Using droplet-based microfluidics to improve the catalytic properties of RNA under multiple-turnover conditions

Abstract

In vitro evolution methodologies are powerful approaches to identify RNA with new functionalities. While Systematic Evolution of Ligands by Exponential enrichment (SELEX) is an efficient approach to generate new RNA aptamers, it is less suited for the isolation of efficient ribozymes as it does not select directly for the catalysis. In vitro compartmentalization (IVC) in aqueous droplets in emulsions allows catalytic RNAs to be selected under multiple-turnover conditions but suffers severe limitations that can be overcome using the droplet-based microfluidics workflow described in this paper. Using microfluidics, millions of genes in a library can be individually compartmentalized in highly monodisperse aqueous droplets and serial operations performed on them. This allows the different steps of the evolution process (gene amplification, transcription, and phenotypic assay) to be uncoupled, making the method highly flexible, applicable to the selection and evolution of a variety of RNAs, and easily adaptable for evolution of DNA or proteins. To demonstrate the method, we performed cycles of random mutagenesis and selection to evolve the X-motif, a ribozyme which, like many ribozymes selected using SELEX, has limited multiple-turnover activity. This led to the selection of variants, likely to be the optimal ribozymes that can be generated using point mutagenesis alone, with a turnover number under multiple-turnover conditions, k ss cat , ∼28-fold higher than the original X-motif, primarily due to an increase in the rate of product release, the rate-limiting step in the multiple-turnover reaction.

Dissecting enzyme function with microfluidic-based deep mutational scanning

“…In addition to glycosidases, emulsion-based methods have been used to screen DNA/RNA polymerases, oxidoreductases, sulfatases, peroxidases, esterases, proteases, and even ribozymes (10,11,(33)(34)(35)(36)(37). The greatest challenge with emulsion-based screening is finding a fluorescent assay for one's particular enzyme of interest.…”

Discovery in Droplets

“…Incubation occurs off-line. Figure adapted from Ryckelynck, M.; Baudrey, S.; Rick, C.; Marin, A.; Coldren, F.; Westhof, E.; Griffiths, A. D. RNA 2015 , 21 , 458–469 (ref 56) under a Creative Commons License.…”

Compartmentalization – A Prerequisite for Maintaining and Changing an Identity

“…The applications for small compartments in life sciences are manifold and range from enzyme [22] and ribozyme engineering [23] via analysis of DNA populations [24] to genome sequencing based on next-generation sequencing technology. [25] The applications can be divided into two parts, in vitro and in vivo screenings.…”

“…as riboswitches) or to catalyze reactions (ribozymes). [23] A sophisticated variation of the protocol includes the use of droplets in a transcriptomics application: mRNA molecules containing the poly-adenosine tail can be captured via poly-thymidine functionalized micro beads from single cells encapsulated into droplets, reverse transcribed and amplified for further single cell transcriptome analysis. [32] Magnetic Beads Magnetic beads can serve as an anchor point for DNA molecules much as a cell gives a first compartment to a bacterial chromosome or plasmids.…”