Algorithms for the selection of fluorescent reporters

Prashant Vaidyanathan,George Church,Douglas Densmore,David Tran,Alexander Vahid,Evan Appleton

doi:10.1038/s42003-020-01599-5

Abstract

Molecular biologists rely on the use of fluorescent probes to take measurements of their model systems. These fluorophores fall into various classes (e.g. fluorescent dyes, fluorescent proteins, etc.), but they all share some general properties (such as excitation and emission spectra, brightness) and require similar equipment for data acquisition. Selecting an ideal set of fluorophores for a particular measurement technology or vice versa is a multidimensional problem that is difficult to solve with ad hoc methods due to the enormous solution space of possible fluorophore panels. Choosing sub-optimal fluorophore panels can result in unreliable or erroneous measurements of biochemical properties in model systems. Here, we describe a set of algorithms, implemented in an open-source software tool, for solving these problems efficiently to arrive at fluorophore panels optimized for maximal signal and minimal bleed-through.

Highlights

Molecular biologists rely on the use of fluorescent probes to take measurements of their model systems
Biologists and laboratories might be limited to panel designs that have already been studied and published or might have to limit the solution space based on an intuitive understanding of the emission and excitation spectra of the fluorophores available, to design a panel
Our software uses search algorithms to explore the solution space of all possible n-panel configurations that can be constructed from a library of fluorophores for a fluorescence measurement instrument to find optimal panel configurations (Supplementary Section 1)

Summary

Introduction

Molecular biologists rely on the use of fluorescent probes to take measurements of their model systems. We created a computational solution housed in an open-source software tool to solve the following problem—given a measurement instrument where the laser and detector configurations are known, and a library of fluorophores under consideration, design an optimized n-color panel of fluorophores by maximizing the amount of signal in each detector and minimizing the amount of bleed-through.

Results

Conclusion