Structure and drug interactions of parallel-stranded DNA studied by infrared spectroscopy and fluorescence

The infrared spectra of three different 25-mer parallel-stranded DNAs (ps-DNA) have been studied. We have used ps-DNAs containing either exclusively dA-dT base pairs or substitution with four dG-dC base pairs and have them compared with their antiparallel-stranded (aps) reference duplexes in a conventional B-DNA conformation. Significant differences have been found in the region of the thymine C = O stretching vibrations. The parallel-stranded duplexes showed characteristic marker bands for the C2 = 02 and C4 = 04 carbonyl stretching vibrations of thymine at 1685 cm-1 and 1668 cm-1, respectively, as compared to values of 1696 cm- 1 and 1663 cm~1 for the antiparallel-stranded reference duplexes. The result