Recognition and cleavage at the DNA major groove

Abstract

DNA recognition agents based on the indole-based aziridinyl eneimine and the cyclopent[b]indole methide species are described. The recognition process involved either selective alkylation or intercalating interactions in the major groove. DNA cleavage resulted from phosphate backbone alkylation (hydrolytic cleavage) and N(7)-alkylation (piperidine cleavage). The formation and fate of the eneimine was studied using enriched 13C NMR spectra and x-ray crystallography. The aziridinyl eneimine specifically alkylates the N(7) position of DNA resulting in direction of the aziridinyl alkylating center to either the 3′- or 5′-phosphate of the alkylated base. The eneimine species forms dimers and trimers that appear to recognize DNA at up to three base pairs. The cyclopent[b]indole quinone methide recognizes the 3′-GT-5′ sequence and alkylates the guanine N(7) and the thymine 6-carbonyl oxygen causing the hydrolytic removal of these bases. New classes of DNA recognition agents have been developed and the utility of 13C-enrichment and 13C-NMR to study DNA alkylation reactions is disclosed.

Dependencies are inferred from the claim text.