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Theoretical basis for stabilizing messenger RNA through secondary structure design.
Wayment-Steele, Hannah K; Kim, Do Soon; Choe, Christian A; Nicol, John J; Wellington-Oguri, Roger; Watkins, Andrew M; Parra Sperberg, R Andres; Huang, Po-Ssu; Participants, Eterna; Das, Rhiju.
  • Wayment-Steele HK; Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
  • Kim DS; Eterna Massive Open Laboratory.
  • Choe CA; Eterna Massive Open Laboratory.
  • Nicol JJ; Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.
  • Wellington-Oguri R; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.
  • Watkins AM; Eterna Massive Open Laboratory.
  • Parra Sperberg RA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
  • Huang PS; Eterna Massive Open Laboratory.
  • Participants E; Eterna Massive Open Laboratory.
  • Das R; Eterna Massive Open Laboratory.
Nucleic Acids Res ; 49(18): 10604-10617, 2021 10 11.
Article in English | MEDLINE | ID: covidwho-1406489
ABSTRACT
RNA hydrolysis presents problems in manufacturing, long-term storage, world-wide delivery and in vivo stability of messenger RNA (mRNA)-based vaccines and therapeutics. A largely unexplored strategy to reduce mRNA hydrolysis is to redesign RNAs to form double-stranded regions, which are protected from in-line cleavage and enzymatic degradation, while coding for the same proteins. The amount of stabilization that this strategy can deliver and the most effective algorithmic approach to achieve stabilization remain poorly understood. Here, we present simple calculations for estimating RNA stability against hydrolysis, and a model that links the average unpaired probability of an mRNA, or AUP, to its overall hydrolysis rate. To characterize the stabilization achievable through structure design, we compare AUP optimization by conventional mRNA design methods to results from more computationally sophisticated algorithms and crowdsourcing through the OpenVaccine challenge on the Eterna platform. We find that rational design on Eterna and the more sophisticated algorithms lead to constructs with low AUP, which we term 'superfolder' mRNAs. These designs exhibit a wide diversity of sequence and structure features that may be desirable for translation, biophysical size, and immunogenicity. Furthermore, their folding is robust to temperature, computer modeling method, choice of flanking untranslated regions, and changes in target protein sequence, as illustrated by rapid redesign of superfolder mRNAs for B.1.351, P.1 and B.1.1.7 variants of the prefusion-stabilized SARS-CoV-2 spike protein. Increases in in vitro mRNA half-life by at least two-fold appear immediately achievable.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Algorithms / RNA, Double-Stranded / RNA, Messenger / RNA, Viral / Spike Glycoprotein, Coronavirus / SARS-CoV-2 Topics: Vaccines / Variants Limits: Humans Language: English Journal: Nucleic Acids Res Year: 2021 Document Type: Article Affiliation country: Nar

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Algorithms / RNA, Double-Stranded / RNA, Messenger / RNA, Viral / Spike Glycoprotein, Coronavirus / SARS-CoV-2 Topics: Vaccines / Variants Limits: Humans Language: English Journal: Nucleic Acids Res Year: 2021 Document Type: Article Affiliation country: Nar