Effect of terminal base pairs on the CD spectra of oligodeoxynucleotide duplexes

Oligodeoxynucleotide duplexes having terminal C:G base pairs and recognition sequences for restriction endonucleases Bgl II and Sau 3Al were synthesized by the solid or liquid phase phosphotriester approach. Among them, the self-complementary oligonucleotides with C or CC at the 5'-end and G or GG at the 3'-end exhibited unusual CD spectra in contrast to those of the usual B-DNA type CD spectra of the oligonucleotide with G or GG at the 5'-end. The spectra are different to those of the Z-DNA, and regarded to the terminal base effect of the C:G pairs.