Sato, Y., Nishizawa, S., Yoshimoto, K., Seino, T., Ichizawa, T., Morita, K. & Teramae, N. Influence of substituent modifications on the binding of 2-amino-1,8-naphthyridines to cytosine opposite an AP site in DNA duplexes: thermodynamic characterization. Nucleic Acids Res. 37, 1411-1422

Department of Chemistry, Graduate School of Science, Tohoku University, CREST, Japan Science and Technology Agency, Aoba-ku, Sendai 980-8578, Japan.
Nucleic Acids Research (Impact Factor: 9.11). 02/2009; 37(5):1411-22. DOI: 10.1093/nar/gkn1079
Source: PubMed


Here, we report on a significant effect of substitutions on the binding affinity of a series of 2-amino-1,8-naphthyridines,
i.e., 2-amino-1,8-naphthyridine (AND), 2-amino-7-methyl-1,8-naphthyridine (AMND), 2-amino-5,7-dimethyl-1,8-naphthyridine (ADMND)
and 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND), all of which can bind to cytosine opposite an AP site in DNA duplexes.
Fluorescence titration experiments show that the binding affinity for cytosine is effectively enhanced by the introduction
of methyl groups to the naphthyridine ring, and the 1:1 binding constant (106 M−1) follows in the order of AND (0.30) < AMND (2.7) < ADMND (6.1) < ATMND (19) in solutions containing 110 mM Na+ (pH 7.0, at 20°C). The thermodynamic parameters obtained by isothermal titration calorimetry experiments indicate that the
introduction of methyl groups effectively reduces the loss of binding entropy, which is indeed responsible for the increase
in the binding affinity. The heat capacity change (ΔCp), as determined from temperature dependence of the binding enthalpy, is found to be significantly different between AND (−161
cal/mol K) and ATMND (−217 cal/mol K). The hydrophobic contribution appears to be a key force to explain the observed effect
of substitutions on the binding affinity when the observed binding free energy (ΔGobs) is dissected into its component terms.

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Available from: Keitaro Yoshimoto, Oct 10, 2014
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