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RNA design rules from a massive open laboratory.

ABSTRACT: Self-assembling RNA molecules present compelling substrates for the rational interrogation and control of living systems. However, imperfect in silico models--even at the secondary structure level--hinder the design of new RNAs that function properly when synthesized. Here, we present a unique and potentially general approach to such empirical problems: the Massive Open Laboratory. The EteRNA project connects 37,000 enthusiasts to RNA design puzzles through an online interface. Uniquely, EteRNA participants not only manipulate simulated molecules but also control a remote experimental pipeline for high-throughput RNA synthesis and structure mapping. We show herein that the EteRNA community leveraged dozens of cycles of continuous wet laboratory feedback to learn strategies for solving in vitro RNA design problems on which automated methods fail. The top strategies--including several previously unrecognized negative design rules--were distilled by machine learning into an algorithm, EteRNABot. Over a rigorous 1-y testing phase, both the EteRNA community and EteRNABot significantly outperformed prior algorithms in a dozen RNA secondary structure design tests, including the creation of dendrimer-like structures and scaffolds for small molecule sensors. These results show that an online community can carry out large-scale experiments, hypothesis generation, and algorithm design to create practical advances in empirical science.

SUBMITTER: Lee J

PROVIDER: S-EPMC3926058 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature

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RNA design rules from a massive open laboratory.

Lee Jeehyung J Kladwang Wipapat W Lee Minjae M Cantu Daniel D Azizyan Martin M Kim Hanjoo H Limpaecher Alex A Yoon Sungroh S Treuille Adrien A Das Rhiju R

Proceedings of the National Academy of Sciences of the United States of America 20140127 6

Self-assembling RNA molecules present compelling substrates for the rational interrogation and control of living systems. However, imperfect in silico models--even at the secondary structure level--hinder the design of new RNAs that function properly when synthesized. Here, we present a unique and potentially general approach to such empirical problems: the Massive Open Laboratory. The EteRNA project connects 37,000 enthusiasts to RNA design puzzles through an online interface. Uniquely, EteRNA ...[more]

PMID: 24469816

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RNA design rules from a massive open laboratory.

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RNA design rules from a massive open laboratory.

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