Complexation of basic amino acids such as arginine, histidine and lysin with plasmid DNA in an aqueous solution: contribution to the capture of radicals under X-irradiation at 1.5 keV

The chemical environment of DNA in real biological situation is complex notably due to the presence of histones, i.e. nuclear proteins which are linked approximately in equal mass balance to the DNA macromolecule to form chromatin. Histones have numerous terminal tails made up of basic (positively charged) amino acids arginine and lysine while DNA is a macro-anion which holds one negative charge per phosphate moiety all along the double-helix. As a first attempt, in this study, the complexity of the nuclear chromatin structure is mimicked through the formation of complexes made up of the basic amino acids Arg, His, Lys (which apart from His are protonated at physiological pH) and a DNA plasmid used as a probe. Those 3 amino acids, when free in aqueous solution are known to be effective radical scavengers, notably for the hydroxyl radical, they might therefore protect DNA against indirect effects when exposed to ionizing radiations. At fixed concentration, the scavenging capacities of free amino acids, σ, for the hydroxyl radical are typically such that σHis ≅ σArg > σLys (σLys ≅ 0.1*σArg). We have measured the yields of single strand breaks per plasmid and per Gray (Χ) during exposure of aqueous solutions of complexes [amino acid - plasmid DNA] to ultra-soft X-rays (1,5 keV). At equal concentrations, the 3 complexed amino acids which also are present in large excess in the solutions do not exhibit DNA protection capabilities that are in line with their scavenging capacities; we find indeed single strand break yields that follow the order ΧHis > ΧArg > ΧLys (ΧLys ≅ 0,01*ΧArg). After having detailed our experimental protocol, we analyze the specific features of basic amino acids interactions with DNA, based on a bibliographic survey. The specificity of Arg interaction with DNA, especially its propensity to create bidentate contacts with bases (principally with the G base) makes it possible to propose a way by which high DNA single strand break damage is favored in the presence of Arg. An inter-molecular radical transfer is suggested which also seems to hold for the Lysine amino acid. As for the unexpected high single strand break yields observed with His, we suggest some possible pathways but complementary experiments still will have to be performed. (authors)