Molecular Life Sciences

Living Edition
| Editors: Robert D. Wells, Judith S. Bond, Judith Klinman, Bettie Sue Siler Masters, Ellis Bell

Base Intercalation in DNA

Living reference work entry


Intercalation is the stacking of a molecule between two bases in DNA (within one strand). This is a common process with a number of aromatic molecules and is driven by π- π, hydrophobic, steric, and other interactions.


One important mechanism in the interaction of carcinogens with DNA is base intercalation. This phenomenon is common with polycyclic aromatic structures, e.g., polycyclic aromatic hydrocarbons and aflatoxin B1. The process involves “stacking” of an aromatic ring(s) between two bases, particularly purines. The physical chemistry involves π interactions between the rings, allowing the carcinogen to slip in between two bases, in a sandwich mode.

Intercalators can be mutagenic themselves in that they can induce frameshift mutations without binding covalently, e.g., ethidium bromide. With reactive molecules such as aflatoxin B 1 8,9-epoxide and benzo[ a]pyrene 8,9-dihydrodiol-9,10-epoxide, intercalation is important in determining the sequence selectivity...


Polycyclic Aromatic Hydrocarbon Ethidium Bromide Aromatic Hydrocarbon Frameshift Mutation Initial Event 
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  1. Gopalakrishnan S, Harris TM, Stone MP (1990) Intercalation of aflatoxin B1 in two oligodeoxynucleotide adducts: comparative 1H NMR analysis of d(ATCAFBGAT).d(ATCGAT) and d(ATAFBGCAT)2. Biochemistry 29:10438–10448PubMedCrossRefGoogle Scholar
  2. Iyer R, Coles B, Raney KD et al (1994) DNA adduction by the potent carcinogen aflatoxin B1: mechanistic studies. J Am Chem Soc 116:1603–1609CrossRefGoogle Scholar

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© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Department of Biochemistry and Center in Molecular ToxicologyBiochemistry and Center in Molecular Toxicology, Vanderbilt University School of MedicineNashvilleUSA