In vitro selection of RNA aptamers derived from a genomic human library against the TAR RNA element of HIV-1.
The transactivating responsive (TAR) element is a RNA hairpin located in the 5' untranslated region of HIV-1 mRNA. It is essential for full-length transcription of the retroviral genome and therefore for HIV-1 replication. Hairpin aptamers that generate highly stable and specific complexes with TAR were previously identified, thus decreasing the level of TAR-dependent expression in cultured cells [Kolb, G., et al. (2006) RNA Biol. 3, 150-156]. We performed genomic SELEX against TAR using a human RNA library to identify human transcripts that might interact with the retroviral genome through loop-loop interactions and potentially contribute to the regulation of TAR-mediated processes. We identified a genomic aptamer termed a1 that folds as a hairpin with an apical loop complementary to five nucleotides of the TAR hexanucleotide loop. Surface plasmon resonance experiments performed on a truncated or mutated version of the a1 aptamer, in the presence of the Rop protein of Escherichia coli, indicate the formation of a highly stable a1-TAR kissing complex. The 5' ACCCAG loop of a1 constitutes a new motif of interaction with the TAR loop.
Watrin
Marguerite
M
Inserm U869, European Institute of Chemistry and Biology, Pessac, France.
Von Pelchrzim
Frederike
F
Dausse
Eric
E
Schroeder
Renée
R
Toulmé
Jean-Jacques
JJ
D052157:Aptamers, Nucleotide / Q000235:genetics / Q000302:isolation & purification* / Q000494:pharmacology*; D001483:Base Sequence; D029968:Escherichia coli Proteins / Q000737:chemistry; D015698:Genomic Library; D016325:HIV Long Terminal Repeat / Q000187:drug effects / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D007700:Kinetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D016601:RNA-Binding Proteins / Q000737:chemistry; D052156:SELEX Aptamer Technique; D020349:Surface Plasmon Resonance
D052157:Aptamers, Nucleotide; D029968:Escherichia coli Proteins; D012333:RNA, Messenger; D012367:RNA, Viral; D016601:RNA-Binding Proteins