Recognition of guanine-guanine mismatches by the dimeric form of 2-amino-1,8-naphthyridine.
Dimeric 2-amino-1,8-naphthyridine selectively binds to a G-G mismatch with high affinity (K(d) = 53 nM). We have investigated a binding mechanism of naphthyridine dimer 2 to a G-G mismatch by spectroscopic studies, thermodynamic analysis, and structure-activity studies for the thermal stabilization of the mismatch. 1H NMR spectra of a complex of 2 with 9-mer duplex d(CATCGGATG)2 containing a G-G mismatch showed that all hydrogens in two naphthyridine rings of 2 were observed upfield compared to those of 2 in a free state. The 2D-NOESY experiments showed that each naphthyridine of 2 binds to a guanine in the G-G mismatch within the pi-stack. In CD spectra, a large conformational change of the G-G mismatch-containing duplex was observed upon complex formation with 2. Isothermal calorimetry titration of 2 binding to the G-G mismatch showed that the stoichiometry for the binding is about 1:1 and that the binding is enthalpy-controlled. It is clarified by structure-activity studies that show (i) the linker connecting two naphthyridine rings was essential for the stabilization of the G-G mismatch, (ii) the binding efficiency was very sensitive to the linker structure, and (iii) the binding of two naphthyridines to each one of two Gs in the G-G mismatch is essential for a strong stabilization. These results strongly supported the intercalation of both naphthyridine rings of 2 into DNA base pairs and the formation of a hydrogen bonded complex with the G-G mismatch.
Nakatani
K
K
Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, CREST, Japan. nakatani@sbchem.kyoto-u.ac.jp
Sando
S
S
Kumasawa
H
H
Kikuchi
J
J
Saito
I
I
D020137:Base Pair Mismatch; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D019281:Dimerization; D006147:Guanine / Q000737:chemistry*; D006860:Hydrogen Bonding; D009287:Naphthyridines / Q000138:chemical synthesis / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D013329:Structure-Activity Relationship; D013816:Thermodynamics
C427025:2-amino-1,8-naphthyridine; D009287:Naphthyridines; D006147:Guanine; D004247:DNA