NanoBlocks: creating fluorescent biosensors from affinity binders using competitive binding

Abstract

Genetically-encoded fluorescent biosensors have revolutionized our understanding of complex systems by permitting the in situ observation of chemical activities. However, only a comparatively small set of chemical activities can be monitored, largely due to the need to identify protein domains that undergo conformational and/or association changes in response to a stimulus. Here, we present a strategy that can convert simple affinity binders such as nanobodies into biosensors for their innate targets by introducing a peptide sequence that competes for the binding site. We demonstrate proof-of-concept implementations of this NanoBlock design, developing sensors based on the ALFA nanobody and on the PDZ domain of Erbin. We show that these sensors can reliably detect their targets in vitro, in mammalian cells, and as part of fluorescence-activated cell sorting (FACS) experiments. In doing so, our strategy offers a way to strongly expand the range of cellular processes that can be probed using fluorescent biosensors.