Literature DB >> 22850726

Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma.

Ichiro Hirao1, Michiko Kimoto.   

Abstract

Toward the expansion of the genetic alphabet of DNA, several artificial third base pairs (unnatural base pairs) have been created. Synthetic DNAs containing the unnatural base pairs can be amplified faithfully by PCR, along with the natural A-T and G-C pairs, and transcribed into RNA. The unnatural base pair systems now have high potential to open the door to next generation biotechnology. The creation of unnatural base pairs is a consequence of repeating "proof of concept" experiments. In the process, initially designed base pairs were modified to address their weak points. Some of them were artificially evolved to ones with higher efficiency and selectivity in polymerase reactions, while others were eliminated from the analysis. Here, we describe the process of unnatural base pair development, as well as the tests of their applications.

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Year:  2012        PMID: 22850726      PMCID: PMC3422687          DOI: 10.2183/pjab.88.345

Source DB:  PubMed          Journal:  Proc Jpn Acad Ser B Phys Biol Sci        ISSN: 0386-2208            Impact factor:   3.493


  82 in total

1.  Molecular biology. Creation's seventh day.

Authors:  R F Service
Journal:  Science       Date:  2000-07-14       Impact factor: 47.728

2.  Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution.

Authors:  Tahir H Tahirov; Dmitry Temiakov; Michael Anikin; Vsevolod Patlan; William T McAllister; Dmitry G Vassylyev; Shigeyuki Yokoyama
Journal:  Nature       Date:  2002-10-09       Impact factor: 49.962

3.  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

Review 4.  Biochemical basis of DNA replication fidelity.

Authors:  M F Goodman; S Creighton; L B Bloom; J Petruska
Journal:  Crit Rev Biochem Mol Biol       Date:  1993       Impact factor: 8.250

5.  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

6.  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

Review 7.  Redesigning the architecture of the base pair: toward biochemical and biological function of new genetic sets.

Authors:  Andrew T Krueger; Eric T Kool
Journal:  Chem Biol       Date:  2009-03-27

8.  Artificial genetic systems: exploiting the "aromaticity" formalism to improve the tautomeric ratio for isoguanosine derivatives.

Authors:  Theodore A Martinot; Steven A Benner
Journal:  J Org Chem       Date:  2004-05-28       Impact factor: 4.354

9.  Exploration of factors driving incorporation of unnatural dNTPS into DNA by Klenow fragment (DNA polymerase I) and DNA polymerase alpha.

Authors:  Kristi Kincaid; Jeff Beckman; Aleksandra Zivkovic; Randall L Halcomb; Joachim W Engels; Robert D Kuchta
Journal:  Nucleic Acids Res       Date:  2005-05-06       Impact factor: 16.971

Review 10.  Synthetic biology.

Authors:  Steven A Benner; A Michael Sismour
Journal:  Nat Rev Genet       Date:  2005-07       Impact factor: 53.242

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  19 in total

Review 1.  Reprogramming the genetic code.

Authors:  Daniel de la Torre; Jason W Chin
Journal:  Nat Rev Genet       Date:  2020-12-14       Impact factor: 53.242

2.  Helix instability and self-pairing prevent unnatural base pairs from expanding the genetic alphabet.

Authors:  Thomas P Hettinger
Journal:  Proc Natl Acad Sci U S A       Date:  2017-08-02       Impact factor: 11.205

3.  Reply to Hettinger: Hydrophobic unnatural base pairs and the expansion of the genetic alphabet.

Authors:  Aaron W Feldman; Michael P Ledbetter; Yorke Zhang; Floyd E Romesberg
Journal:  Proc Natl Acad Sci U S A       Date:  2017-08-02       Impact factor: 11.205

4.  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

Review 5.  Nucleoside analogs in the study of the epitranscriptome.

Authors:  Cody M Palumbo; Peter A Beal
Journal:  Methods       Date:  2018-10-26       Impact factor: 3.608

Review 6.  Synthetic Biological Circuits within an Orthogonal Central Dogma.

Authors:  Alan Costello; Ahmed H Badran
Journal:  Trends Biotechnol       Date:  2020-06-22       Impact factor: 19.536

7.  Optimization of Replication, Transcription, and Translation in a Semi-Synthetic Organism.

Authors:  Aaron W Feldman; Vivian T Dien; Rebekah J Karadeema; Emil C Fischer; Yanbo You; Brooke A Anderson; Ramanarayanan Krishnamurthy; Jason S Chen; Lingjun Li; Floyd E Romesberg
Journal:  J Am Chem Soc       Date:  2019-06-26       Impact factor: 15.419

Review 8.  Directed polymerase evolution.

Authors:  Tingjian Chen; Floyd E Romesberg
Journal:  FEBS Lett       Date:  2013-11-05       Impact factor: 4.124

9.  Generation of high-affinity DNA aptamers using an expanded genetic alphabet.

Authors:  Michiko Kimoto; Rie Yamashige; Ken-ichiro Matsunaga; Shigeyuki Yokoyama; Ichiro Hirao
Journal:  Nat Biotechnol       Date:  2013-04-07       Impact factor: 54.908

Review 10.  Overcoming Challenges in Engineering the Genetic Code.

Authors:  M J Lajoie; D Söll; G M Church
Journal:  J Mol Biol       Date:  2015-09-05       Impact factor: 5.469

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