Mechanisms of drug–DNA recognition distinguished by Raman spectroscopy, ,†‡

The highly chromophoric drugs, ethidium bromide (EtBr), 9-aminoacridine (9AA) and proflavine (PF) (3,6-diaminoacridine) bind to DNA by insertion of a polycyclic aromatic ring between adjacent base pairs of the double helix. Despite similar intercalative mechanisms, these drugs exhibit distinct DNA affinities and produce characteristic mutagenic effects. Complexes of the intercalants with small nucleotide fragments have been investigated by various methods, including X-ray crystallography. However, the structural impact of drug intercalation on a DNA molecule of genetic consequence has not yet been reported. Here, we employ near-infrared laser excitation (752 nm) and a DNA target of genomic size to obtain and compare Raman spectra of complexes of EtBr, 9AA and PF with DNA. Raman signatures of solution complexes have been analyzed by difference methods to reveal the specific structural changes induced at the drug/DNA intercalation sites. Perturbation of the DNA backbone geometry, as reflected in the Raman marker diagnostic of the phosphodiester group (800–880 cm−1), ranges from disruption of the B-form duplex in favor of either the A-form duplex, or separated strands, or a combination of altered DNA backbone geometries. The acridine intercalants, PF and 9AA, also perturb hydrogen-bonding interactions between the paired bases of duplex DNA, although in distinct ways. Conversely, base pairing is relatively unperturbed by ethidium intercalation. The results are discussed in relation to frameshift mutagenic activities of the intercalating drugs. Copyright © 2008 John Wiley & Sons, Ltd.