|M.Sc Thesis||Department of Biology|
I have examined the gel-migration properties of sequences containing both A-tracts as well as G,C-rich motifs (i.e., sequences of the form GnCm or CnGm n+m>4) in various sequence settings. I show that A-tracts influence their flanking sequences in a differential manner. Whereas they suppress the intrinsic bending characteristics of any sequence placed immediately 3` to them (and hence by definition any sequence placed between two phased A-tracts), they do not have any influence on sequences adjoining them on their 5`-end. I 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 that the DNA structure is complex and can not be analyzed by simple models that refer only to the interactions between base pairs of nearest neighbors.
In further investigations I have examined the affect of MPD on the gel-migration properties of random B-DNA molecules as well as A-tract-containing DNA molecules using ligation ladder analysis. Here I found that MPD influences the gel-migration properties of both random B-DNA and A-tract-containing DNA molecules and that the magnitude of the change is the same in both cases. Hence we can not use RL (relative length) values as the analytic tool to always analyze the experimental results. These studies have resolved a long standing open question on the discrepancy between solution and crystal studies on sequence-directed DNA bending.