Literature DB >> 26304162

The expanded genetic alphabet.

Denis A Malyshev1, Floyd E Romesberg2.   

Abstract

All biological information, since the last common ancestor of all life on Earth, has been encoded by a genetic alphabet consisting of only four nucleotides that form two base pairs. Long-standing efforts to develop two synthetic nucleotides that form a third, unnatural base pair (UBP) have recently yielded three promising candidates, one based on alternative hydrogen bonding, and two based on hydrophobic and packing forces. All three of these UBPs are replicated and transcribed with remarkable efficiency and fidelity, and the latter two thus demonstrate that hydrogen bonding is not unique in its ability to underlie the storage and retrieval of genetic information. This Review highlights these recent developments as well as the applications enabled by the UBPs, including the expansion of the evolution process to include new functionality and the creation of semi-synthetic life that stores increased information.
© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Entities:  

Keywords:  DNA; base pairs; hydrophobicity; semi-synthetic organism; unnatural nucleotides

Mesh:

Substances:

Year:  2015        PMID: 26304162      PMCID: PMC4798003          DOI: 10.1002/anie.201502890

Source DB:  PubMed          Journal:  Angew Chem Int Ed Engl        ISSN: 1433-7851            Impact factor:   15.336


  169 in total

Review 1.  Non-mitochondrial ATP transport.

Authors:  H H Winkler; H E Neuhaus
Journal:  Trends Biochem Sci       Date:  1999-02       Impact factor: 13.807

2.  (1)H NMR investigation of solvent effects in aromatic stacking interactions.

Authors:  M S Cubberley; B L Iverson
Journal:  J Am Chem Soc       Date:  2001-08-08       Impact factor: 15.419

3.  Deep origin of plastid/parasite ATP/ADP translocases.

Authors:  Haleh Amiri; Olof Karlberg; Siv G E Andersson
Journal:  J Mol Evol       Date:  2003-02       Impact factor: 2.395

4.  Unnatural base pairs for specific transcription.

Authors:  T Ohtsuki; M Kimoto; M Ishikawa; T Mitsui; I Hirao; S Yokoyama
Journal:  Proc Natl Acad Sci U S A       Date:  2001-04-24       Impact factor: 11.205

5.  Hydrogen bonding revisited: geometric selection as a principal determinant of DNA replication fidelity.

Authors:  M F Goodman
Journal:  Proc Natl Acad Sci U S A       Date:  1997-09-30       Impact factor: 11.205

6.  A thymidine triphosphate shape analog lacking Watson-Crick pairing ability is replicated with high sequence selectivity.

Authors:  S Moran; R X Ren; E T Kool
Journal:  Proc Natl Acad Sci U S A       Date:  1997-09-30       Impact factor: 11.205

7.  Synthesis of 6-(2-thienyl)purine nucleoside derivatives that form unnatural base pairs with pyridin-2-one nucleosides.

Authors:  T Fujiwara; M Kimoto; H Sugiyama; I Hirao; S Yokoyama
Journal:  Bioorg Med Chem Lett       Date:  2001-08-20       Impact factor: 2.823

8.  PCR with an expanded genetic alphabet.

Authors:  Denis A Malyshev; Young Jun Seo; Phillip Ordoukhanian; Floyd E Romesberg
Journal:  J Am Chem Soc       Date:  2009-10-21       Impact factor: 15.419

9.  Site-specific incorporation of functional components into RNA by transcription using unnatural base pair systems.

Authors:  Michiko Kimoto; Akira Sato; Rie Kawai; Shigeyuki Yokoyama; Ichiro Hirao
Journal:  Nucleic Acids Symp Ser (Oxf)       Date:  2009

10.  Major groove derivatization of an unnatural base pair.

Authors:  Young Jun Seo; Floyd E Romesberg
Journal:  Chembiochem       Date:  2009-09-21       Impact factor: 3.164

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  47 in total

Review 1.  Strategic labelling approaches for RNA single-molecule spectroscopy.

Authors:  Gerd Hanspach; Sven Trucks; Martin Hengesbach
Journal:  RNA Biol       Date:  2019-04-21       Impact factor: 4.652

2.  Structure-activity relationships of the ATP cofactor in ligase-catalysed oligonucleotide polymerisations.

Authors:  Yi Lei; Ryan Hili
Journal:  Org Biomol Chem       Date:  2017-02-28       Impact factor: 3.876

Review 3.  Toward an Expanded Genome: Structural and Computational Characterization of an Artificially Expanded Genetic Information System.

Authors:  Nigel G J Richards; Millie M Georgiadis
Journal:  Acc Chem Res       Date:  2017-06-08       Impact factor: 22.384

4.  A metallo-DNA nanowire with uninterrupted one-dimensional silver array.

Authors:  Jiro Kondo; Yoshinari Tada; Takenori Dairaku; Yoshikazu Hattori; Hisao Saneyoshi; Akira Ono; Yoshiyuki Tanaka
Journal:  Nat Chem       Date:  2017-07-03       Impact factor: 24.427

5.  Progress Toward a Semi-Synthetic Organism with an Unrestricted Expanded Genetic Alphabet.

Authors:  Vivian T Dien; Matthew Holcomb; Aaron W Feldman; Emil C Fischer; Tammy J Dwyer; Floyd E Romesberg
Journal:  J Am Chem Soc       Date:  2018-11-12       Impact factor: 15.419

6.  Tautomeric Equilibria of Nucleobases in the Hachimoji Expanded Genetic Alphabet.

Authors:  Lukas Eberlein; Frank R Beierlein; Nico J R van Eikema Hommes; Ashish Radadiya; Jochen Heil; Steven A Benner; Timothy Clark; Stefan M Kast; Nigel G J Richards
Journal:  J Chem Theory Comput       Date:  2020-03-20       Impact factor: 6.006

7.  Synthetic Biology Parts for the Storage of Increased Genetic Information in Cells.

Authors:  Sydney E Morris; Aaron W Feldman; Floyd E Romesberg
Journal:  ACS Synth Biol       Date:  2017-06-27       Impact factor: 5.110

8.  Site-specific covalent labeling of large RNAs with nanoparticles empowered by expanded genetic alphabet transcription.

Authors:  Yan Wang; Yaoyi Chen; Yanping Hu; Xianyang Fang
Journal:  Proc Natl Acad Sci U S A       Date:  2020-08-31       Impact factor: 11.205

Review 9.  The expanding world of DNA and RNA.

Authors:  Tingjian Chen; Narupat Hongdilokkul; Zhixia Liu; Deepak Thirunavukarasu; Floyd E Romesberg
Journal:  Curr Opin Chem Biol       Date:  2016-08-24       Impact factor: 8.822

10.  Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease.

Authors:  Markus Probst; Walter Aeschimann; Thi T H Chau; Simon M Langenegger; Achim Stocker; Robert Häner
Journal:  Nucleic Acids Res       Date:  2016-07-15       Impact factor: 16.971

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