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 x 10(5) 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.
Pasic
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Department of Biology, Biotechnical Faculty, University of Ljubljana, Veccna pot 111, Ljubljana, 1000, Slovenia.
Sepcic
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Turk
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Macek
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Poklar
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N
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D002417:Cattle; D003508:Cycloheptanes / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D017931:DNA Primers / Q000235:genetics; D019641:DNA, Archaeal / Q000096:biosynthesis; D004259:DNA-Directed DNA Polymerase / Q000235:genetics; D004355:Drug Stability; D066298:In Vitro Techniques; D007700:Kinetics; D008297:Male; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D019384:Nucleic Acid Synthesis Inhibitors; D011067:Poly dA-dT / Q000737:chemistry / Q000378:metabolism; D011089:Polydeoxyribonucleotides / Q000737:chemistry / Q000378:metabolism; D012474:Salmon; D013050:Spectrometry, Fluorescence; D013056:Spectrophotometry, Ultraviolet; D019712:Thermococcus / Q000187:drug effects / Q000235:genetics / Q000378:metabolism
D003508:Cycloheptanes; D017931:DNA Primers; D019641:DNA, Archaeal; D019384:Nucleic Acid Synthesis Inhibitors; D011089:Polydeoxyribonucleotides; C114237:parazoanthoxanthin A; D011067:Poly dA-dT; C019530:poly(dC-dG); D004247:DNA; D004259:DNA-Directed DNA Polymerase