ArticleNucleic acids research2004
Probing alternative foldings of the HIV-1 leader RNA by antisense oligonucleotide scanning arrays.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 45 citations in OpenAlex.
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- HIV-1 spliced RNAs display transcription start site bias.RNA (New York, N.Y.) · 2020Article
- Intrinsic conformational dynamics of the HIV-1 genomic RNA 5'UTR.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- The Life-Cycle of the HIV-1 Gag-RNA Complex.Viruses · 2016Review
- Progress and outlook in structural biology of large viral RNAs.Virus research · 2014Review
- End-to-end crosstalk within the hepatitis C virus genome mediates the conformational switch of the 3'X-tail region.Nucleic acids research · 2014Article
- Annealing to sequences within the primer binding site loop promotes an HIV-1 RNA conformation favoring RNA dimerization and packaging.RNA (New York, N.Y.) · 2013Article
- The folding of the hepatitis C virus internal ribosome entry site depends on the 3'-end of the viral genome.Nucleic acids research · 2012Article
- In vitro and in vivo analysis of the interaction between RNA helicase A and HIV-1 RNA.Journal of virology · 2012Article
- Mapping targetable sites on human telomerase RNA pseudoknot/template domain using 2'-OMe RNA-interacting polynucleotide (RIPtide) microarrays.The Journal of biological chemistry · 2012Article
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- An antisense microwalk reveals critical role of an intronic position linked to a unique long-distance interaction in pre-mRNA splicing.RNA (New York, N.Y.) · 2010Article
- The PKR-binding domain of adenovirus VA RNAI exists as a mixture of two functionally non-equivalent structures.Nucleic acids research · 2009Article
- Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function.Nucleic acids research · 2008Article
- A chemical synthesis of LNA-2,6-diaminopurine riboside, and the influence of 2'-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes.Nucleic acids research · 2007Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Scanning arrays of antisense DNA oligonucleotides provide a novel and systematic means to study structural features within an RNA molecule. We used this approach to probe the structure of the untranslated leader of the human immunodeficiency virus type 1 (HIV-1) RNA genome. This 335 nt RNA encodes multiple important replication signals and adopts two mutually exclusive conformations. The poly(A) and the dimer initiation signal (DIS) sequences of the leader RNA are base-paired in the long-distance interaction (LDI) conformation, but both domains form distinct hairpins in the branched multiple hairpins (BMH) conformation. An RNA switch mechanism has been proposed to regulate the activity of the DIS dimerization signal that is masked in one, yet exposed in the other conformation. The two RNA conformations demonstrate discrete differences in the array-based hybridization patterns. LDI shows increased hybridization in the poly(A) region and decreased hybridization in the DIS region when compared with BMH. These results provide additional evidence for the structure models of the two alternative leader RNA conformations. We also found a correlation between the efficiency of oligonucleotide hybridization and the accessibility of the RNA structure as determined by chemical and enzymatic probing in previous studies. The array approach therefore provides a very sensitive method to detect structural differences in related transcripts.
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