Alteration in DNA binding pattern of conformationally locked NC(O)N system: A spectroscopic investigation.

The binding mode of a conformationally locked NC(O)N planar system with deoxyribonucleic acid (DNA) is investigated using various spectroscopic and enzymatic assays. Compound 1 and its four different salts (comp. 2-5) were prepared for this purpose. They showed certain changes in their respective DNA-compound complex at ground state and excited state as measured by UV-vis and fluorescence emission spectra. The Stern-Volmer quenching constant (KSV) for the neutral species (1) is found 8545 M(-1), whereas, for its salts 2, 3, 4 and 5 the quenching constants were 33510 M(-1), 11352 M(-1), 19693 M(-1) and 27270 M(-1) respectively. Nevertheless, the binding constant values remain comparable in neutral and salt forms except for 5. To elucidate the reason we took their CD spectra and ran a topoisomerase I (Topo I) assay. These experimental data revel the fact that compound 1 (neutral form) binds at the minor groove of DNA, whereas, its salt (2) has an extended intercalating property.

Temperature dependence of Congo red binding to amyloid ß12-28.

Because Congo red (CR) can bind to critical intermediate structural forms of amyloid beta (Aß), 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 Aß(12-28) was investigated by use of isothermal titration calorimetry (ITC). Studies conducted between 15 and 35 °C show that binding of CR to Aß(12-28) was strongly dependent on temperature, with a decrease in CR-Aß(12-28) complexation as temperature increases, presumably because of conformational changes within Aß(12-28) 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 Aß(12-28) was associated with favorable changes in both enthalpy and entropy that resulted in binding constants (K) of between 10(5) and 10(6) M (-1). An early (and more intense) entropy-driven CR disaggregation phase (K ~10(7)-10(8) M (-1)) was observed before the onset of CR-Aß(12-28) complexation. Only CR disaggregation was observed at 35 °C. These results may provide further insights into the ability of CR to inhibit Aß toxicity in neurodegenerative diseases.

Substituent effect on the preferred DNA binding mode and affinity of a homologous series of naphthalene diimides.

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)).

Substituent control of DNA binding modes in a series of chalcogenoxanthylium photosensitizers as determined by isothermal titration calorimetry and topoisomerase I DNA unwinding assay.

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 <10(-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 approximately 2 x 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.

Synthesis of analogues of a flexible thiopyrylium photosensitizer for purging blood-borne pathogens and binding mode and affinity studies of their complexes with DNA.

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 >600nm, which avoids the hemoglobin band I maximum at 575nm. 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.

Binding mode and affinity studies of DNA-binding agents using topoisomerase I DNA unwinding assay.

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 T(m)) 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.

Binding of a homologous series of anthraquinones to DNA.

The DNA binding characteristics of a series of homologous 2,6-disubstituted anthraquinone threading intercalators bearing one to four ethylene glycol units in their side chains have been studied. Binding constants were measured via surface plasmon resonance (SPR). These compounds bind to an AT-rich hairpin with slightly higher affinity than to a GC-rich hairpin. The binding constants decrease as the length of the side chain increases.