The biological process of transcription creates from a template DNA strand (i.e., the gene) copies of short-lived mRNA. The amount of mRNA produced determines the gene's expression in the cell, which affects the activity of the gene at a given time. Transcription factors are proteins which bind to the DNA in the neighborhood of the gene in order to regulate the location and rate of transcription. An important biological question is therefore to find binding locations and binding strengths for transcription factors.

This has traditionally been a laborious experimental process, but a new technology called a protein-binding microarray allows us to assay the binding affinities of a given transcription factor for many different DNA sequences in parallel. This thesis addresses a suitable combinatorial design for these microarrays that is both effective and economical.