CD spectra and some properties of deoxyoligonucleotide duplexes having a C:G terminus (nucleosides and nucleotides. Part 69).

In the course of an investigation of the mode of recognition of nucleotide sequences with restriction endonucleases, several deoxyoligonucleotide duplexes having G:C terminal base pairs were synthesized. The oligonucleotides having a 5'-C (3'-G) terminus showed unusual CD spectra with a negative band at the longer wavelength region, when compared to those of the same internal sequences but a 5'-G (3'-C) terminus, which showed a positive band like the B- or A-DNA type. The nature of these CD spectra was compared with those of the Z-DNAs on the effect of salt concentrations, intercalation with ethidium bromide, or 31P-NMR spectra. These unusual spectra may be attributed to the terminal effect of the 5'-C:3'-G pairs.