Book of Abstracts: Albany 2003
June 17-21 2003
Inter-relationships Between A-tracts, G-tracts and Divalent Ions and Their Effect on the Intrinsic Bending Phenomenon
We have previously shown that nucleotide sequences between phased A4-6-tracts (at 10-11 bp intervals) have only a slight effect on overall curvature (1). To explore the phenomenon we have constructed a series of molecules containing various combinations of G,C-rich sequence motifs of the general form GnCm or CnGm (n+m>4, collectively called ?G-tracts?) and A-tracts and have looked at their gel-electrophoretic migration pattern (2). We use these sequences to examine the inter-relationship of G tracts and A-tracts in various sequence settings. Our findings demonstrate the non-uniformity of A-tract structure and its differential effect on sequences placed at the 3? versus the 5? side of A-tracts. Whereas A-tracts suppress, or make constant, the intrinsic bending characteristics of any sequence placed immediately 3? to them (and hence by definition any sequence placed between two phased A-tracts), sequences adjoining them on their 5?-side are free to modulate the overall curvature. We interpret these results as evidence for the dominant nature of the unique and non-uniform structure adopted by tracts of four adenines or more. The effects of A-tracts extend at least five base pairs into the adjoining 3? region. This is further evidence for the complexity of DNA structure, and the inadequacy of simple nearest-neighbor models to explain all its manifestations. In addition, the extent of bending by the GGGCCC motif, used in our studies, is significantly more pronounced than previously observed, and amount to 60% that of an A6-tract, in the absence of divalent ions. In contrast to previous studies we do not observe a significant effect of divalent ions on DNA curvature, when the experiments are carried out on sequences with various repeats. The significant effect of divalent ions on G-tract sequences is on the helical repeat of the studied sequences. Whereas it is more than 11bp/turn without divalent ions, it is less than 11 with divalent ions.
Department of Biology