Recognition and cleavage at the DNA major groove

Edward B. Skibo, Chenggou Xing, Thomas Groy

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


DNA recognition agents based on the indole-based aziridinyl eneimine and the cyclopent[b]indole methide species were designed and evaluated. 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. In summary new classes of DNA recognition agents are described and the utility of 13 C-enrichment and 13 C NMR to study DNA alkylation reactions is illustrated.

Original languageEnglish (US)
Pages (from-to)2445-2459
Number of pages15
JournalBioorganic and Medicinal Chemistry
Issue number9
StatePublished - 2001

Bibliographical note

Funding Information:
The authors gratefully acknowledge support from the National Institutes of Health, National Science Foundation, and the Arizona Disease Control Research Commission.


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