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Intercalation of daunomycin into d(CG)4 oligomer duplex containing G·T mismatches by vibrational circular dichroism and infrared absorption spectroscopy

The vibrational circular dichroism (VCD) and infrared absorption (IR) spectra of the mismatched octamer oligonucleotides d(CGTGCGCG)2 (CGT) and d(CGCGTGCG)2 (CGC) and their complexes with the antitumor drug daunomycin were measured in D2O, interpreted, and compared to the octamer d(CGCGCGCG)2 (CG). The IR spectra of the mismatched octamers in the carbonyl‐stretching region are similar to those of the parent CG, whereas the VCD spectra differ in several respects between each other. The main VCD feature due to carbonyl stretching is informative for the mismatches and CG. Vibrational modes in the sugar–phosphate region remain essentially unchanged especially for PO2− symmetric stretching. Differences between the free and complexed mismatch octamers occurred mainly in the carbonyl‐stretching region (1700–1600 cm−1). The absorption intensity of the CO peak of G is more prominent for CGC than CGT and resembles CG in this respect. The detailed composition of this doublet is clearly visible, indicating the geometric rearrangement of the base pairs in the presence of the mismatch and upon forming the daunomycin complex. © 2005 Wiley Periodicals, Inc. Biopolymers 82: 189–198, 2006