In vitro selection identifies key determinants for loop–loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1

Abstract

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 (K_d = 30 nM at 23 °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 α and β 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.