Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 107, Issue 9, Pages 4004-4009Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0910781107
Keywords
protein engineering; compartmentalization; emulsion; horseradish peroxidase
Categories
Funding
- Human Frontier Science Program (HFSP) [RGP0004/2005-C102]
- National Science Foundation [DMR-0602684, DBI-0649865]
- Harvard Materials Research Science and Engineering Center [DMR-0820484]
- Centre National de la Recherche Scientifique
- Massachusetts Life Sciences Center
- Agence National de la Recherche [ANR-05-BLAN-0397]
- European Molecular Biology Organization
- European Commission
- Division Of Materials Research
- Direct For Mathematical & Physical Scien [820484] Funding Source: National Science Foundation
- Agence Nationale de la Recherche (ANR) [ANR-05-BLAN-0397] Funding Source: Agence Nationale de la Recherche (ANR)
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The explosive growth in our knowledge of genomes, proteomes, and metabolomes is driving ever-increasing fundamental understanding of the biochemistry of life, enabling qualitatively new studies of complex biological systems and their evolution. This knowledge also drives modern biotechnologies, such as molecular engineering and synthetic biology, which have enormous potential to address urgent problems, including developing potent new drugs and providing environmentally friendly energy. Many of these studies, however, are ultimately limited by their need for even-higher-throughput measurements of biochemical reactions. We present a general ultrahigh-throughput screening platform using drop-based microfluidics that overcomes these limitations and revolutionizes both the scale and speed of screening. We use aqueous drops dispersed in oil as picoliter-volume reaction vessels and screen them at rates of thousands per second. To demonstrate its power, we apply the system to directed evolution, identifying new mutants of the enzyme horseradish peroxidase exhibiting catalytic rates more than 10 times faster than their parent, which is already a very efficient enzyme. We exploit the ultrahigh throughput to use an initial purifying selection that removes inactive mutants; we identify similar to 100 variants comparable in activity to the parent from an initial population of similar to 10(7). After a second generation of mutagenesis and high-stringency screening, we identify several significantly improved mutants, some approaching diffusion-limited efficiency. In total, we screen similar to 10(8) individual enzyme reactions in only 10 h, using <150 mu L of total reagent volume; compared to state-of-the-art robotic screening systems, we perform the entire assay with a 1,000-fold increase in speed and a 1-million-fold reduction in cost.
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