Thermodynamic characterization of the binding of naphthyridines to the AP site-containing DNA duplexes.
We here report on the thermodynamics of the hydrogen bond-mediated binding of 2-amino-7-methyl-1,8-naphthyridine (AMND) to a cytosine base opposite an abasic site (AP site) in a 21-meric DNA duplex (5'-GCA GCT CCC GXG GTC TCC TCG-3'/3'-CGT CGA GGG CCC CAG AGG AGC-5', X= AP site, C = target). The examination by fluorescence titration experiments shows a 1:1 binding constant of 2.7x10(6) M(-1) at 20 degrees C in solutions containing 110 mM Na(+) (pH 7.0). From the analysis of salt dependence of binding constants, polyelectrolyte (DeltaG(pe)) and non-polyelectrolyte (DeltaG(t)) contributions are calculated as -1.7 kcal/mol and -6.9 kcal/mol, respectively, at 110 mM Na(+) concentration. The binding enthalpy determined by isothermal titration calorimetry (ITC) is -18.5 kcal/mol in 110 mM Na(+) at 20 degrees C. We discuss these results with a view towards further development of our ligand-based fluorescence assay for SNPs (single nucleotide polymorphisms) typing.
Sato
Yusuke
Y
Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.
Seino
Takehiro
T
Nishizawa
Seiichi
S
Teramae
Norio
N
D001665:Binding Sites; D002151:Calorimetry; D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D015342:DNA Probes / Q000737:chemistry; D005456:Fluorescent Dyes / Q000737:chemistry*; D009287:Naphthyridines / Q000737:chemistry*; D020641:Polymorphism, Single Nucleotide; D013050:Spectrometry, Fluorescence; D013816:Thermodynamics
C520210:2-amino-7-methyl-1,8-naphthyridine; D015342:DNA Probes; D005456:Fluorescent Dyes; D009287:Naphthyridines; D003596:Cytosine; D004247:DNA