Binding site for ethidium cation in the major groove of b-form dna

Regina R. Monaco, Fred H. Hausheer

Research output: Contribution to journalArticlepeer-review

13 Scopus citations


Molecular modeling of the system composed of ethidium cation initially intercalated through the major and minor grooves of the B-DNA form of 5’GCATGC3’ into the central AT pairs, with the phenyl group oriented either toward or away from the helical axis, led upon energy minimization to intercalation complexes only when the phenyl group was initially oriented away from the helical axis. For the other two cases, energy minimization led to extrusion of the ethidium from the helix to form unanticipated outside-bound complexes stabilized by specific hydrogen bonds. It is suggested that outside-bound major groove complexes involving the GXXXG sequence may play important roles in the reaction mechanism of ethidium intercalation and in its action as a drug.

Original languageEnglish (US)
Pages (from-to)675-680
Number of pages6
JournalJournal of Biomolecular Structure and Dynamics
Issue number4
StatePublished - 1993
Externally publishedYes

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology


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