Literature DB >> 27528667

Amplification of RNA by an RNA polymerase ribozyme.

David P Horning1, Gerald F Joyce2.   

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.

Keywords:  PCR; RNA enzyme; in vitro evolution; ribozyme; self-replication

Mesh:

Substances:

Year:  2016        PMID: 27528667      PMCID: PMC5024611          DOI: 10.1073/pnas.1610103113

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  39 in total

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Authors:  R C Cadwell; G F Joyce
Journal:  PCR Methods Appl       Date:  1992-08

2.  Genome evolution and adaptation in a long-term experiment with Escherichia coli.

Authors:  Jeffrey E Barrick; Dong Su Yu; Sung Ho Yoon; Haeyoung Jeong; Tae Kwang Oh; Dominique Schneider; Richard E Lenski; Jihyun F Kim
Journal:  Nature       Date:  2009-10-18       Impact factor: 49.962

3.  Ribozyme-catalyzed transcription of an active ribozyme.

Authors:  Aniela Wochner; James Attwater; Alan Coulson; Philipp Holliger
Journal:  Science       Date:  2011-04-08       Impact factor: 47.728

4.  Heat flux across an open pore enables the continuous replication and selection of oligonucleotides towards increasing length.

Authors:  Moritz Kreysing; Lorenz Keil; Simon Lanzmich; Dieter Braun
Journal:  Nat Chem       Date:  2015-01-26       Impact factor: 24.427

5.  Fast gapped-read alignment with Bowtie 2.

Authors:  Ben Langmead; Steven L Salzberg
Journal:  Nat Methods       Date:  2012-03-04       Impact factor: 28.547

6.  In vitro selection of RNA aptamers specific for cyanocobalamin.

Authors:  J R Lorsch; J W Szostak
Journal:  Biochemistry       Date:  1994-02-01       Impact factor: 3.162

7.  The effects of tetraalkylammonium salts on helix-coil transition parameters in natural and synthetic ribo- and deoxyribo-polynucleotides.

Authors:  T Golaś; M Miller; D Shugar
Journal:  Chem Biol Interact       Date:  1980-05       Impact factor: 5.192

Review 8.  Genome dynamics during experimental evolution.

Authors:  Jeffrey E Barrick; Richard E Lenski
Journal:  Nat Rev Genet       Date:  2013-10-29       Impact factor: 53.242

9.  A synthetic approach to abiogenesis.

Authors:  James Attwater; Philipp Holliger
Journal:  Nat Methods       Date:  2014-05       Impact factor: 28.547

10.  Generation of functional RNAs from inactive oligonucleotide complexes by non-enzymatic primer extension.

Authors:  Katarzyna Adamala; Aaron E Engelhart; Jack W Szostak
Journal:  J Am Chem Soc       Date:  2014-12-31       Impact factor: 15.419

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  64 in total

1.  An RNA polymerase ribozyme that synthesizes its own ancestor.

Authors:  Katrina F Tjhung; Maxim N Shokhirev; David P Horning; Gerald F Joyce
Journal:  Proc Natl Acad Sci U S A       Date:  2020-01-27       Impact factor: 11.205

Review 2.  Beyond DNA and RNA: The Expanding Toolbox of Synthetic Genetics.

Authors:  Alexander I Taylor; Gillian Houlihan; Philipp Holliger
Journal:  Cold Spring Harb Perspect Biol       Date:  2019-06-03       Impact factor: 10.005

3.  RNA-Catalyzed Polymerization of Deoxyribose, Threose, and Arabinose Nucleic Acids.

Authors:  David P Horning; Saikat Bala; John C Chaput; Gerald F Joyce
Journal:  ACS Synth Biol       Date:  2019-05-03       Impact factor: 5.110

4.  Kinetic Effects of β,γ-Modified Deoxynucleoside 5'-Triphosphate Analogues on RNA-Catalyzed Polymerization of DNA.

Authors:  Noah A Setterholm; Pouya Haratipour; Boris A Kashemirov; Charles E McKenna; Gerald F Joyce
Journal:  Biochemistry       Date:  2020-12-27       Impact factor: 3.162

5.  Autocatalytic Sets and RNA Secondary Structure.

Authors:  Wim Hordijk
Journal:  J Mol Evol       Date:  2017-04-04       Impact factor: 2.395

Review 6.  Protocells and RNA Self-Replication.

Authors:  Gerald F Joyce; Jack W Szostak
Journal:  Cold Spring Harb Perspect Biol       Date:  2018-09-04       Impact factor: 10.005

7.  Reconstruction and Characterization of Thermally Stable and Catalytically Active Proteins Comprising an Alphabet of ~ 13 Amino Acids.

Authors:  Madoka Kimura; Satoshi Akanuma
Journal:  J Mol Evol       Date:  2020-03-23       Impact factor: 2.395

8.  Exploration of RNA Sequence Space in the Absence of a Replicase.

Authors:  Madhan R Tirumalai; Quyen Tran; Maxim Paci; Dimple Chavan; Anuradha Marathe; George E Fox
Journal:  J Mol Evol       Date:  2018-05-11       Impact factor: 2.395

9.  Emerging Frontiers in the Study of Molecular Evolution.

Authors:  David A Liberles; Belinda Chang; Kerry Geiler-Samerotte; Aaron Goldman; Jody Hey; Betül Kaçar; Michelle Meyer; William Murphy; David Posada; Andrew Storfer
Journal:  J Mol Evol       Date:  2020-04       Impact factor: 2.395

Review 10.  Insuperable problems of the genetic code initially emerging in an RNA world.

Authors:  Peter R Wills; Charles W Carter
Journal:  Biosystems       Date:  2017-09-10       Impact factor: 1.973

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