Nuclease resistance and RNase H sensitivity of oligonucleotides bridged byoligomethylenediol and oligoethylene glycol linkers

The properties of new chimeric oligodeoxynucleotides made of short sequence s (tetramers, pentamers, octamers, and decamers) bridged by hexamethylenedi ol and hexaethylene glycol linkers have been investigated. These chimeric o ligonucleotides showed an improved resistance toward snake venom 3'-phospho diesterase, with an increased stability when a terminal 3'-3'-internucleoti de phosphodiester bond is present. It also has been demonstrated that the h ybrid complexes formed by bridged oligonucleotides and a complementary 20-m er RNA are able to elicit the activity of ribonuclease H (RNase H) from Esc herichia coli, The substrate properties of chimeric oligonucleotides depend on the length of the oligonucleotide fragments bridged by linkers. Introdu ction of a nonnucleotide spacer into the native oligonucleotide only slight ly hampers the extent of the RNA hydrolysis in the hybrid complexes, wherea s a modification of the site of reaction is observed as a possible conseque nce of the steric disturbance due to the aliphatic linkers, Hence, these ne w chimeric oligonucleotides, namely, short oligonucleotide fragments bridge d by nonnucleotide linkers, demonstrate a favorable combination of exonucle ase resistance and high substrate activity toward RNase H, As a consequence , these chimeric oligonucleotides could be proposed as new, promising analo gs to be used in the antisense strategy.