Efficient PNA double-duplex invasion using preQ₁•G-clamp as a pseudo-complementary G•C base pair

We report a highly useful pseudo-complementary G•C base pair based on electrostatic repulsion between preQ₁ and G-clamp. While pseudo-complementary (pc) PNA oligomers containing preQ₁•G-clamp base pairs suppressed PNA homoduplex formation, they formed very stable PNA-DNA heteroduplexes. We demonstrated that double-duplex invasion proceeded with 100% efficiency when less than 2 equivalents of pcPNAs were used under low salt conditions, and furthermore, an invasion efficiency of 97-100% was achieved under physiological salt conditions and at 37 °C by using a larger amount of pcPNAs.