Faculty of Natural Sciences

TY - JOUR

T1 - RNA interactions in the 5' region of the HIV-1 genome

AU - Damgaard, Christian Kroun

AU - Andersen, Ebbe Sloth

AU - Knudsen, Bjarne

AU - Gorodkin, Jan

AU - Kjems, Jørgen

PY - 2004/2/13

Y1 - 2004/2/13

N2 - 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.

AB - 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.

KW - Algorithms

KW - Base Sequence

KW - Codon, Initiator

KW - Computational Biology

KW - Genome, Viral

KW - HIV-1

KW - Molecular Sequence Data

KW - Nuclease Protection Assays

KW - Nucleic Acid Conformation

KW - Nucleotides

KW - Phylogeny

KW - RNA Stability

KW - RNA, Viral

KW - Ultraviolet Rays

U2 - 10.1016/j.jmb.2003.12.010

DO - 10.1016/j.jmb.2003.12.010

M3 - Journal article

C2 - 14757051

VL - 336

SP - 369

EP - 379

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 2

ER -