Temporal DNA Barcodes: A Time-Based Approach for Single-Molecule Imaging

Improved Optical Multiplexing with Temporal DNA Barcodes

Many biochemical events of importance are complex and dynamic. Fluorescence microscopy offers a versatile solution to study the dynamics of biology at the mesoscale. An important challenge in the field is the simultaneous study of several objects of interest, referred to as optical multiplexing. For improved multiplexing, some prior techniques used repeated reporter washing or the geometry of nanostructures; however, these techniques require complex nanostructure assembly, multiple reporters, or advanced multistep drift correction. Here we propose a time-based approach, for improved optical multiplexing, that uses readily available inexpensive reporters and requires minimal preparation efforts. We program short DNA strands, referred hereby as DNA devices, such that they undergo unique conformation changes in the presence of the dye-labeled reporters. The universal fluorescent reporter transiently binds with the devices to report their activity. Since each device is programmed to exhibit different hybridization kinetics, their fluorescent time trace, referred to as the temporal barcode, will be unique. We model our devices using continuous-time Markov chains and use stochastic simulation algorithm to generate their temporal patterns. We first ran simulation experiments with a small number of DNA devices, demonstrating several distinct temporal barcodes, all of which use a single dye color. Later, using nanostructure-based devices, we designed a much larger pool of temporal barcodes and used machine learning for classification of these barcodes. Our simulation experiments and design principles can aid in the experimental demonstration of the DNA devices.

Programming Temporal DNA Barcodes for Single-Molecule Fingerprinting

Fluorescence microscopy enables simultaneous observation of the dynamics of single molecules in a large region of interest. Most traditional techniques employ either the geometry or the color of single molecules to uniquely identify (or barcode) different species of interest. However, these techniques require complex sample preparation and multicolor hardware setup. In this work, we introduce a time-based amplification-free single-molecule barcoding technique using easy-to-design nucleic acid strands. A dye-labeled complementary reporter strand transiently binds to the programmed nucleic acid strands to emit temporal intensity signals. We program the DNA strands to emit uniquely identifiable temporal signals for molecular-scale fingerprinting. Since the reporters bind transiently to DNA devices, our method offers relative immunity to photobleaching. We use a single universal reporter strand for all DNA devices making our design extremely cost-effective. We show DNA strands can be programmed for generating a multitude of uniquely identifiable molecular barcodes. Our technique can be easily incorporated with the existing orthogonal methods that use wavelength or geometry to generate a large pool of distinguishable molecular barcodes thereby enhancing the overall multiplexing capabilities of single-molecule imaging.