Bending and torsional flexibility of G/C-rich sequences as determined by cyclization assays

Abstract

The structural polymorphism of DNA is a vital aspect of its biological function. However, it has become increasingly apparent in recent years that DNA polymorphism is a complicated, multidimensional phenomenon that includes not only static sequence-directed structures but dynamic effects as well, including influences of counterions and sequence context. In order to address some of these additional factors that govern DNA conformation, we have used T4 ligase-mediated cyclization to investigate bending in a series of DNA sequences containing the GGGCCC·GGGCCC motif in different sequence contexts including various helical phasings with (A)5-tracts. We present evidence for curvature in GGGCCC·GGGCCC and (A)5-tract motifs in the presence of physiological levels of Mg2+ and show that these motifs curve through similar but oppositely directed bending angles under those ionic strength conditions. Although these two sequence motifs appear to bend similarly, our results suggest significant differences in stiffness and stability of curvature between them. We also show that under the same experimental conditions, the CTAG·CTAG sequence element possesses unusual torsional flexibility and that this appears to be associated with the central TA·TA dinucleotide. The results underscore the need to include sequence context and specific ion effects as well as a dynamic basis in more complete predictive models for functionally related DNA polymorphism.