A transcriptional reporting system for sensing interactions of small molecules with proteins

Characterizing binding interactions of small molecules with proteins is important in many areas of
chemistry and biology. We show here that a transcriptional activation sequence from Escherichia Coli
(E. coli) can be exploited to create a binding sensor for small molecule/protein interactions. The system
requires two key components: small molecules connected to a DNA bearing a transcriptional activation
sequence (TAS) and proteins of interest (POIs) expressed as fusions with the transcriptional activation
domain (TAD) from the phage shock protein F (PspF). If the DNA bound small molecule binds to the
POI, the induced proximity of the TAD to the TAS initiates transcription, with the number of copies of
RNA produced proportional to the binding affinity. Although numerous direct binding measurement
techniques are known, very few of these amplify binding signals, or convert the binding signal to a
different molecular form which is then easy to handle and quantify. We demonstrate several
circumstances where the technique will prove valuable, such as in characterizing binders, identifying
molecular glues, high-throughput screening, or as a reporter in DNA encoded library (DEL) selections.