ArticleMethods (San Diego, Calif.)2009
Dissecting structural transitions in the HIV-1 dimerization initiation site RNA using 2-aminopurine fluorescence.
Article in Methods (San Diego, Calif.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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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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Who cites it
3 citing papers in PubMed, 12 citations in OpenAlex.
- Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway.RNA (New York, N.Y.) · 2019Article
- Molecular determinants of HIV-1 NCp7 chaperone activity in maturation of the HIV-1 dimerization initiation site.Nucleic acids research · 2013Article
- Hepatitis C virus RNA: molecular switches mediated by long-range RNA-RNA interactions?Nucleic acids research · 2013Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
A highly conserved 35 nucleotide RNA stem-loop, the dimerization initiation site (DIS), in the 5' untranslated region (UTR) of the human immunodeficiency virus type I (HIV-1) genome has been identified as the sequence primarily responsible for initiation of viral genome dimerization. The DIS initiates viral genome dimerization through a loop-loop 'kissing' interaction and is converted from an intermediate 'kissing' to a more thermodynamically stable extended duplex dimer in a conformational rearrangement that is chaperoned by the HIV-1 nucleocapsid protein (NCp7). Here we describe fluorescence methods designed to probe local RNA dynamics and structural transitions associated with the DIS dimer formation and its NCp7 chaperoned structural conversion. These methods take advantage of the exquisite sensitivity of the quantum yield of the fluorescent nucleotide base analog, 2-aminopurine (2-AP), to its immediate structural and dynamic environment. The 2-AP fluorescence methods described allow a detailed kinetic and thermodynamic examination of this type of RNA-RNA interaction, as well as an analysis of the molecular mechanism of NCp7 chaperone activity.
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