BENDING AND TORSIONAL FLEXIBILITY OF G C-RICH SEQUENCES AS DETERMINEDBY CYCLIZATION ASSAYS/

The structural polymorphism of DNA is a vital aspect of its biological function. However, it has become increasingly apparent in recent year s 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 con text. In order to address some of these additional factors that govern DNA conformation, we have used T4 ligase-mediated cyclization to inve stigate bending in a series of DNA sequences containing the GGGCCC . G GGCCC motif in different sequence contexts including various helical p hasings with (A)(5)-tracts. We present evidence for curvature in GGGCC C . GGGCCC and (A)(5)-tract motifs in the presence of physiological le vels of Mg2+ and show that these motifs curve through similar but oppo sitely directed bending angles under these ionic strength conditions. Although these two sequence motifs appear to bend similarly, our resul ts suggest significant differences in stiffness and stability of curva ture between them. We also show that under the same experimental condi tions, the CTAG . CTAG sequence element possesses unusual torsional fl exibility 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 co mplete predictive models for functionally related DNA polymorphism.