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RNA interactions in the 5 region of the HIV-1 genome
RNA interactions in the 5 region of the HIV-1 genome
7333
The untranslated leader of the dimeric HIV-1 RNA genome is folded into a complex structure that plays multiple and essential roles in the viral replication cycle. Here, we have investigated secondary and tertiary structural elements within the 5' 744 nucleotides of the HIV-1 genome using a combination of bioinformatics, enzymatic probing, native gel electrophoresis, and UV-crosslinking experiments. We used a recently developed RNA folding algorithm (Pfold) to predict the common secondary structure of an alignment of 20 divergent HIV-1 sequences. Combining this analysis with biochemical data, we present a secondary structure model for the entire 744 nucleotide fragment, which incorporates previously recognized and novel structural elements. In particular, our data provided strong evidence for a long-distance interaction between the region encompassing the AUG Gag initiation codon and an upstream region and we demonstrate that this feature is highly conserved in distantly related human and animal retroviruses. To obtain information about tertiary interactions we applied an intramolecular UV-crosslinking strategy and identified a novel tertiary interaction within the PBS hairpin structure.
Damgaard CK, Andersen ES, Knudsen B, Gorodkin J, Kjems J
Journal of molecular biology
2004-02-13 00:00
336
2
369-79
Algorithms,Base Sequence,Codon, Initiator,Computational Biology,Genome, Viral,HIV-1,Molecular Sequence Data,Nuclease Protection Assays,Nucleic Acid Conformation,Nucleotides,Phylogeny,RNA Stability,RNA, Viral,Ultraviolet Rays,Codon, Initiator,Nucleotides,RNA, Viral
Department of Molecular Biology, University of Aarhus, C.F. Møllers Allé, Building 130, DK-8000 C, Arhus, Denmark.
J. Mol. Biol.
0022-2836
S0022283603014797
0
False
14757051
