Literature DB >> 27565457

The expanding world of DNA and RNA.

Tingjian Chen1, Narupat Hongdilokkul1, Zhixia Liu1, Deepak Thirunavukarasu1, Floyd E Romesberg2.   

Abstract

DNA and RNA are remarkable because they can both encode information and possess desired properties, including the ability to bind specific targets or catalyze specific reactions. Nucleotide modifications that do not interfere with enzymatic synthesis are now being used to bestow DNA or RNA with properties that further increase their utility, including phosphate and sugar modifications that increase nuclease resistance, nucleobase modifications that increase the range of activities possible, and even whole nucleobase replacement that results in selective pairing and the creation of unnatural base pairs that increase the information content. These modifications are increasingly being applied both in vitro and in vivo, including in efforts to create semi-synthetic organisms with altered or expanded genetic alphabets.
Copyright © 2016 Elsevier Ltd. All rights reserved.

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Year:  2016        PMID: 27565457      PMCID: PMC5107331          DOI: 10.1016/j.cbpa.2016.08.001

Source DB:  PubMed          Journal:  Curr Opin Chem Biol        ISSN: 1367-5931            Impact factor:   8.822


  45 in total

1.  An unnatural base pair for incorporating amino acid analogs into proteins.

Authors:  Ichiro Hirao; Takashi Ohtsuki; Tsuyoshi Fujiwara; Tsuneo Mitsui; Tomoko Yokogawa; Taeko Okuni; Hiroshi Nakayama; Koji Takio; Takashi Yabuki; Takanori Kigawa; Koichiro Kodama; Takashi Yokogawa; Kazuya Nishikawa; Shigeyuki Yokoyama
Journal:  Nat Biotechnol       Date:  2002-02       Impact factor: 54.908

2.  Site-specifically arraying small molecules or proteins on DNA using an expanded genetic alphabet.

Authors:  Zhengtao Li; Thomas Lavergne; Denis A Malyshev; Jörg Zimmermann; Ramkrishna Adhikary; Kirandeep Dhami; Phillip Ordoukhanian; Zhelin Sun; Jie Xiang; Floyd E Romesberg
Journal:  Chemistry       Date:  2013-09-11       Impact factor: 5.236

3.  In vitro selection with artificial expanded genetic information systems.

Authors:  Kwame Sefah; Zunyi Yang; Kevin M Bradley; Shuichi Hoshika; Elizabeth Jiménez; Liqin Zhang; Guizhi Zhu; Savita Shanker; Fahong Yu; Diane Turek; Weihong Tan; Steven A Benner
Journal:  Proc Natl Acad Sci U S A       Date:  2013-12-30       Impact factor: 11.205

4.  Identification of a T7 RNA polymerase variant that permits the enzymatic synthesis of fully 2'-O-methyl-modified RNA.

Authors:  Jenny Ibach; Laura Dietrich; Kyra R M Koopmans; Nico Nöbel; Marc Skoupi; Susanne Brakmann
Journal:  J Biotechnol       Date:  2013-07-17       Impact factor: 3.307

5.  Evolution of functional six-nucleotide DNA.

Authors:  Liqin Zhang; Zunyi Yang; Kwame Sefah; Kevin M Bradley; Shuichi Hoshika; Myong-Jung Kim; Hyo-Joong Kim; Guizhi Zhu; Elizabeth Jiménez; Sena Cansiz; I-Ting Teng; Carole Champanhac; Christopher McLendon; Chen Liu; Wen Zhang; Dietlind L Gerloff; Zhen Huang; Weihong Tan; Steven A Benner
Journal:  J Am Chem Soc       Date:  2015-05-20       Impact factor: 15.419

6.  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

7.  Synthetic genetic polymers capable of heredity and evolution.

Authors:  Vitor B Pinheiro; Alexander I Taylor; Christopher Cozens; Mikhail Abramov; Marleen Renders; Su Zhang; John C Chaput; Jesper Wengel; Sew-Yeu Peak-Chew; Stephen H McLaughlin; Piet Herdewijn; Philipp Holliger
Journal:  Science       Date:  2012-04-20       Impact factor: 47.728

Review 8.  Nucleic Acid Ligands With Protein-like Side Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents.

