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Computational Design of Asymmetric Three-dimensional RNA Structures and Machines.

Joseph D Yesselman, Daniel Eiler, Erik D Carlson, Alexandra N Ooms, Wipapat Kladwang, Xuesong Shi, David A Costantino, Daniel Herschlag, Michael C Jewett, Jeffrey S Kieft, Rhiju Das
doi: https://doi.org/10.1101/223479
Joseph D Yesselman
Department of Biochemistry, Stanford University School of Medicine;
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Daniel Eiler
Dept of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine;
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Erik D Carlson
Department of Chemical and Biological Engineering, Northwestern University;
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Alexandra N Ooms
Department of Cancer Genetics & Genomics, Stanford University School of Medicine
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Wipapat Kladwang
Department of Biochemistry, Stanford University School of Medicine;
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Xuesong Shi
Department of Biochemistry, Stanford University School of Medicine;
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David A Costantino
Dept of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine;
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Daniel Herschlag
Department of Biochemistry, Stanford University School of Medicine;
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Michael C Jewett
Department of Chemical and Biological Engineering, Northwestern University;
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Jeffrey S Kieft
Dept of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine;
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Rhiju Das
Department of Biochemistry, Stanford University School of Medicine;
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  • For correspondence: rhiju@stanford.edu
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Abstract

The emerging field of RNA nanotechnology seeks to create nanoscale 3D machines by repurposing natural RNA modules, but successes have been limited to symmetric assemblies of single repeating motifs. We present RNAMake, a suite that automates design of RNA molecules with complex 3D folds. We first challenged RNAMake with the paradigmatic problem of aligning a tetraloop and sequence-distal receptor, previously only solved via symmetry. Single-nucleotide-resolution chemical mapping, native gel electrophoresis, and solution x-ray scattering confirmed that 11 of the 16 (miniTTR) designs successfully achieved clothespin-like folds. A 2.55 Å diffraction-resolution crystal structure of one design verified formation of the target asymmetric nanostructure, with large sections achieving near-atomic accuracy (< 2.0 Å). Finally, RNAMake designed asymmetric segments to tether the 16S and 23S rRNAs together into a synthetic single-stranded ribosome that remains uncleaved by ribonucleases and supports life in Escherichia coli, a challenge previously requiring several rounds of trial-and-error.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted November 21, 2017.
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Computational Design of Asymmetric Three-dimensional RNA Structures and Machines.
Joseph D Yesselman, Daniel Eiler, Erik D Carlson, Alexandra N Ooms, Wipapat Kladwang, Xuesong Shi, David A Costantino, Daniel Herschlag, Michael C Jewett, Jeffrey S Kieft, Rhiju Das
bioRxiv 223479; doi: https://doi.org/10.1101/223479
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Computational Design of Asymmetric Three-dimensional RNA Structures and Machines.
Joseph D Yesselman, Daniel Eiler, Erik D Carlson, Alexandra N Ooms, Wipapat Kladwang, Xuesong Shi, David A Costantino, Daniel Herschlag, Michael C Jewett, Jeffrey S Kieft, Rhiju Das
bioRxiv 223479; doi: https://doi.org/10.1101/223479

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