Characterization of Parazoanthoxanthin A Binding to a Series of Natural and Synthetic Host DNA Duplexes

Parazoanthoxanthin A is a fluorescent yellow nitrogenous pigment of the group of zoanthoxanthins, which show a broad range of biological activity. These include, among others, the ability to bind to DNA. In this study we have used a variety of spectroscopic (intrinsic fluorescence emission and UV-spectroscopy) and hydrodynamic techniques (viscometry) to characterize in more detail the binding of parazoanthoxanthin A to a variety of natural and synthetic DNA duplexes in different buffer conditions. Our results reveal the following five significant features: (i) Parazoanthoxanthin A exhibits two modes of DNA binding: One binding mode exhibits properties of intercalation, while the second binding mode is predominantly electrostatic in origin. (ii) The apparent binding “site size” for parazoanthoxanthin A near physiological salt concentration (100 mM NaCl) is in the range of 7 ± 1 base pairs for natural genomic DNA duplexes (calf thymus and salmon testes DNA) and alternating synthetic polynucleotides (poly[d(AT)] · poly[d(AT)] and poly[d(GC)] · poly[d(GC)]). A slightly larger apparent binding site size of 9 ± 1 bp was obtained for parazoanthoxanthin A binding to the synthetic homopolymer poly[d(A)] · poly[d(T)]. (iii) Near physiological salt concentration (100 mM NaCl) parazoanthoxanthin A binds with the same approximate binding affinity of 2–5 × 105 M−1 to all DNA polymers studied. (iv) At low salt concentration, parazoanthoxanthin A preferentially binds alternating poly[d(AT)] · poly[d(AT)] and poly[d(GC)] · poly[d(GC)] host duplexes. (v) Parazoanthoxanthin A inhibits DNA polymerase in vitro.