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Huber LB, Betz K, Marx A. Reverse Transcriptases: From Discovery and Applications to Xenobiology. Chembiochem 2023; 24:e202200521. [PMID: 36354312 DOI: 10.1002/cbic.202200521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/09/2022] [Indexed: 11/12/2022]
Abstract
Reverse transcriptases are DNA polymerases that can use RNA as a template for DNA synthesis. They thus catalyze the reverse of transcription. Although discovered in 1970, reverse transcriptases are still of great interest and are constantly being further developed for numerous modern research approaches. They are frequently used in biotechnological and molecular diagnostic applications. In this review, we describe the discovery of these fascinating enzymes and summarize research results and applications ranging from molecular cloning, direct virus detection, and modern sequencing methods to xenobiology.
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Affiliation(s)
- Luisa B Huber
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
| | - Karin Betz
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
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2
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Eggert F, Kurscheidt K, Hoffmann E, Kath‐Schorr S. Towards Reverse Transcription with an Expanded Genetic Alphabet. Chembiochem 2019; 20:1642-1645. [DOI: 10.1002/cbic.201800808] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Frank Eggert
- LIMES Institute, Chemical Biology and Medicinal Chemistry UnitUniversity of Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Katharina Kurscheidt
- LIMES Institute, Chemical Biology and Medicinal Chemistry UnitUniversity of Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Eva Hoffmann
- LIMES Institute, Chemical Biology and Medicinal Chemistry UnitUniversity of Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Stephanie Kath‐Schorr
- LIMES Institute, Chemical Biology and Medicinal Chemistry UnitUniversity of Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
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Aschenbrenner J, Werner S, Marchand V, Adam M, Motorin Y, Helm M, Marx A. Engineering of a DNA Polymerase for Direct m 6 A Sequencing. Angew Chem Int Ed Engl 2018; 57:417-421. [PMID: 29115744 PMCID: PMC5768020 DOI: 10.1002/anie.201710209] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Indexed: 12/16/2022]
Abstract
Methods for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N6 -methyladenosine (m6 A) is the most abundant RNA modification in mammalian mRNA and is involved in the regulation of gene expression. Current detection techniques are laborious and rely on antibody-based enrichment of m6 A-containing RNA prior to sequencing, since m6 A modifications are generally "erased" during reverse transcription (RT). To overcome the drawbacks associated with indirect detection, we aimed to generate novel DNA polymerase variants for direct m6 A sequencing. Therefore, we developed a screen to evolve an RT-active KlenTaq DNA polymerase variant that sets a mark for N6 -methylation. We identified a mutant that exhibits increased misincorporation opposite m6 A compared to unmodified A. Application of the generated DNA polymerase in next-generation sequencing allowed the identification of m6 A sites directly from the sequencing data of untreated RNA samples.
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Affiliation(s)
- Joos Aschenbrenner
- Department of Chemistry, Konstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Stephan Werner
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University MainzStaudingerweg 555128MainzGermany
| | - Virginie Marchand
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire, IMoPA, UMR7365 CNRS-ULBiopôle de L'Université de Lorraine9, Avenue de la Forêt de Haye54505Vandoeuvre-les-NancyFrance
| | - Martina Adam
- Department of Chemistry, Konstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Yuri Motorin
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire, IMoPA, UMR7365 CNRS-ULBiopôle de L'Université de Lorraine9, Avenue de la Forêt de Haye54505Vandoeuvre-les-NancyFrance
| | - Mark Helm
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University MainzStaudingerweg 555128MainzGermany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
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4
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Aschenbrenner J, Werner S, Marchand V, Adam M, Motorin Y, Helm M, Marx A. Entwicklung einer DNA-Polymerase für die direkte m6A-Sequenzierung. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201710209] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Joos Aschenbrenner
- Fachbereich Chemie, Konstanz Research School Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Stephan Werner
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudingerweg 5 55128 Mainz Deutschland
| | - Virginie Marchand
- Laboratoire Ingénierie Moléculaire et Physiopathologie, Articulaire, IMoPA, UMR7365 CNRS-UL; Biopôle de L'Université de Lorraine; 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy Frankreich
| | - Martina Adam
- Fachbereich Chemie, Konstanz Research School Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Yuri Motorin
