DNA barcoding for parallelised single-molecule characterisation of kinetic phenotypes

Single-molecule techniques provide exceptional resolution of biomolecular dynamics but are limited by low-throughput. We present a barcoding strategy that enables simultaneous kinetic profiling of multiple protein variants at the single-molecule level. Each protein is covalently linked to a unique DNA barcode, decoded via transient hybridisation of fluorescent probes distinguished by colour and binding duration. We applied this method to a library of 16 ClpS variants to systematically explore evolutionary trajectories towards a variant adapted to recognise N-terminal amino acids with binding kinetics optimised for single-molecule peptide sequencing. The approach uncovered ~5-fold variation in median dissociation rates across variants. Several variants displayed bimodal kinetics, likely reflecting structural subpopulations, and differences in kinetic properties arose primarily from the relative abundance of these phenotypes. This approach offers a general framework for screening and optimising proteins for single-molecule applications, while revealing mechanistic insights that are inaccessible to traditional ensemble methods.