Table 1.

Thermodynamic parameters for the 1,8-naphthyridine binding to cytosine in the 21-meric AP site-containing DNA duplex^a

	K11 (M−1)	ΔGobs (kcal/mol)	SK	ΔGpe (kcal/mol)	ΔGt (kcal/mol)	ΔHobs (kcal/mol)	TΔSobs (kcal/mol)
AND	3.0 (±0.2) × 105	−7.3 (±0.1)	−1.15	−1.4	−5.9	−20.5 ± 0.6	−13.2 (±0.6)
AMND	2.7 (±0.2) × 106	−8.6 (±0.1)	−1.31	−1.7	−6.9	−19.8 ± 0.4	−11.2 (±0.4)
ADMND	6.1 (±0.5) × 106	−9.1 (±0.1)	−1.36	−1.8	−7.3	−16.7 ± 0.3	−7.6 (±0.3)
ATMND	1.9 (±0.2) × 107	−9.8 (±0.1)	−1.42	−1.8	−8.0	−12.8 ± 0.7	−3.0 (±0.7)

^aK₁₁ (M⁻¹), determined by fluorescence titration experiments (cf. Figures 3 and 4), is the 1 : 1 binding constant in 110 mM Na⁺ at 20°C ([sodium cacodylate] = 10 mM, [EDTA] = 1.0 mM, [NaCl] = 100 mM, pH 7.0) with the standard deviations obtained from three independent experiments. ΔG_obs is the observed binding free energy calculated from ΔG_obs = −RTlnK₁₁. SK is the slope of the plot of log K₁₁ versus log [Na⁺] (cf. Supplementary Figure S3): fitting error is within 0.02. ΔG_pe and ΔG_t are the polyelectrolyte and nonpolyelectrolyte contributions to the observed binding free energy (ΔG_obs) evaluated at 110 mM Na⁺ (ΔG_obs = ΔG_pe + ΔG_t, ΔG_pe = −SKRT ln [Na⁺]). ΔH_obs was directly determined by ITC at 20°C (cf. Figure 5): Errors are the standard deviations obtained from three independent measurements. TΔS_obs was calculated from TΔS_obs = ΔH_obs − ΔG_obs. DNA duplex: 5′-GCA GCT CCC GXG GTC TCC TCG-3′/3′-CGT CGA GGG CCC CAG AGG AGC-5′, X = AP site (dSpacer), C = target cytosine.