Recognition of a Single Guanine Bulge by 2-Acylamino-1,8-naphthyridine

2-Acylamino-1,8-naphthyridine (1), which possesses hydrogen bonding groups fully complementary to guanine (G), selectively binds to a single G bulge of duplex DNA. The melting temperature (T m) of the duplex containing a G bulge was increased by the presence of 1, whereas no increase of T m was observed for the duplexes containing adenine (A) and thymine (T) bulges as well as for normal duplex. Riboflavin-sensitized photooxidation of DNA containing GG steps opposite to G and A bulges was selectively inhibited by the presence of 1 at the G bulge. DNase I footprinting titration indicated a selective binding of 1 to the G bulge with an association constant of 3.4 ± 1 × 104 M-1. In the presence of 1, CD spectra of the G bulge-containing duplex noticeably changed, being accompanied by the induced CD at 300−350 nm, whereas no CD spectral change was observed for the duplex containing A bulge. Both the hydrogen bonding groups complementary to G and the planar bicyclic ring system are essential for the complex formation between G bulge and 1.