Triple helix formation inhibits DNA gyrase activity

The goal of this work was to examine the effect of triple helix-forming oli gonucleotides on a gyrase target region and on the activity of the enzyme. Using melting temperature measurements and gel mobility shift analysis, it was found that modified oligonucleotides can form a triple helix along the 29-nucleotide region of a 32-bp duplex representing part of the gyrase DNA- target sequence of the 162-bp fragment from pBR322. Tripler formation with this target region has been achieved at pH 7.5 by using a synthetic oligonu cleotide in which cytosine was replaced by the C-nucleoside of 2-aminopyrid ine. The results of the enzymic experiments in vitro with the 162-bp fragme nt demonstrated that the cleavage reaction mediated by gyrase can be effici ently inhibited by the tripler-forming oligonucleotide modified with 2-amin opyridine. A possible inhibitory mechanism is discussed.