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In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1.
Duconge F; Toulme JJ; Institut National de la Sante et de la Recherche
March 30, 2000
RNA. 1999 Dec;5(12):1605-14. Unique Identifier : AIDSLINE MED/20072287

We selected RNA aptamers specific for the trans-activation responsive (TAR) RNA, a stem-loop structure crucial for the transcription of the integrated genome of the human immunodeficiency virus. Most of the selected sequences could be folded as imperfect hairpins and displayed a 5'-GUCCCAGA-3' consensus motif constituting the apical loop. The six central bases of this consensus sequence are complementary to the entire TAR loop, leading to the formation of TAR RNA-aptamer "kissing" complexes. The consensus G and A residues closing the aptamer loop contributed to the high affinity (Kd = 30 nM at 23 degrees C) of the aptamers for the TAR RNA. This G A pair was shown to be crucial for binding to TAR at a low magnesium concentration. The selection also identified 5'-PuPy and 5'-PyPu base pairs at alpha and beta positions of the stem, next to the loop, respectively. This strategy offered a way to identify key determinants of loop-loop interactions and to generate high affinity ligands of TAR RNA structure.

JOURNAL ARTICLE Base Pairing Base Sequence Binding Sites Consensus Sequence DNA Primers Human HIV Long Terminal Repeat/*GENETICS HIV-1/*GENETICS Kinetics Molecular Sequence Data *Nucleic Acid Conformation Oligoribonucleotides/*CHEMISTRY Polymerase Chain Reaction RNA, Viral/*CHEMISTRY/*GENETICS Structure-Activity Relationship Support, Non-U.S. Gov't