Selected deoxyoctanucleotides and their daunomycin complexes: Infrared absorption and vibrational circular dichroism spectra

The infrared absorption (IR) and vibrational circular dichroism (VCD) spectra are reported for six self-complementary deoxyoctanucleotides complexed with the anthracycline drug daunomycin. The oligomers included d(CGCGCGCG) d(CGCGCGCG), d(CGCATGCG) d(CGCATGCG) and d(CGCTAGCG) d(CGCTAGCG), which possess a 50CGC triplet, and d(CGATATCG) d(CGATATCG), d(CGTATACG) d(CGTATACG) and d(CGAATTCG) d(CGAATTCG), which have either 50CGA or 50CGT triplets. The latter three triplets were said to be favorable intercalation sites for this drug, while the former three were considered to be non-preferred. Changes in the VCD spectra upon drug binding indicate a perturbation of the structure at the base step involving cytosine (Cy) and guanine (Gu), which appears to comprise the daunomycin intercalation site. The VCD spectra also show distinct changes as the drug binds with base sequences that contain 50CGC triplets compared to those with either 50CGA or 50CGT triplets. These differences are attributed to specific binding interactions of the DNA components with the functional groups of the aglycone chromophore and its amino sugar moiety. # 2006 Elsevier B.V. All rights reserved.