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• W2128744040 abstract "Thermodynamic studies on the interactions between intercalator−neomycin conjugates and a DNA polynucleotide triplex [poly(dA)·2poly(dT)] were conducted. To draw a complete picture of such interactions, naphthalene diimide−neomycin (3) and anthraquinone−neomycin (4) conjugates were synthesized and used together with two other analogues, previously synthesized pyrene−neomycin (1) and BQQ−neomycin (2) conjugates, in our investigations. A combination of experiments, including UV denaturation, circular dichroism (CD) titration, differential scanning calorimetry (DSC), and isothermal titration calorimetry (ITC), revealed that all four conjugates (1−4) stabilized poly(dA)·2poly(dT) much more than its parent compound, neomycin. UV melting experiments clearly showed that the temperature (Tm3→2) at which poly(dA)·2poly(dT) dissociated into poly(dA)·poly(dT) and poly(dT) increased dramatically (>12 °C) in the presence of intercalator−neomycin conjugates (1−4) even at a very low concentration (2 μM). In contrast to intercalator−neomycin conjugates, the increment of Tm3→2 of poly(dA)·2poly(dT) induced by neomycin was negligible under the same conditions. The binding preference of intercalator−neomycin conjugates (1−4) to poly(dA)·2poly(dT) was also confirmed by competition dialysis and a fluorescent intercalator displacement assay. Circular dichroism titration studies revealed that compounds 1−4 had slightly larger binding site size (∼7−7.5) with poly(dA)·2poly(dT) as compared to neomycin (∼6.5). The thermodynamic parameters of these intercalator−neomycin conjugates with poly(dA)·2poly(dT) were derived from an integrated van’t Hoff equation using the Tm3→2 values, the binding site size numbers, and other parameters obtained from DSC and ITC. The binding affinity of all tested ligands with poly(dA)·2poly(dT) increased in the following order: neomycin < 1 < 3 < 4 < 2. Among them, the binding constant [(2.7 ± 0.3) × 108 M−1] of 2 with poly(dA)·2poly(dT) was the highest, almost 1000-fold greater than that of neomycin. The binding of compounds 1−4 with poly(dA)·2poly(dT) was mostly enthalpy-driven and gave negative ΔCp values. The results described here suggest that the binding affinity of intercalator−neomycin conjugates for poly(dA)·2poly(dT) increases as a function of the surface area of the intercalator moiety." @default.
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• W2128744040 date "2010-06-14" @default.
• W2128744040 modified "2023-10-01" @default.
• W2128744040 title "Probing the Recognition Surface of a DNA Triplex: Binding Studies with Intercalator−Neomycin Conjugates" @default.
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• W2128744040 doi "https://doi.org/10.1021/bi100071j" @default.
• W2128744040 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3641831" @default.
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