Abstract
Tandem repeats make up a small fraction of the human genome, but due to their high rates of expansion and contraction, they are predicted to be highly polymorphic. When tandem repeats are found within functional regions of the genome, these polymorphisms can modulate phenotypes, which can result in disease. This thesis investigates tandem repeats composed of short subunits, called microsatellites, short tandem repeats, or simple sequence repeats. Part of this thesis investigates how these tandem repeats can be conserved in mammals, and explains how the most conserved of these repeats are found in regions of the genome that regulate gene expression and mRNA translation. Many of these highly conserved microsatellites are found in genes that regulate development, highlighting the exciting possibility that mammalian development can be modulated by these hypermutable elements. Some regulatory microsatellites have the potential to form unusual DNA structures, and these structures are known to regulate RNA production and DNA replication. To further investigate how tandem repeats can form alternative DNA structures, this thesis examines how DNA polymerase interacts with repeats known to form various structures. A relatively new method of DNA sequencing, from Pacific Biosciences, records polymerase activity in real-time and at single-molecule resolution. The sequencer kinetics are used to study the interaction between polymerase and two structures: G-quadruplex DNA, known for its ability to pause polymerase and its prevalence in regulatory regions; and Z-DNA, a left-handed double helix that is also prevalent in regulatory regions. In total, this thesis examines how human microsatellites can be sources of phenotypic variation, and discusses methods for genotyping and interpreting the genetic variation prevalent in these repeats.