RNA-aptamers-in-droplets (RAPID) high-throughput screening for secretory phenotypes

Nat Commun. 2017 Aug 23;8(1):332. doi: 10.1038/s41467-017-00425-7.


Synthetic biology and metabolic engineering seek to re-engineer microbes into "living foundries" for the production of high value chemicals. Through a "design-build-test" cycle paradigm, massive libraries of genetically engineered microbes can be constructed and tested for metabolite overproduction and secretion. However, library generation capacity outpaces the rate of high-throughput testing and screening. Well plate assays are flexible but with limited throughput, whereas droplet microfluidic techniques are ultrahigh-throughput but require a custom assay for each target. Here we present RNA-aptamers-in-droplets (RAPID), a method that greatly expands the generality of ultrahigh-throughput microfluidic screening. Using aptamers, we transduce extracellular product titer into fluorescence, allowing ultrahigh-throughput screening of millions of variants. We demonstrate the RAPID approach by enhancing production of tyrosine and secretion of a recombinant protein in Saccharomyces cerevisiae by up to 28- and 3-fold, respectively. Aptamers-in-droplets affords a general approach for evolving microbes to synthesize and secrete value-added chemicals.Screening libraries of genetically engineered microbes for secreted products is limited by the available assay throughput. Here the authors combine aptamer-based fluorescent detection with droplet microfluidics to achieve high throughput screening of yeast strains engineered for enhanced tyrosine or streptavidin production.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Aptamers, Nucleotide / genetics*
  • High-Throughput Screening Assays / methods*
  • Metabolic Engineering / methods*
  • Microfluidic Analytical Techniques / methods*
  • Microscopy, Fluorescence
  • Phenotype
  • Recombinant Proteins / biosynthesis
  • Reproducibility of Results
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Streptavidin / biosynthesis
  • Tyrosine / biosynthesis


  • Aptamers, Nucleotide
  • Recombinant Proteins
  • Tyrosine
  • Streptavidin