Split-Protein Systems for the Detection and Interrogation of Protein-Nucleic Acid Interactions

Abstract

Cys2-His2 zinc fingers constitute one of the largest classes of DNA-binding domains in the human genome. The modularity of these domains has been recently exploited to design artificial zinc fingers, capable of targeting virtually any sequence. However, the resultant zinc fingers have had significantly high failure rate, owing to low binding affinity and selectivity. Despite much research on the topic, a proper understanding of all the factors involved in zinc finger selectivity, be they natural or artificial, has proved elusive. Here, we present a modification of our previously reported SEquence-Enabled Reassembly (SEER) methodology, allowing us to study zinc finger selectivity with base pair resolution. Using this modified strategy, we show that the natural 3-finger zinc finger Zif268 binding to its consensus site is highly dependent on the availability of specific base pairs, or 'hot spots,' and independent of mutations at adjacent positions. Additionally, we show that positional interdependence plays a large role in the selectivity of both Zif268 and the artificial 6-finger zinc finger Aart for their respective targets. We envision that this technique can be easily applied towards the interrogation of any DNA-binding domain in a high throughput and accurate manner.