A novel class of polymeric fluorescent dyes assembled using a DNA synthesizer.

Tracy Matray,Erin Kwang,Hesham Sherif,Sharat Singh,Hiroaki Yada,Eriko Matsui,Michael Vanbrunt,Kenneth Farber,Marco Bonizzoni

doi:10.1371/journal.pone.0243218

Abstract

In the pursuit of a novel class of fluorescent dyes we have developed a programmable polymer system that enables the rational design and control of macromolecular constructs through simple control of polymer primary sequence. These polymers are assembled using standard phosphoramidite chemistry on a DNA synthesizer which allows for extremely rapid prototyping and enables many permutations due to the large selection of phosphoramidite monomers presently available on the market. This programmability to some extent allows us to control the interactions/spacing of payload molecules distributed along the designed polymeric backbone. Control of molecular architecture using this technology has allowed us to address the long-standing technical issue of contact quenching between fluorescent dyes offering new possibilities in the life sciences arena. Much like peptidic sequences coding for enzymes, cofactors, and receptors (all needing control of tertiary structure for proper function via primary sequence) our programmable system approaches a similar endpoint using a phosphate based polymeric backbone assembled in a completely automated fashion. Using this novel technology, we have efficiently synthesized several types of fluorescent dyes and demonstrated the programmability in molecule design, including the increases in brightness of the fluorescence emission.

Highlights

Fluorescent dyes are ubiquitous in modern day science due to their intrinsic ability to function as a reporter group enabling easy and efficient detection of target species in an extremely sensitive manner
It is our belief that this system will have far reaching impact due to the variety of “payloads” that can be loaded onto the prepositioned attachment points
We believe that many fields of research will benefit from this technology platform including materials science, probe based IVD assay development, imaging, and many others

Summary

Introduction

Fluorescent dyes are ubiquitous in modern day science due to their intrinsic ability to function as a reporter group enabling easy and efficient detection of target species in an extremely sensitive manner. Creative use of fluorescent molecules has promoted rapid growth in a multitude of areas including sequencing, imaging, PCR, flow cytometry, proteomics and FISH. While these unique molecules continue to play a critical role in scientific research, relatively few new classes have been developed beyond the classical small organic molecules such as xanthates, coumarins, cyanines and the protein type dyes like Phycoerythrin (PE). Additional fluorescent molecules with high absorptivity and emission characteristics that are excitable using currently available lasers are needed to improve ultrasensitive multiplexed biomarker detection.

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