4.16. DNA Intercalation

Definition: There are several ways molecules (in this case, also known as ligands) can interact with DNA. Ligands may interact with DNA by covalently binding, electrostatically binding, or intercalating. Intercalation occurs when ligands of an appropriate size and chemical nature fit themselves in between base pairs of DNA. These ligands are mostly polycyclic, aromatic, and planar, and therefore often make good nucleic acid stains. Intensively studied DNA intercalators include berberine, ethidium bromide, proflavine, daunomycin, doxorubicin, and thalidomide. DNA intercalators are used in chemotherapeutic treatment to inhibit DNA replication in rapidly growing cancer cells. Examples include doxorubicin (adriamycin) and daunorubicin (both of which are used in treatment of Hodgkin's lymphoma), and dactinomycin (used in Wilm's tumour, Ewing's Sarcoma, rhabdomyosarcoma).
In order for an intercalator to fit between base pairs, the DNA must dynamically open a space between its base pairs by unwinding.

4.16.1. Types of Intercallators

DNA-binding agents tend to interact noncovalently with the host DNA molecule through two general modes: (i) Threading Intercalation: in a groove-bound fashion stabilized by a mixture of hydrophobic, electrostatic, and hydrogen-bonding interactions and (ii) Classical Intercalation: through an intercalative association in which a planar, heteroaromatic moiety slides between the DNA base pairs.
Intercalative binding, the most commonly studied, is the noncovalent stacking interaction resulting from the insertion of a planar heterocyclic aromatic ring between the base pairs of the DNA double helix.

4.16.2. The Mechanism of Intercalation
Intercalation as a mechanism of interaction between cationic, planar, polycyclic aromatic systems of the correct size (on the order of a base pair) was first proposed by Leonard Lerman in 1961. One proposed mechanism of intercalation is as follows: In aqueous isotonic solution, the cationic intercalator is attracted electrostatically to the polyanionic DNA. The ligand displaces a sodium and/or magnesium cation that always surrounds DNA (to balance its charge), forming a weak electrostatic bond with the outer surface of DNA. From this position, the ligand may then slide into the hydrophobic environment found between the base pairs and away from the hydrophilic outer environment surrounding the DNA. The base pairs transiently form such openings due to energy absorbed during collisions with solvent molecules.

4.16.3. Effect of Intercalation

Intercalation stabilizes, lengthens, stiffens, and unwinds the DNA double helix. The degree of unwinding varies depending on the intercalator. As for example, the ethidium cation unwinds DNA by about 26° and proflavine by about 17°.
These structural modifications can lead to functional changes, often to inhibition of transcription and replication and DNA repair processes, which make intercalators potent mutagens. There is much interest in the ability of intercalators to inhibit nucleic acid synthesis in vivo, leading to activity as mutagens, antibiotics, antibacterials, trypanocides, schistosomicides, and antitumor agents. Intercalative interactions between DNA duplexes and planar polycyclic aromatic organic intercalators, such as ethidium bromide, acridine and its derivatives, and benzo[a]pyrene (BP), have been thoroughly studied. Studies of bulky intercalators are rare. Bis-intercalators have also been reported, such as bisnaphthalimide, which exhibits antitumor activity. A tetraintercalator has been reported by Iverson, et al. Some of the potent polycyclic aromatic intercalators are listed in Figure 4.17 as a representative example.

Figure 4.17: Example of some DNA intercalators with their structures and applications.