ArticleNucleic acids research2005
Structural polymorphism of the HIV-1 leader region explored by computational methods.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 26 citations in OpenAlex.
- Short- and long-range interactions in the HIV-1 5' UTR regulate genome dimerization and packaging.Nature structural & molecular biology · 2022Article
- MPGAfold in dengue secondary structure prediction.Methods in molecular biology (Clifton, N.J.) · 2014Article
- In-gel probing of individual RNA conformers within a mixed population reveals a dimerization structural switch in the HIV-1 leader.Nucleic acids research · 2013Article
- In vitro and in vivo analysis of the interaction between RNA helicase A and HIV-1 RNA.Journal of virology · 2012Article
- Article
- Ensemble of secondary structures for encapsidated satellite tobacco mosaic virus RNA consistent with chemical probing and crystallography constraints.Biophysical journal · 2011Article
- Identification of cis-acting elements in the 3'-untranslated region of the dengue virus type 2 RNA that modulate translation and replication.The Journal of biological chemistry · 2011Article
- Inhibition of HIV-1 replication and dimerization interference by dual inhibitory RNAs.Molecules (Basel, Switzerland) · 2010Article
- Article
- The fraction of RNA that folds into the correct branched secondary structure determines hepatitis delta virus type 3 RNA editing levels.RNA (New York, N.Y.) · 2009Article
- Regulation of primate lentiviral RNA dimerization by structural entrapment.Retrovirology · 2008Article
- High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states.PLoS biology · 2008Article
- An extended stem-loop 1 is necessary for human immunodeficiency virus type 2 replication and affects genomic RNA encapsidation.Journal of virology · 2007Article
- The role of a metastable RNA secondary structure in hepatitis delta virus genotype III RNA editing.RNA (New York, N.Y.) · 2006Article
- HIV-1 RNA dimerization: It takes two to tango.AIDS reviewsReview
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Experimental studies revealed that the elements of the human immunodeficiency virus type 1 (HIV-1) 5'-untranslated leader region (5'-UTR) can fold in vitro into two alternative conformations, branched (BMH) and 'linearized' (LDI) and switch between them to achieve different functionality. In this study we computationally explored in detail, with our massively parallel genetic algorithm (MPGAfold), the propensity of 13 HIV-1 5'-UTRs to fold into the BMH and the LDI conformation types. Besides the BMH conformations these results predict the existence of two functionally equivalent types of LDI conformations. One is similar to what has been shown in vitro to exist in HIV-1 LAI, the other is a novel conformation exemplified by HIV-1 MAL long-distance interactions. These novel MPGAfold results are further corroborated by a consensus probability matrix algorithm applied to a set of 155 HIV-1 sequences. We also have determined in detail the impact of various strain mutations, domain sizes and folds of elongating sequences simulating folding during transcription on HIV-1 RNA secondary structure folding dynamics.
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