|M.Sc Student||Allon Karin Zipora|
|Subject||Cooperative Sequence Dependent Binding of p53DBD to its|
|Department||Department of Biology||Supervisor||Professor Tali Haran|
|Full Thesis text|
The tumor suppressor protein p53 is a transcription factor that in response to various types of cellular stress regulates the expression of a variety of genes involved in cell cycle control, apoptosis, DNA repair and cell differentiation, by binding sequence-specifically to defined DNA targets. Abrogation of p53 sequence-dependent binding is implicated in approximately 50% of all known cancers. The p53 consensus binding site consists of two decameric sequences, or half sites, with the general form RRRCWWGYYY (R=A, G; W=A, T; Y=C, T). Between the two decamers there are between zero to thirteen bases. Most p53 natural targets differ from the consensus sequence in at least one position.
The WW motif at the center of each decamer is highly conserved, even though it does not bind directly to p53. The aim of my work was to quantitatively study the influence of changes in the WW motif and in the spacer sequences between two decamers on the affinity and cooperativity of p53 binding to its consensus binding sites. My results showed that there is a connection between an increase in the torsional flexibility in the WW motive to an increase in the binding affinity and a decrease in the binding cooperativity of p53 to its target sites.
Since most of the p53 native binding sites differ from the consensus sequence in at least one site, I also studied the binding site activity and cooperativity of p53 to some of its native binding sites. I did not quantify the changes in binding affinity and cooperativity, but from looking at the gels I saw compatibility between the results I got from the consensus binding site and the results I got from the native binding sites.