Authors:  John C Rohloff; Amy D Gelinas; Thale C Jarvis; Urs A Ochsner; Daniel J Schneider; Larry Gold; Nebojsa Janjic
Journal:  Mol Ther Nucleic Acids       Date:  2014-10-07       Impact factor: 10.183

9.  Evolution of thermophilic DNA polymerases for the recognition and amplification of C2'-modified DNA.

Authors:  Tingjian Chen; Narupat Hongdilokkul; Zhixia Liu; Ramkrishna Adhikary; Shujian S Tsuen; Floyd E Romesberg
Journal:  Nat Chem       Date:  2016-04-18       Impact factor: 24.427

Review 10.  The structural diversity of artificial genetic polymers.

Authors:  Irina Anosova; Ewa A Kowal; Matthew R Dunn; John C Chaput; Wade D Van Horn; Martin Egli
Journal:  Nucleic Acids Res       Date:  2015-12-15       Impact factor: 16.971

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  10 in total

Review 1.  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

Review 2.  Physics-based all-atom modeling of RNA energetics and structure.

Authors:  Louis G Smith; Jianbo Zhao; David H Mathews; Douglas H Turner
Journal:  Wiley Interdiscip Rev RNA       Date:  2017-09       Impact factor: 9.957

Review 3.  Rewriting the Genetic Code.

Authors:  Takahito Mukai; Marc J Lajoie; Markus Englert; Dieter Söll
Journal:  Annu Rev Microbiol       Date:  2017-07-11       Impact factor: 15.500

4.  A Tool for the Import of Natural and Unnatural Nucleoside Triphosphates into Bacteria.

Authors:  Aaron W Feldman; Emil C Fischer; Michael P Ledbetter; Jen-Yu Liao; John C Chaput; Floyd E Romesberg
Journal:  J Am Chem Soc       Date:  2018-01-17       Impact factor: 15.419

Review 5.  Nucleic Acid Aptamers: Emerging Applications in Medical Imaging, Nanotechnology, Neurosciences, and Drug Delivery.

Authors:  Pascal Röthlisberger; Cécile Gasse; Marcel Hollenstein
Journal:  Int J Mol Sci       Date:  2017-11-16       Impact factor: 5.923

Review 6.  Key Aspects of Nucleic Acid Library Design for in Vitro Selection.

Authors:  Maria A Vorobyeva; Anna S Davydova; Pavel E Vorobjev; Alya G Venyaminova
Journal:  Int J Mol Sci       Date:  2018-02-05       Impact factor: 5.923

7.  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

Review 8.  Chemical Modification of Aptamers for Increased Binding Affinity in Diagnostic Applications: Current Status and Future Prospects.

Authors:  Jan P Elskens; Joke M Elskens; Annemieke Madder
Journal:  Int J Mol Sci       Date:  2020-06-25       Impact factor: 5.923

9.  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

10.  7,8-Dihydro-8-oxo-1,N6-ethenoadenine: an exclusively Hoogsteen-paired thymine mimic in DNA that induces A→T transversions in Escherichia coli.

Authors:  Andrey V Aralov; Nina Gubina; Cristina Cabrero; Vladimir B Tsvetkov; Anton V Turaev; Bogdan I Fedeles; Robert G Croy; Ekaterina A Isaakova; Denis Melnik; Svetlana Dukova; Dmitriy Y Ryazantsev; Alexei A Khrulev; Anna M Varizhuk; Carlos González; Timofei S Zatsepin; John M Essigmann
Journal:  Nucleic Acids Res       Date:  2022-04-08       Impact factor: 16.971

  10 in total

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