Poly (ADP-ribose) polymerase 1: DNA complexes are dependent on DNA sequence and secondary structure

Cell dysfunction leads to over-production of proteins, uncontrolled growth, and tumor formation. This dysfunction is the calling card of cancer. In this thesis study I examine a multifunctional DNA binding protein, PARP1, to characterize the effect that unique DNA structures, G-quadruplexes, have on DNA binding and activation of PARP1 self-assembly of poly (ADP-ribose) chains. I will demonstrate that this activity is influenced by the structure and sequence of the DNA bound by PARP1 and using a technique to monitor binding of PARP1 protein to a single DNA molecule. I will highlight the important details of these interactions by a novel ratio of PARP1 binding to G-quadruplex DNA. I will then demonstrate a new technique combining single-molecule experiments with next generation DNA sequencing, using Illumina sequencing flow cells. While still in developmental stages, this technique can reveal a host of new information about PARP1 binding and self-modification, or autoPARylation on binding to G-quadruplex DNA. After demonstrating preliminary studies, I will make a case for continued improvement in the data analysis tools used in these experiments, with an end goal of creating a tool that any scientific lab can use as part of a routine workflow.