LNA/DNA chimeric oligomers mimics RNA aptamers targeted to the TAR RNA element of HIV-1

One of the major limitations of the use of phospho-diester oligonucleotides in cells is their rapid degradation by nucleases. To date, several chemical modi®cations have been employed to overcome this issue but insuf®cient ef®cacy and/or speci®city have limited their in vivo usefulness. In this work conformationally restricted nucleotides, locked nucleic acid (LNA), were investigated to design nuclease resistant aptamers targeted against the HIV-1 TAR RNA. LNA/DNA chimeras were synthe-sized from a shortened version of the hairpin RNA aptamer identi®ed by in vitro selection against TAR. The results indicate that these modi®cations confer good protection towards nuclease digestion. Electrophoretic mobility shift assays, thermal dena-turation monitored by UV-spectroscopy and surface plasmon resonance experiments identi®ed LNA/ DNA TAR ligands that bind to TAR with a dis-sociation constant in the low nanomolar range as the parent RNA aptamer. The crucial G, A residues that close the aptamer loop remain a key structural determinant for stable LNA/DNA chimera±TAR com-plexes. This work provides evidence that LNA modi-®cations alternated with DNA can generate stable structured RNA mimics for interacting with folded RNA targets