DNA-protein binding specificity remains insufficiently comprehended to enable quantitative and accurate predictions of interactions between arbitrary nucleotide and peptide sequences. Yet, specificity in binding between DNA and protein is imperative for life as we know it. A myriad of different disease states are linked to mutations, either in regulatory DNA regions or in the transcription factors that bind them. To develop effective treatments against diseases with a causal relationship to altered DNA-protein interaction dynamics, it is crucial that we understand the underlying mechanisms that govern their binding. High-throughput quantitative methods will likely play a major role in the deciphering of the dually encoded information in DNA and protein sequences.   In the last decade new methodologies that repurpose Illumina’s next generation sequencing systems for high-throughput quantitative studies of interactions between a wide range of biomolecules have emerged. While these new assays have truly revolutionized our ability to study biomolecular interactions, they suffer from limitations that restrict their current applications. Most notably, they suffer from an inherent noise level that limits the user to only detect interactions of high enough affinities, and they only allow for deep mutational screening of one of the interacting partners. In this degree project, method development for improved quantitative high-throughput affinity measurements of DNA-protein interactions has been started.  Herein it is demonstrated that dCas9-transcription factor fusion proteins and DNA anchors with dCas9 and transcription factor binding sites required for implementation of the improved method, can be created by recombinant production in Escherichia coli and by PCR respectively. Furthermore, it is shown that each partner may be robustly and site-specifically labeled with FRET compatible fluorophores, a necessity for the proposed implementation, by Halo-tag labeling for the fusion protein and by fluorogenic PCR for the DNA anchor. Lastly, it is found that some required activities of the parts are retained but that others require further optimization.