MODULATION OF OLIGONUCLEOTIDE DUPLEX AND TRIPLEX STABILITY VIA HYDROPHOBIC INTERACTIONS

Synthetic oligonucleotides have been proposed as a new rationally desi gned class of pharmaceuticals with a mechanism of action based upon a Watson - Crick and/or Hoogsteen type of base pairing with RNA or DNA r egions of interest. Two series of 3'-cholesterol and/or 5'-cholesterol conjugated oligonucleotides have been synthesized. The primary struct ure of these compounds was conceived in a way that should allow a hydr ophobic interaction to take place upon bringing the cholesteryl moieti es into proximity via a hybridization event. In the first group of com pounds the cholesteryl group was tethered to the opposite ends of two oligonucleotides, tandemly addressed to the same complementary strand. An increase in the Tm of duplexes up to 13.3 degrees C was observed i n comparison to unmodified oligomers. We observed a higher level of mi smatch discrimination for the two contiguous oligonucleotide cholester ol conjugates compared to one continuous oligomer of the same length. A second group of compounds was synthesized as 5',3'-bischolesterol co ntaining oligomers, capable of forming 'clamp-shaped' triple-stranded complexes, where cholesterol groups were attached to the termini of du plex and tripler forming domains. Stabilization of triplexes by up to 30 degrees C due to inter-cholesteryl interaction was observed. We det ected no tripler formation with a mismatched target. These data sugges t that significant stabilization of complexes of nucleic acids could b e achieved through inter-cholesteryl hydrophobic interaction.