Binding Modes

In general, two binding modes are possible between guest molecules and the host DNA: (a) minor or major groove binding, and (b) intercalation (Figure 2.5.1). A third binding mode, external binding, is also known; this results exclusively from attractive electrostatic interactions between a positively charged molecule and the negatively charged phosphate backbone of the DNA. In contrast, groove binding

Intercalation Groove Binding

Fig. 2.5.1. Binding modes of small molecules with DNA

and intercalation may be viewed as the formation of a supramolecular assembly based on associative interactions such as p stacking, hydrogen bonding, attractive van der Waals, or hydrophobic interactions. Each binding interaction is usually initiated by hydrophobic transfer of the DNA binder from the polar aqueous solution into the less polar environment of the DNA. If the DNA binder carries a positive charge, association with DNA also leads to a release of DNA counter cations from the DNA grooves.

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