Noncovalent DNA Binding and the Mechanism of Oxidative DNA Damage by Fecapentaene-12

Abstract

The fecapentaenes are a group of mutagenic, polyunsaturated lipids that are produced endogenously in the human gastrointestinal tract. Previous studies show that the fecapentaenes cause oxidative DNA damage, but the chemical mechanisms by which this occurs remain unclear. The data presented here indicate that fecapentaene-12 causes direct oxidative DNA damage via production of the reactive oxygen species O2*-, H2O2, and HO*. In addition, evidence is presented indicating that fecapentaene-12 associates noncovalently with duplex DNA. Fecapentaene-12 provides an interesting new example highlighting the potential for hydrophobic long chain hydrocarbons to associate noncovalently with duplex DNA.

Supramolecular Self-Assembling Cyanine as an Alternative to Ethidium Bromide Displacement in DNA-Drug Model Interactions during High Throughput Screening

“…The association constant (Ka) was calculated from the reciprocal of the IC50. 11,12 The data were calculated as signal minus background (S -B) or as signal divided by background (S/B). To facilitate data comparison, the graphs also depict % changes to S -B or S/B.…”

“…In studies with EB, polyamines were used for DNA-model drug interactions or as potential gene delivery vehicles. 9,11,12,[22][23][24] Similar to DNA-drug interactions, cyanines can intercalate or self-assemble upon DNA double helix. 7,10,25 Despite extensive studies, the exact mechanism of polyamines binding to DNA remains to be finalized; 9,21 our studies might aid in the further elucidation of these interactions.…”

“…Cyanine displacement is thus useful for studying DNA-drug interactions. Reciprocal of IC50 transforming into Ka 11,12,28,29 assumes that spermine and cyanine compete for the same/similar binding sites on DNA, like the widely employed EB. 2,6,[12][13][14][22][23][24] However, this Ka is only an estimate, since affinity is influenced by several factors (vide supra), and we did not factor the Ka of cyanine for DNA during affinity calculations.…”

“…Reciprocal of IC50 transforming into Ka 11,12,28,29 assumes that spermine and cyanine compete for the same/similar binding sites on DNA, like the widely employed EB. 2,6,[12][13][14][22][23][24] However, this Ka is only an estimate, since affinity is influenced by several factors (vide supra), and we did not factor the Ka of cyanine for DNA during affinity calculations. 12,28,29 Our Ka of ~10 6 M -1 is within the 10 5 to 10 11 M -1 range for DNA-drug interactions using EB 2 and similar to the 1.4 × 10 6 M -1 Ka for spermine binding to λDNA at 17 mM ionic strength 26 compared to the 20 mM NaCl we used.…”

“…2,6,[12][13][14][22][23][24] However, this Ka is only an estimate, since affinity is influenced by several factors (vide supra), and we did not factor the Ka of cyanine for DNA during affinity calculations. 12,28,29 Our Ka of ~10 6 M -1 is within the 10 5 to 10 11 M -1 range for DNA-drug interactions using EB 2 and similar to the 1.4 × 10 6 M -1 Ka for spermine binding to λDNA at 17 mM ionic strength 26 compared to the 20 mM NaCl we used. Our Ka is similar to the 5 × 10 6 M -1 calculated for spermine binding to calf thymus DNA using EB, 28 but differs from the mutually exclusive affinity values of 2.3 × 10 5 , 1.97 × 10 7 and 5.7 × 10 4 M -1 reported using the exact same reagents, 21,29,30 thereby echoing the difficulties in comparing literature Ka values.…”