Democratizing single-molecule fret: an open-source microscope for measuring precise distances and biomolecular dynamics

B Ambrose, J Baxter, J Cully, M Willmott, BC Bateman… - Biophysical …, 2020 - cell.com
B Ambrose, J Baxter, J Cully, M Willmott, BC Bateman, E Steele, AJ Cadby, J Shewring…
Biophysical Journal, 2020cell.com
Single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful technique
capable of resolving relative and absolute distances within and between dynamic
biomolecules. However, its broad application by non-specialists is limited by the high costs
of commercial instruments, and a lack of open-source hardware and acquisition software.
Here, we present the smfBox, a confocal smFRET microscope constructed from readily
available optical components. We replaced the expensive microscope body with machined …
Single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful technique capable of resolving relative and absolute distances within and between dynamic biomolecules. However, its broad application by non-specialists is limited by the high costs of commercial instruments, and a lack of open-source hardware and acquisition software. Here, we present the smfBox, a confocal smFRET microscope constructed from readily available optical components. We replaced the expensive microscope body with machined aluminium and 3D-printed parts, forming a fully enclosed instrument that can be operated under ambient light conditions. We provide detailed assembly instructions and open-source acquisition software GitHub:(https://craggslab. github. io/smfBox/index. html), which outputs time-stamped photon arrivals in the photon-HDF5 file format. We show that the smfBox is capable of accurate absolute FRET measurements, reproducing the FRET efficiencies from our recent multi-lab benchmarking study, providing all the required analysis protocols as Jupyter notebooks. Additionally, we validate our microscope for measuring biomolecular conformational dynamics, by determining the opening and closing rates for DNA hairpins across a wide range of salt concentrations (using dynamic Photon Distribution Analysis). By varying the labelling position on the hairpin, we quantify the error in the rate measurements for different differences in FRET efficiency between the two interconverting conformations. Finally, we have developed a new single-molecule method sensitive to structural changes below 3 nm, Quantitative Quenchable FRET. Our data reveal a quantitative relationship between the overlap of the accessible volumes of donor and acceptor dyes, and quenching efficiency, which is well described by a simple kinetic model involving the local viscosity. This new tool extends the FRET toolbox for measurement of shorter distances, and also provides a single-molecule viscosity sensor, which we are exploiting in studies of membrane fluidity and liquid-liquid phase separation.
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