Literature DB >> 31160351

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

Alexander I Taylor1, Gillian Houlihan1, Philipp Holliger1.   

Abstract

The remarkable physicochemical properties of the natural nucleic acids, DNA and RNA, define modern biology at the molecular level and are widely believed to have been central to life's origins. However, their ability to form repositories of information as well as functional structures such as ligands (aptamers) and catalysts (ribozymes/DNAzymes) is not unique. A range of nonnatural alternatives, collectively termed xeno nucleic acids (XNAs), are also capable of supporting genetic information storage and propagation as well as evolution. This gives rise to a new field of "synthetic genetics," which seeks to expand the nucleic acid chemical toolbox for applications in both biotechnology and molecular medicine. In this review, we outline XNA polymerase and reverse transcriptase engineering as a key enabling technology and summarize the application of "synthetic genetics" to the development of aptamers, enzymes, and nanostructures.
Copyright © 2019 Cold Spring Harbor Laboratory Press; all rights reserved.

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Year:  2019        PMID: 31160351      PMCID: PMC6546049          DOI: 10.1101/cshperspect.a032490

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Biol        ISSN: 1943-0264            Impact factor:   10.005


  78 in total

1.  A ribozyme composed of only two different nucleotides.

Authors:  John S Reader; Gerald F Joyce
Journal:  Nature       Date:  2002 Dec 19-26       Impact factor: 49.962

2.  Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor.

Authors:  Hanyang Yu; Su Zhang; John C Chaput
Journal:  Nat Chem       Date:  2012-01-10       Impact factor: 24.427

Review 3.  DNA enzymes as potential therapeutics: towards clinical application of 10-23 DNAzymes.

Authors:  Alesya A Fokina; Dmitry A Stetsenko; Jean-Christophe François
Journal:  Expert Opin Biol Ther       Date:  2015-03-14       Impact factor: 4.388

Review 4.  The chemical evolution of oligonucleotide therapies of clinical utility.

Authors:  Anastasia Khvorova; Jonathan K Watts
Journal:  Nat Biotechnol       Date:  2017-02-27       Impact factor: 54.908

Review 5.  Aptamer chemistry.

Authors:  Pascal Röthlisberger; Marcel Hollenstein
Journal:  Adv Drug Deliv Rev       Date:  2018-04-04       Impact factor: 15.470

6.  Highly stable aptamers selected from a 2'-fully modified fGmH RNA library for targeting biomaterials.

Authors:  Adam D Friedman; Dongwook Kim; Rihe Liu
Journal:  Biomaterials       Date:  2015-01       Impact factor: 12.479

7.  A short adaptive path from DNA to RNA polymerases.

Authors:  Christopher Cozens; Vitor B Pinheiro; Alexandra Vaisman; Roger Woodgate; Philipp Holliger
Journal:  Proc Natl Acad Sci U S A       Date:  2012-05-07       Impact factor: 11.205

8.  Synthesis and polymerase activity of a fluorescent cytidine TNA triphosphate analogue.

Authors:  Hui Mei; Changhua Shi; Randi M Jimenez; Yajun Wang; Miramar Kardouh; John C Chaput
Journal:  Nucleic Acids Res       Date:  2017-06-02       Impact factor: 16.971

9.  Evolved polymerases facilitate selection of fully 2'-OMe-modified aptamers.

Authors:  Zhixia Liu; Tingjian Chen; Floyd E Romesberg
Journal:  Chem Sci       Date:  2017-10-16       Impact factor: 9.825

10.  Directed evolution of artificial enzymes (XNAzymes) from diverse repertoires of synthetic genetic polymers.

Authors:  Alexander I Taylor; Philipp Holliger
Journal:  Nat Protoc       Date:  2015-09-24       Impact factor: 13.491

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  11 in total

1.  Evolution of abiotic cubane chemistries in a nucleic acid aptamer allows selective recognition of a malaria biomarker.

Authors:  Yee-Wai Cheung; Pascal Röthlisberger; Ariel E Mechaly; Patrick Weber; Fabienne Levi-Acobas; Young Lo; Alvin W C Wong; Andrew B Kinghorn; Ahmed Haouz; G Paul Savage; Marcel Hollenstein; Julian A Tanner
Journal:  Proc Natl Acad Sci U S A       Date:  2020-07-06       Impact factor: 11.205

2.  A two-residue nascent-strand steric gate controls synthesis of 2'-O-methyl- and 2'-O-(2-methoxyethyl)-RNA.

Authors:  Niklas Freund; Alexander I Taylor; Sebastian Arangundy-Franklin; Nithya Subramanian; Sew-Yeu Peak-Chew; Amy M Whitaker; Bret D Freudenthal; Mikhail Abramov; Piet Herdewijn; Philipp Holliger
Journal:  Nat Chem       Date:  2022-10-13       Impact factor: 24.274

3.  A modular XNAzyme cleaves long, structured RNAs under physiological conditions and enables allele-specific gene silencing.

Authors:  Alexander I Taylor; Christopher J K Wan; Maria J Donde; Sew-Yeu Peak-Chew; Philipp Holliger
Journal:  Nat Chem       Date:  2022-09-05       Impact factor: 24.274

4.  Discovery and evolution of RNA and XNA reverse transcriptase function and fidelity.

Authors:  Gillian Houlihan; Sebastian Arangundy-Franklin; Benjamin T Porebski; Nithya Subramanian; Alexander I Taylor; Philipp Holliger
Journal:  Nat Chem       Date:  2020-07-20       Impact factor: 24.427

5.  Ligand-Guided Selection with Artificially Expanded Genetic Information Systems against TCR-CD3ε.

Authors:  Hasan Zumrut; Zunyi Yang; Nicole Williams; Joekeem Arizala; Sana Batool; Steven A Benner; Prabodhika Mallikaratchy
Journal:  Biochemistry       Date:  2020-01-08       Impact factor: 3.162

Review 6.  Oligonucleotide-Based Approaches to Inhibit Dengue Virus Replication.

Authors:  Kingshuk Panda; Kalichamy Alagarasu; Deepti Parashar
Journal:  Molecules       Date:  2021-02-11       Impact factor: 4.411

7.  The proto-Nucleic Acid Builder: a software tool for constructing nucleic acid analogs.

Authors:  Asem Alenaizan; Joshua L Barnett; Nicholas V Hud; C David Sherrill; Anton S Petrov
Journal:  Nucleic Acids Res       Date:  2021-01-11       Impact factor: 16.971

8.  Energy Landscapes of Deoxyxylo- and Xylo-Nucleic Acid Octamers.

Authors:  Daniel J Sharpe; Konstantin Röder; David J Wales
Journal:  J Phys Chem B       Date:  2020-05-06       Impact factor: 2.991

Review 9.  Building better polymerases: Engineering the replication of expanded genetic alphabets.

Authors:  Zahra Ouaray; Steven A Benner; Millie M Georgiadis; Nigel G J Richards
Journal:  J Biol Chem       Date:  2020-10-01       Impact factor: 5.157

Review 10.  In vitro Selection of Chemically Modified DNAzymes.

Authors:  Po-Jung Jimmy Huang; Juewen Liu
Journal:  ChemistryOpen       Date:  2020-10-19       Impact factor: 2.630

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