Dynamics of Bent Molecules in Gels

The unique structure of A-tracts and intrinsic DNA bending

Short runs of adenines are a ubiquitous DNA element in regulatory regions of many organisms. When runs of 4–6 adenine base pairs (‘A-tracts’) are repeated with the helical periodicity, they give rise to global curvature of the DNA double helix, which can be macroscopically characterized by anomalously slow migration on polyacrylamide gels. The molecular structure of these DNA tracts is unusual and distinct from that of canonical B-DNA. We review here our current knowledge about the molecular details of A-tract structure and its interaction with sequences flanking them of either side and with the environment. Various molecular models were proposed to describe A-tract structure and how it causes global deflection of the DNA helical axis. We review old and recent findings that enable us to amalgamate the various findings to one model that conforms to the experimental data. Sequences containing phased repeats of A-tracts have from the very beginning been synonymous with global intrinsic DNA bending. In this review, we show that very often it is the unique structure of A-tracts that is at the basis of their widespread occurrence in regulatory regions of many organisms. Thus, the biological importance of A-tracts may often be residing in their distinct structure rather than in the global curvature that they induce on sequences containing them.