- Laboratoire Ingénierie Moléculaire et Physiopathologie, Articulaire, IMoPA, UMR7365 CNRS-UL; Biopôle de L'Université de Lorraine; 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy Frankreich
| | - Mark Helm
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudingerweg 5 55128 Mainz Deutschland
| | - Andreas Marx
- Fachbereich Chemie, Konstanz Research School Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
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Rosenblum SL, Weiden AG, Lewis EL, Ogonowsky AL, Chia HE, Barrett SE, Liu MD, Leconte AM. Design and Discovery of New Combinations of Mutant DNA Polymerases and Modified DNA Substrates. Chembiochem 2017; 18:816-823. [PMID: 28160372 DOI: 10.1002/cbic.201600701] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Indexed: 11/06/2022]
Abstract
Chemical modifications can enhance the properties of DNA by imparting nuclease resistance and generating more-diverse physical structures. However, native DNA polymerases generally cannot synthesize significant lengths of DNA with modified nucleotide triphosphates. Previous efforts have identified a mutant of DNA polymerase I from Thermus aquaticus DNA (SFM19) as capable of synthesizing a range of short, 2'-modified DNAs; however, it is limited in the length of the products it can synthesize. Here, we rationally designed and characterized ten mutants of SFM19. From this, we identified enzymes with substantially improved activity for the synthesis of 2'F-, 2'OH-, 2'OMe-, and 3'OMe-modified DNA as well as for reverse transcription of 2'OMe DNA. We also evaluated mutant DNA polymerases previously only tested for synthesis for 2'OMe DNA and showed that they are capable of an expanded range of modified DNA synthesis. This work significantly expands the known combinations of modified DNA and Taq DNA polymerase mutants.
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Affiliation(s)
- Sydney L Rosenblum
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Aurora G Weiden
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Eliza L Lewis
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Alexie L Ogonowsky
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Hannah E Chia
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Susanna E Barrett
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Mira D Liu
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Aaron M Leconte
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
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Virdee S. 2016 EMBO Chemical Biology Conference. Chembiochem 2016; 18:66-71. [PMID: 27862792 DOI: 10.1002/cbic.201600597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Indexed: 11/07/2022]
Abstract
The full breadth of the field: The 2016 EMBO Chemical Biology Conference, covering topics from tool development to biological applications and from computational drug design to synthetic chemistry, took place in Heidelberg from 31st August to 3rd September.
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Affiliation(s)
- Satpal Virdee
- University of Dundee, MRC Protein Phosphorylation and Ubiquitylation Unit, Dow Street, Dundee, DD1 5EH, UK
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Welter M, Verga D, Marx A. Sequence-Specific Incorporation of Enzyme-Nucleotide Chimera by DNA Polymerases. Angew Chem Int Ed Engl 2016; 55:10131-5. [PMID: 27392211 DOI: 10.1002/anie.201604641] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Indexed: 02/06/2023]
Abstract
DNA polymerases select the right nucleotide for the growing polynucleotide chain based on the shape and geometry of the nascent nucleotide pairs and thereby ensure high DNA replication selectivity. High-fidelity DNA polymerases are believed to possess tight active sites that allow little deviation from the canonical structures. However, DNA polymerases are known to use nucleotides with small modifications as substrates, which is key for numerous core biotechnology applications. We show that even high-fidelity DNA polymerases are capable of efficiently using nucleotide chimera modified with a large protein like horseradish peroxidase as substrates for template-dependent DNA synthesis, despite this "cargo" being more than 100-fold larger than the natural substrates. We exploited this capability for the development of systems that enable naked-eye detection of DNA and RNA at single nucleotide resolution.
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Affiliation(s)
- Moritz Welter
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Daniela Verga
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany.
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Welter M, Verga D, Marx A. Sequenz-spezifischer Einbau von Enzym-Nukleotid-Chimären durch DNA-Polymerasen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Moritz Welter
- Fachbereich Chemie, Graduiertenschule Chemische Biologie Konstanz; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Daniela Verga
- Fachbereich Chemie, Graduiertenschule Chemische Biologie Konstanz; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Andreas Marx
- Fachbereich Chemie, Graduiertenschule Chemische Biologie Konstanz; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
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