Quantifying the performance of high-throughput directed evolution protocols

Most protocols for the high-throughput directed evolution of enzymes rely on random encapsulation to link phenotype and genotype. In order to optimize these approaches, or compare one to another, one needs a measure of their performance at extracting the best variants. We introduce here a new metric...

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Bibliographic Details
Published in:arXiv.org 2018-11
Main Authors: Dramé-Maigné, Adèle, Zadorin, Anton, Golovkova, Iaroslava, Rondelez, Yannick
Format: Article
Language:English
Subjects:
Encapsulation
Evolution
Online Access:Get full text
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Summary:Most protocols for the high-throughput directed evolution of enzymes rely on random encapsulation to link phenotype and genotype. In order to optimize these approaches, or compare one to another, one needs a measure of their performance at extracting the best variants. We introduce here a new metric named the Selection Quality Index (SQI), which can be computed from a simple mock experiment with a known initial fraction of active variants. As opposed to previous approaches, our index integrates the random co-encapsulation of entities in compartments and comes with a straightforward experimental interpretation. We further show how this new metric can be used to extract general trends of protocol efficiency, or reveal hidden mechanisms such as a counterintuitive form of beneficial poisoning in the Compartmentalized Self-Replication protocol.
ISSN:2331-8422