Specific recognition of a single guanine bulge in dsDNA using a surface plasmon resonance sensor with immobilized 2-(2-aminoacetyl)amino-5,6,7-trimethyl-1,8-naphthyridine

A surface plasmon resonance (SPR) assay for the specific recognition of a single guanine (G) bulge in DNA using an SPR sensor with an immobilized small-molecule ligand was developed. The synthesized ligand, 2-(2-aminoacetyl)amino-5,6,7-trimethyl-1,8 naphthyridine, can selectively binds to a G bulge of duplex DNA (dsDNA) through hydrogen bonding. The melting temperature (Tm) of the duplex containing a G bulge increased by 7.9 °C in the presence of the ligand, whereas a moderate increase in Tm was observed for duplexes containing cytosine, thymine and adenine bulges as well as for normal duplex. An SPR sensor with immobilized ligand on surface achieved an almost specific response for the G-bulged dsDNA, among four types of bulged dsDNA and the fully matched duplex. An examination of the effect of flanking bases on the SPR responses reveals that the present sensor is suitable for the selective detection of G-bulged dsDNA, although the SPR response was affected by the bases that flank the bulge site. The linear detection range of the G-bulged dsDNA was from 0.02 μM to 1.0 μM. The recognition of G bulge in dsDNA by the SPR sensor can be utilized for the SPR typing of G-related single nucleotide polymorphisms.