Kazuhiko Nakatani

Enantiomeric DNA termed as L-DNA has unique properties. One is the ability of hybridizing to the complementary DNA as natural D-DNA. Another property is that the L-DNA could be recognized much more weakly by enzymes than D-DNA. We have focused our attention on these properties and applied L-DNA as a molecular tag. Here, we report that L-D chimera DNA is useful for PCR primers and subsequent separation and hybridization. Precise investigation revealed that in the process of PCR, L-DNA region could not be the PCR template and the polymerase extension reaction stopped at the boundary between L- and D-DNA region. As a result, L-DNA region formed like a “sticky end” and played a role of molecular tag. According to the L-DNA tag sequence, the produced L-DNA-tagged PCR products were easily separated or hybridized on the solid surface where the complementary L-DNA was pre-immobilized.

NMR structure of the first identified ligand, naphthyridine–azaquinolone (NA), complexed with the CAG-CAG triad is reported. The determined structure revealed the invasive ligands binding to the A-A mismatch and flanking G-C base pairs, causing the widowed cytosines to flip out from π-stack. Hydrogen-bond pairs between NA and DNA, naphthyridine-guanine and azaquinolone-adenine, are well stacked in the right-handed DNA helix, showing structural mimicry of Watson–Crick base pairing. This is the first observation that the small molecular ligand induced the base flipping of the nucleotide base in the Watson-Crick base pair.

Kinetics and thermodynamics studies of the binding between naphthyridine dimer and DNAduplexes having a G-G mismatch sequence were performed by using Surface Plasmon Resonance (SPR) assay. Naphthyridine dimers possessing a different length of PEG linker were synthesized and immobilized to the dextran surface of the sensor chip to obtain an improved sensitivity of the SPR sensor toward a G-G mismatch. The effect of the directly neighboring base pair to the G-G mismatch was estimated from the thermodynamic parameters of the complex. These results indicate that stacking with adjacent base pair and naphthyridine dimer is the key roll for the formation of the complex between mismatched base pair and naphthyridine dimer.