HIV-1 Transcription Inhibition Using Small RNA-Binding Molecules.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Progress in 7SK ribonucleoprotein structural biology.Frontiers in molecular biosciences · 2023Review
- An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb.Nucleic acids research · 2019Article
- Development of Small Molecules with a Noncanonical Binding Mode to HIV-1 Trans Activation Response (TAR) RNA.Journal of medicinal chemistry · 2016Article
- hLARP7 C-terminal domain contains an xRRM that binds the 3' hairpin of 7SK RNA.Nucleic acids research · 2016Article
- A Phylogenetic Survey on the Structure of the HIV-1 Leader RNA Domain That Encodes the Splice Donor Signal.Viruses · 2016Article
- Tat-dependent production of an HIV-1 TAR-encoded miRNA-like small RNA.Nucleic acids research · 2016Article
- Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein.RNA (New York, N.Y.) · 2016Article
- Molecular organization of the 5S rDNA gene type II in elasmobranchs.RNA biology · 2016Article
- Thermodynamic examination of 1- to 5-nt purine bulge loops in RNA and DNA constructs.RNA (New York, N.Y.) · 2015Article
- Characterizing RNA ensembles from NMR data with kinematic models.Nucleic acids research · 2014Article
- Life of psi: how full-length HIV-1 RNAs become packaged genomes in the viral particles.Virology · 2014Review
- HMGA1 directly interacts with TAR to modulate basal and Tat-dependent HIV transcription.RNA biology · 2013Article
- Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis.Biophysical journal · 2008Article
- Measurement of the effect of monovalent cations on RNA hairpin stability.Journal of the American Chemical Society · 2007Article
- iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge.Biophysical journal · 2007Article
- Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation signals.Nucleic acids research · 2007Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We propose the existence of a novel base triple in the HIV-1 TAR hairpin. This triple is supported by covariation of loop residue 31 with residue 22, which is part of an unusual base pair with U40 below the 3-nucleotide bulge. A set of mutants was constructed to test the involvement of bases A22, U31, and U40 in a triple interaction. RNA structure probing, trans-activation assays, and structure modeling are consistent with the existence of this base triple in a bent conformation of the free TAR element. However, disruption of the base triple does not affect binding of a Tat-derived peptide. We therefore compared the structure of free and Tat-bound TAR RNA by footprinting and site-specific cross-linking analyses. These studies indicate that the Tat arginine-rich motif, in addition to its known binding site at the bulge, is in close contact with U31 in the TAR loop. Because binding of Tat to TAR is known to coincide with the formation of a base triple with residues U23, A27, and U38, we hypothesize that Tat binding and the associated straightening of TAR triggers the disruption of the (A22-U40)U31 triple.
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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.