B-Z Transition of Synthetic Oligonucleotides Containing Non-Z Forming Elements

Abstract

Ten oligonucleotides of the length 8–12 base pairs have been synthesized, which contain, in addition to the obligatory sequences CG/CG, sequences not favorable for the transition to the Z conformation (AT pairs, GG/CC or AA/TT sequences). Conformational transitions of these oligonucleotides in high concentrations of NaClO₄ in the absence and in the presence of Ni²⁺ were investigated using CD spectroscopy.

The B-Z transition is affected by the length and sequence of the oligonucleotide. Increasing the NaC1O₄ concentration alone the transition of only one of the oligonucleotides studied, (CGCGCGTGC ACGCGCG)₂, can be induced. Other oligonucleotides remain in the B conformation or only partial transition to the Z conformation can be observed.

Most other oligonucleotides can be converted into the Z conformation at intermediate concentrations of NaC1O₄ (2.0−3.2 M) by an addition of Ni²⁺ ions. In some cases, however, Ni²⁺ can destabilize the double stranded structure of the sample. We have studied the effect of the presence of A.T pairs in the G.C containing oligonucleotides and the effect of the presence of pu-pu/pyr-pyr sequences. The presence of the latter sequences in the Z form implicates the formation of a Z-Z′ junction which makes the transition quite difficult. Despite the fact that some oligonucleotides contained several structural elements not favorable for the transition, we did not find any sequence which would completely block the ability of the oligonucleotide to adopt the Z conformation.