Abstract
Intercalating nucleic acids (INAยฎs) with insertions of (R)โ1โOโ(1โpyrenylmethyl)glycerol were hybridized with locked nucleic acids (LNAs). INA/LNA duplexes were found to be less stable than the corresponding DNA/LNA duplexes when the INA monomer was inserted as a bulge close to the LNA monomers in the opposite strand. This property was used to make โquenchedโ complements that possess LNA in hairpins and in duplexes and are consequently more accessible for targeting native DNA. The duplex between a fully modified 13โmer LNA sequence and a complementary INA with six pyrene residues inserted after every second base as a bulge was found to be very unstable (T~m~=30.1โยฐC) in comparison with the unmodified doubleโstranded DNA (T~m~=48.7โยฐC) and the corresponding duplexes of LNA/DNA (T~m~=81.6โยฐC) and INA/DNA (T~m~=66.4โยฐC). A thermal melting experiment of a mixture of an LNA hairpin, with five LNA nucleotides in the stem, and its complementary DNA sequence gave a transition with an extremely low increase in optical density (hyperchromicity). When two INA monomers were inserted into the stem of the LNA hairpin, the same experiment resulted in a significant hyperchromicity comparable with the one obtained for the corresponding DNA/DNA duplex.