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The stabilization of G-Quadruplex DNA structures by ligands is a promising strategy for telomerase inhibition in cancer therapy since this enzyme is responsible for the unlimited proliferation of cancer cells. To assess the potential of a compound as a telomerase inhibitor, selectivity for quadruplex over duplex DNA is a fundamental attribute, as the drug must be able to recognize quadruplex DNA in the presence of a large amount of duplex DNA, in the cellular nucleus. By using different spectroscopic techniques, such as ultraviolet-visible, fluorescence and circular dichroism, this work evaluates the potential of a series of multicharged phthalocyanines, bearing four or eight positive charges, as G-Quadruplex stabilizing ligands. This work led us to conclude that the existence of a balance between the number and position of the positive charges in the phthalocyanine structure is a fundamental attribute for its selectivity for G-Quadruplex structures over duplex DNA structures. Two of the studied phthalocyanines, one with four peripheral positive charges (ZnPc1) and the other with less exposed eight positive charges (ZnPc4) showed high selectivity and affinity for G-Quadruplex over duplex DNA structures and were able to accumulate in the nucleus of UM-UC-3 bladder cancer cells.

The absorbance at 260 nm (A ₂₆₀) is ubiquitously used for nucleic acid quantification. We show that following oxygenation, DNA solutions experience alterations in both spectral properties (hyperchromism in the UV region, λ max 260 nm) and DNA conformation. The spectral changes caused by oxygen-DNA complexation are stable for at least several weeks at room temperature or several hours at 37 °C, but are also reversible by purging with nitrogen. Our data indicate that DNA in working solutions might already exist in the oxygen-complexed state, potentially confounding spectrophotometric analyses. Further, the presence of these complexes does not appear to impart cell toxicity in vitro or affect the biophysical functional behaviour (e.g. hybridisation) of DNA. Interestingly, our work also suggests that hybridisation could determine a release of bound oxygen, a phenomenon that could open the way to the use of such systems as oxygen carriers. [graphic removed]

A quantitative analysis of the excitonic intensity borrowing for the J-/H-aggregates of the bacteriochlorophylls/chlorophylls (BChls/Chls) in specific, and of porphyrins in general, is presented. The analysis is based on the argument that the mixing between the two energetically well-separated bands, such as the Q and B bands of BChls/Chls, should be considered important if the aggregated system possesses an excitonic superstate. A remarkably simple explanation of the significance of the excitonic intensity borrowing is given: superhyperchromism is manifested by the mediation of interband coupling between the superstates in the two well-separated bands of such aggregates. A comprehensive discussion on the significance of superhyperchromism and on its size-dependence is provided in connection with its effects on the absorption spectra of the BChl/Chl J- and H-aggregates.

Sensitive methods of differential UV spectrophotometry and differential scanning microcalorimetry were used to study the interaction of small and large quantities of the natural antitumor antibiotic actinomycin D with clusters of native and fragmented calf thymus DNA during thermal melting. At micromolar (physiological) concentrations, actinomycin is incorporated in untwisted sites of DNA rather than in the double helix. Actinomycin stabilizes these sites and therefore slightly increases the overall melting temperature of DNA. The antibiotic effectively interacts with the nucleotides of native DNA at a ratio of 1: 868, especially strongly with the clusters of satellite fractions and DNA fragments. At low concentrations, it stabilizes the «loose» bilizes the double helix and causes DNA aggregation.

This chapter contains sections titled: Introduction A Simplified Account of the Physical Basis of UV Absorption Definitions and Nomenclature Well‐Known and Less Well‐Known Characteristics of UV Absorption by Nucleic Acid Bases The Basis of UV Melting Experiments for Thermodynamic Studies The Two‐State Approximation and Its Limitations Equilibrium and Non‐equilibrium A Common Pitfall with Self‐Complementary Sequences Extracting Thermodynamic Information from Melting Curves of Large RNAs Parameters Influencing the Melting Temperature Practical Problems A Neat Experimental Solution to the Sloping Baseline References