The TATA-binding protein (TBP) is a key regulator of eukaryotic transcription initiation. The TBP homolog from Giardia intestinalis (gTBP) is highly divergent among all TBPs; notably lacking three of the four phenylalanine residues to unwind double- stranded DNA. I show that gTBP preferentially binds to single-stranded DNA (ssDNA) in two modes based on sequence and protein concentration. The proposed A mode likely represents multimeric binding of gTBP to ssDNA with four or more consecutive guanine bases. The B mode involves monomeric binding utilizing the structural properties of the ssDNA. To demonstrate this, I developed a novel technique using base stacking energy potentials to approximate the per-nucleotide flexibility of ssDNA. I also attempted to create a polynomial regression model to predict binding; however, further work is required to improve accuracy. Overall, this thesis presents a new perspective on eukaryotic transcription regulation based on the discovery of unconventional binding between gTBP and ssDNA.
Author Keywords: computer modelling, DNA binding protein, DNA structure, DNA transcription, general transcription factor (GTF), parasite