Small Circles of Helical DNA Obtained on the Basis of Transcriptional Pause Sites Sequence

Abstract

The 21-base pair synthetic DNA duplexes with basic ‘pause-motif’ site (‘CATGC’) were ligated head-to-tail to produce linear and circular multimers. This also was done from other closely related sequences. Electrophoretic mobilities of the linear multimers in Polyacrylamide gels were determined under the standard and modified conditions. We revealed that small linear multimers (∼ 90 bp) were characterized by comparable value of gel retardation relative to the well known curved DNA, while longer multimers (130–170 bp) had only slightly expressed mobility anomaly. Nevertheless these multimers containing nontruncated ‘pause-motif were capable of cyclization, in particular, formation of unusually small circles while truncated ones were not. We conclude that basic ‘pause-motif site increases the closure ability while the multimers based on truncated ‘pause motif fail to curve into the small circles. We tend to explain this situation as a result of intrinsic bending as well as the influence of the thermal fluctuations of DNA, the latter most probably can be associated with ‘pause motif. We have estimated the equilibrial and maximal bend angles per 10.5 bp to be 12°∼16° and 32° accordingly under experimental conditions of our study.