Rates of Aziridinium Alkylation of Polynucleotides and Ribonucleic Acid

Physical association modeling of DNA alkylation. Some DNA conformational aspects

The widespread occurrence of physical binding between biological macromolecules and small molecules has prompted us to hypothesize that physical binding contributes to DNA alkylation specificity. The preferred physical binding sites for a CH+3-like test probe were predicted for several sequences of DNA using molecular mechanics free space calculation methods. Sequences containing A = T basepairs direct physical binding to the minor groove, whereas sequences containing G identical to C basepairs direct physical binding to the major groove. Physical binding calculations were also performed for model 'unwound' DNA conformations. The results of the test probe studies were subsequently employed as starting points to predict the preferred physical binding sites for the more complicated case of an actual alkylating agent, the dimethylaziridinium ion. These studies demonstrate that physical binding specificity is highly dependent upon DNA sequence and conformation, and correlates well with the DNA alkylation site specificity observed for alkylating agents in th dimethylaziridine class.

The interaction of chromatin with alkylating agents. The monofunctional action of bis(2-chloroethyl)methylamine

The reaction of L5178Y lymphoblast cell chromatin with the alkylating agent bis(2-chloroethyl)methylamine has been studied as a function of time, pH and reagent concentration. The reaction with DNA of chromatin from which the proteins were dissociated, as well as with purified calf thymus DNA, was studied in parallel. The extent of alkylation of DNA in intact chromatin was 4--5 times as much as in parallel free DNA samples; up to 4% of nucleotide base pairs were substituted. The extent of monofunctional substitution of the proteins was similar, on a weight basis, to that of DNA. Chromatographic analysis of the depurinated products showed that in chromatin, as in DNA, position N-7 of guanine is the major site of reaction. Up to 25% of the reaction products were guanines cross-linked as bis(2-guanin-7-yl-ethyl)methylamine, indicating a considerable degree of DNA-DNA cross linking. Column analysis shows that up to 40% of the nuclear proteins are cross-linked to DNA at 10 mM bis(2-chloroethyl)methylamine. The increased reactivity of intact chromatin is interpreted in terms of a conformational change in the position of the DNA bases when in the organized nucleohistone complex.