Cyclization duplex

Form I, may undergo various transformations that are readily assayed, this DNA is of particular utility as a probe of binding of small molecules. The basic feature is that, upon cyclization of a helical duplex, the total number of turns of one strand about the other remains a topological constant therefore, changes in the number of Watson—Crick turns in the closed form will be uniquely related to the number of supercoil turns. This is expressed [36, 37] as... 

It is now well known that certain base sequences lead to intrinsic curvature of duplex DNA. This is notably the case for tracts of four or more AT base pairs placed so that they occur in phase with the helical repeat of the duplex. This leads to the conclusion that certain base pair steps, or certain base pair tracts, should be associated with specific conformations able to deflect the axis of the double helix. An early analysis by Trifonov and Sussman showed that AA (and TT) steps had a clear tendency to be separated from one another by one helical turn within nucleosome binding sequences. Gel mobility studies, cyclization experiments and electron microscopy all subsequently confirmed that sequences containing repeated A-tracts were indeed intrinsically curved. Since this time other sequences have also been shown to produce curvature, although the effect of repeated AA steps still appears to be dominant. 

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