Optical crosstalk in SPAD arrays for high-throughput single-molecule fluorescence spectroscopy

Modeling for Single-Photon Avalanche Diodes: State-of-the-Art and Research Challenges

With the growing importance of single-photon-counting (SPC) techniques, researchers are now designing high-performance systems based on single-photon avalanche diodes (SPADs). SPADs with high performances and low cost allow the popularity of SPC-based systems for medical and industrial applications. However, few efforts were put into the design optimization of SPADs due to limited calibrated models of the SPAD itself and its related circuits. This paper provides a perspective on improving SPAD-based system design by reviewing the development of SPAD models. First, important SPAD principles such as photon detection probability (PDP), dark count rate (DCR), afterpulsing probability (AP), and timing jitter (TJ) are discussed. Then a comprehensive discussion of various SPAD models focusing on each of the parameters is provided. Finally, important research challenges regarding the development of more advanced SPAD models are summarized, followed by the outlook for the future development of SPAD models and emerging SPAD modeling methods.

High-throughput smFRET analysis of freely diffusing nucleic acid molecules and associated proteins

Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique for nanometer-scale studies of single molecules. Solution-based smFRET, in particular, can be used to study equilibrium intra- and intermolecular conformations, binding/unbinding events and conformational changes under biologically relevant conditions without ensemble averaging. However, single-spot smFRET measurements in solution are slow. Here, we detail a high-throughput smFRET approach that extends the traditional single-spot confocal geometry to a multispot one. The excitation spots are optically conjugated to two custom silicon single photon avalanche diode (SPAD) arrays. Two-color excitation is implemented using a periodic acceptor excitation (PAX), allowing distinguishing between singly- and doubly-labeled molecules. We demonstrate the ability of this setup to rapidly and accurately determine FRET efficiencies and population stoichiometries by pooling the data collected independently from the multiple spots. We also show how the high throughput of this approach can be used o increase the temporal resolution of single-molecule FRET population characterization from minutes to seconds. Combined with microfluidics, this high-throughput approach will enable simple real-time kinetic studies as well as powerful molecular screening applications.