Amplification of RNA by an RNA polymerase ribozyme
David P. Horning a,b and Gerald F. Joyce a,b,1
Author Affiliations
a Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037;
b Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
Contributed by Gerald F. Joyce, June 23, 2016 (sent for review May 17, 2016; reviewed by Ronald R. Breaker and Peter J. Unrau)
Significance
Darwinian life requires the ability to replicate genotypes and express phenotypes. Although all extant life relies on protein enzymes to accomplish these tasks, life in the ancestral RNA world would have used only RNA enzymes. Here, we report the in vitro evolution of an improved RNA polymerase ribozyme that is able to synthesize structured functional RNAs, including aptamers and ribozymes, and replicate short RNA sequences in a protein-free form of the PCR. Thus, the replication of RNA and the expression of functional RNA can be accomplished with RNA alone. Combining and improving these activities may enable the self-sustained evolution of RNA and offers a potential route to a synthetic form of RNA life.
Abstract
In all extant life, genetic information is stored in nucleic acids that are replicated by polymerase proteins. In the hypothesized RNA world, before the evolution of genetically encoded proteins, ancestral organisms contained RNA genes that were replicated by an RNA polymerase ribozyme. In an effort toward reconstructing RNA-based life in the laboratory, in vitro evolution was used to improve dramatically the activity and generality of an RNA polymerase ribozyme by selecting variants that can synthesize functional RNA molecules from an RNA template. The improved polymerase ribozyme is able to synthesize a variety of complex structured RNAs, including aptamers, ribozymes, and, in low yield, even tRNA. Furthermore, the polymerase can replicate nucleic acids, amplifying short RNA templates by more than 10,000-fold in an RNA-catalyzed form of the PCR. Thus, the two prerequisites of Darwinian life—the replication of genetic information and its conversion into functional molecules—can now be accomplished with RNA in the complete absence of proteins.
self-replication ribozyme RNA enzyme PCR in vitro evolution
Footnotes
1To whom correspondence should be addressed. Email: gjoyce@scripps.edu.
Author contributions: D.P.H. and G.F.J. designed research; D.P.H. performed research; D.P.H. and G.F.J. analyzed data; and D.P.H. and G.F.J. wrote the paper.
Reviewers: R.R.B., Yale University; and P.J.U., Simon Fraser University.
Conflict of interest statement: R.R.B. and G.F.J. appeared as coauthors of a paper published as Breaker RR, Joyce GF (2014) The expanding view of RNA and DNA function. Chem Biol 21(9):1059–1065. This paper was a Perspective commemorating the 20th anniversary of the journal.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1610103113/-/DCSupplemental.
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