Extending conventional TIRF microscopy to image single molecules in micromolar analyte backgrounds

Abstract

Weak, reversible interactions underpin biomolecular recognition, and single-molecule fluorescence (smF) imaging techniques can provide unprecedented insight into those biological processes. Unfortunately, such studies often require micromolar concentrations of fluorophore-labeled biomolecules, which is beyond the accessible range of conventional smF microscopies. Here, we describe a surface-functionalization method based on cloud-point polyethylene glycol (PEG) grafting that enables widefield smF microscopy measurements at micromolar concentrations without the use of nanophotonic devices. Using conventional total internal reflection fluorescence (TIRF) microscopy, we detected single-molecule fluorescence resonance energy transfer (smFRET) from surface-tethered, donor-labeled target molecules with up to 8 μM concentrations of freely diffusing, acceptor-labeled analyte molecules in the background—two orders of magnitude higher than typical studies in the literature. Weak, DNA-hybridization and protein-RNA binding equilibria were measured across micromolar range titrations. Together with advances in high-background data analysis, the robust method presented here enables kinetic and thermodynamic analyses of weak biomolecular interactions, especially those limited by nonspecific adsorption and high fluorescence backgrounds, using only standard smF instrumentation.