Recognition of left-handed Z-DNA of short unmodified oligonucleotides under physiological ionic strength conditions

Abstract

The left-handed Z-DNA form of the short unmodified alternating guanine–cytosine oligonucleotides, 5′-(dGdC)24 and 5′-(dGdC)18, was selectively detected under physiological ionic strength and pH conditions using the anionic nickel(II) porphyrin, NiTPPS. No spectroscopic signal was observed for NiTPPS with any right-handed oligonucleotides under identical conditions. The 48mer 5′-(dGdC)24 Z-form was detected at concentrations as low as 100nM. The binding of NiTPPS to the B- and Z-oligonucleotides was studied quantitatively by UV–vis absorption and circular dichroism spectroscopies. NiTPPS was found to be a universal DNA binder, with binding affinity and geometry depending on the ionic composition of the solution, rather than on the DNA helical twist. This is the first example of a successful spectroscopic detection of the Z-DNA of short unmodified oligonucleotides under physiological pH and ionic strength conditions.