Base Intercalation in DNA

Definition

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.

Discussion

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 B₁ 8,9-epoxide and benzo[a]pyrene 8,9-dihydrodiol-9,10-epoxide, intercalation is important in determining the sequence selectivity...