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Because Congo red (CR) can bind to critical intermediate structural forms of amyloid beta (Aβ), it has been suggested as a potential therapeutic agent against neurodegenerative disorders such as Alzheimer’s disease. In this study, the interaction of CR with Aβ12–28 was investigated by use of isothermal titration calorimetry (ITC). Studies conducted between 15 and 35 °C show that binding of CR to Aβ12–28 was strongly dependent on temperature, with a decrease in CR–Aβ12–28 complexation as temperature increases, presumably because of conformational changes within Aβ12–28 at the highest temperatures, that conceal the CR binding sites. In fact, no CR binding was observed at 35 °C. The binding of CR to Aβ12–28 was associated with favorable changes in both enthalpy and entropy that resulted in binding constants (K) of between 105 and 106 M −1. An early (and more intense) entropy-driven CR disaggregation phase (K ~107–108 M −1) was observed before the onset of CR–Aβ12–28 complexation. Only CR disaggregation was observed at 35 °C. These results may provide further insights into the ability of CR to inhibit Aβ toxicity in neurodegenerative diseases.

A series of thio- and selenopyrylium analogues of 2,4-di(4-dimethylaminophen-yl)-6-methylthiopyrylium iodide were prepared in five steps from 4-dimethylaminophenyl-propargyl aldehyde and the corresponding lithium acetylide. When bound to DNA, all of the dyes absorb at wavelengths >600 nm, which avoids the hemoglobin band I maximum at 575 nm. The binding of the series of dyes to double-stranded DNA was examined spectrophotometrically and by isothermal titration calorimetry to determine binding constants, by a topoisomerase I DNA unwinding assay, by competition dialysis with [poly(dGdC)] 2 and [poly(dAdT)] 2 , and by ethidium bromide displacement studies to examine propensities for intercalation, and by circular dichroism studies. The dyes were found to show mixed binding modes.

A topoisomerase I DNA unwinding assay has been used to determine the relative DNA-binding affinities of a model pair of homologous naphthalene diimides. Binding affinity data were corroborated using calorimetric (ITC) and spectrophotometric (titration and Tm) studies, with substituent size playing a significant role in binding. The assay was also used to investigate the mode of binding adopted by several known DNA-binding agents, including SYBR Green and PicoGreen. Some of the compounds exhibited unexpected binding modes.

A combination of isothermal titration calorimetry (ITC), topoisomerase I DNA unwinding assays, and ethidium bromide displacement studies were employed to investigate the binding of a homologous series of naphthalene diimides (NDI) to DNA. Our results suggest that the nature of the substituent plays a significant role in both the preferred binding mode and relative binding affinity of the compounds of this study. Only intercalative-type binding (K=15±3×10(6)M(-1)) was observed for the NDI with the smallest substituent (trimethyl-ethylamino), while larger members of the series (diethylmethyl-, dipropylmethyl- and dibutylmethyl-ethylamino substituents) adopted an additional binding mode of higher affinity (K(1)=31-78×10(6)M(-1)).

The DNA binding efficacy and preferred mode of binding of a series of rhodamine-related chalcogenoxanthylium dyes was investigated by isothermal titration calorimetry (ITC) using ctDNA, [poly(dCdG)] 2 and [poly(dAdT)] 2 , and by a topoisomerase I DNA unwinding (Topo I) assay. The dyes of this study showed tight binding to ctDNA with binding constants, K b , on the order of 10 6 –10 7 M −1 . The ITC and Topo I assay studies suggested that the 9-substituent has a strong impact on binding modes ranging from an apparent preference for intercalation with a 9-2-thienyl substituent (similar binding to [poly(dCdG)] 2 and [poly(dAdT)] 2 , re-supercoiling of DNA in the Topo I assay at −5 M dye), to mixed binding modes with 9-phenyl derivatives (2- to 3-fold preference for binding to [poly(dAdT)] 2 , re-supercoiling of DNA in the Topo I assay at ∼2 × 10 −5 M dye), to minor groove binding in a 9-(2-thienyl-5-diethylcarboxamide) derivative (strong preference for binding to [poly(dAdT)] 2 , did not show complete re-supercoiling in the Topo I assay). No binding to ctDNA was observed in one derivative with a 9-(3-thienyl-2-diethylcarboxamide) substituent, which cannot be co-planar with the xanthylium core. In series of dyes where the chalcogen atom was varied, the selenoxanthylium derivatives had 2- to 3-fold higher values of K b than the corresponding xanthylium, thioxanthylium, or telluroxanthylium derivatives, which all showed comparable values of K b . The chalcogen atom appeared to have little influence on binding mode.