FLUORESCENCE RESONANCE ENERGY-TRANSFER ANALYSIS OF THE DEGRADATION OFAN OLIGONUCLEOTIDE PROTECTED BY A VERY STABLE HAIRPIN

In vitro degradation of antisense oligonucleotides protected or not on their 3' side against enzymatic attack by a naturally forming hairpin has been studied by fluorescence resonance energy transfer (FRET). Th e two oligonucleotides d(5'TTCTCGCGAAGC3') forming the hairpin and d(5 'TTCTCCGGAAGC3') as a control were labeled on their 5' side by tetrame thylrhodamine and on their 3' side by fluorescein. Fluorescein has bee n shown not to hinder the hairpin formation and to give an additional protection against nucleases. The FRET technique proved adequate for a n in situ study of these protected antisense oligonucleotides in livin g cells.