Literature DB >> 31985216

Nanopore Sequencing of an Expanded Genetic Alphabet Reveals High-Fidelity Replication of a Predominantly Hydrophobic Unnatural Base Pair.

Michael P Ledbetter1, Jonathan M Craig2, Rebekah J Karadeema1, Matthew T Noakes2, Hwanhee C Kim2, Sarah J Abell2, Jesse R Huang2, Brooke A Anderson1, Ramanarayanan Krishnamurthy1, Jens H Gundlach2, Floyd E Romesberg1.   

Abstract

Unnatural base pairs (UBPs) have been developed and used for a variety of in vitro applications as well as for the engineering of semisynthetic organisms (SSOs) that store and retrieve increased information. However, these applications are limited by the availability of methods to rapidly and accurately determine the sequence of unnatural DNA. Here we report the development and application of the MspA nanopore to sequence DNA containing the dTPT3-dNaM UBP. Analysis of two sequence contexts reveals that DNA containing the UBP is replicated with an efficiency and fidelity similar to that of natural DNA and sufficient for use as the basis of an SSO that produces proteins with noncanonical amino acids.

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Year:  2020        PMID： 31985216      PMCID： PMC7263177          DOI： 10.1021/jacs.9b09808

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN： 0002-7863            Impact factor:   15.419


  28 in total

1.  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

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.  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

4.  High Fidelity, Efficiency and Functionalization of Ds-Px Unnatural Base Pairs in PCR Amplification for a Genetic Alphabet Expansion System.

Authors:  Itaru Okamoto; Yuya Miyatake; Michiko Kimoto; Ichiro Hirao
Journal:  ACS Synth Biol       Date:  2016-02-05       Impact factor: 5.110

5.  Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity.

Authors:  Fei Chen; Zunyi Yang; Maocai Yan; J Brian Alvarado; Ganggang Wang; Steven A Benner
Journal:  Nucleic Acids Res       Date:  2011-01-17       Impact factor: 16.971

6.  Nanopores discriminate among five C5-cytosine variants in DNA.

Authors:  Zachary L Wescoe; Jacob Schreiber; Mark Akeson
Journal:  J Am Chem Soc       Date:  2014-11-14       Impact factor: 15.419

7.  A semi-synthetic organism that stores and retrieves increased genetic information.

Authors:  Yorke Zhang; Jerod L Ptacin; Emil C Fischer; Hans R Aerni; Carolina E Caffaro; Kristine San Jose; Aaron W Feldman; Court R Turner; Floyd E Romesberg
Journal:  Nature       Date:  2017-11-29       Impact factor: 49.962

8.  Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage.

Authors:  Matthew T Noakes; Henry Brinkerhoff; Andrew H Laszlo; Ian M Derrington; Kyle W Langford; Jonathan W Mount; Jasmine L Bowman; Katherine S Baker; Kenji M Doering; Benjamin I Tickman; Jens H Gundlach
Journal:  Nat Biotechnol       Date:  2019-04-22       Impact factor: 54.908

9.  Decoding long nanopore sequencing reads of natural DNA.

Authors:  Andrew H Laszlo; Ian M Derrington; Brian C Ross; Henry Brinkerhoff; Andrew Adey; Ian C Nova; Jonathan M Craig; Kyle W Langford; Jenny Mae Samson; Riza Daza; Kenji Doering; Jay Shendure; Jens H Gundlach
Journal:  Nat Biotechnol       Date:  2014-06-25       Impact factor: 54.908

10.  Subangstrom single-molecule measurements of motor proteins using a nanopore.

Authors:  Ian M Derrington; Jonathan M Craig; Eric Stava; Andrew H Laszlo; Brian C Ross; Henry Brinkerhoff; Ian C Nova; Kenji Doering; Benjamin I Tickman; Mostafa Ronaghi; Jeffrey G Mandell; Kevin L Gunderson; Jens H Gundlach
Journal:  Nat Biotechnol       Date:  2015-09-28       Impact factor: 54.908
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  4 in total

1.  Control of subunit stoichiometry in single-chain MspA nanopores.

Authors:  Mikhail Pavlenok; Luning Yu; Dominik Herrmann; Meni Wanunu; Michael Niederweis
Journal:  Biophys J       Date:  2022-01-31       Impact factor: 4.033

Review 2.  Biological Nanopores: Engineering on Demand.

Authors:  Ana Crnković; Marija Srnko; Gregor Anderluh
Journal:  Life (Basel)       Date:  2021-01-05

3.  Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing.

Authors:  S Kasra Tabatabaei; Bach Pham; Chao Pan; Jingqian Liu; Shubham Chandak; Spencer A Shorkey; Alvaro G Hernandez; Aleksei Aksimentiev; Min Chen; Charles M Schroeder; Olgica Milenkovic
Journal:  Nano Lett       Date:  2022-02-25       Impact factor: 11.189

Review 4.  Recent advances in biological nanopores for nanopore sequencing, sensing and comparison of functional variations in MspA mutants.

Authors:  Huma Bhatti; Rohil Jawed; Irshad Ali; Khurshid Iqbal; Yan Han; Zuhong Lu; Quanjun Liu
Journal:  RSC Adv       Date:  2021-08-31       Impact factor: 4.036
  4 in total

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