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Rodríguez-Robles E, Müller D, Künzl T, Nemat SJ, Edelmann MP, Srivastava P, Louis D, Groaz E, Tiefenbacher K, Roberts TM, Herdewijn P, Marlière P, Panke S. Rational design of a bacterial import system for new-to-nature molecules. Metab Eng 2024:S1096-7176(24)00071-5. [PMID: 38802041 DOI: 10.1016/j.ymben.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/27/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Integration of novel compounds into biological processes holds significant potential for modifying or expanding existing cellular functions. However, the cellular uptake of these compounds is often hindered by selectively permeable membranes. We present a novel bacterial transport system that has been rationally designed to address this challenge. Our approach utilizes a highly promiscuous sulfonate membrane transporter, which allows the passage of cargo molecules attached as amides to a sulfobutanoate transport vector molecule into the cytoplasm of the cell. These cargoes can then be unloaded from the sulfobutanoyl amides using an engineered variant of the enzyme γ-glutamyl transferase, which hydrolyzes the amide bond and releases the cargo molecule within the cell. Here, we provide evidence for the broad substrate specificity of both components of the system by evaluating a panel of structurally diverse sulfobutanoyl amides. Furthermore, we successfully implement the synthetic uptake system in vivo and showcase its functionality by importing an impermeant non-canonical amino acid.
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Affiliation(s)
- Emilio Rodríguez-Robles
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - David Müller
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Tilmann Künzl
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Suren J Nemat
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Martin Peter Edelmann
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Puneet Srivastava
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Elisabetta Groaz
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Tania Michelle Roberts
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Sven Panke
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
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2
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Blanchard A, Abramov M, Hassan C, Marlière P, Herdewijn P, Pezo V. A microbiological system for screening the interference of XNA monomers with DNA and RNA metabolism. RSC Adv 2023; 13:29862-29865. [PMID: 37842681 PMCID: PMC10568403 DOI: 10.1039/d3ra06172h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023] Open
Abstract
We explored the toxicity and mutagenicity of a wide range of xenobiotic nucleoside triphosphates to an Escherichia coli strain equipped with a nucleoside triphosphate transporter. This bacterial test provides a tool to evaluate and guide the synthesis of nucleotides for applications such as the propagation of non-natural genetic information or the selection of potential drugs.
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Affiliation(s)
- Aude Blanchard
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay 2 Rue Gaston Crémieux 91057 Evry France
| | - Mikhail Abramov
- Laboratory for Medicinal Chemistry, Rega Institute Herestraat 49, KU Leuven Leuven Belgium
| | - Camille Hassan
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay 2 Rue Gaston Crémieux 91057 Evry France
| | - Philippe Marlière
- Theraxen SA 296 route de Longwy L-1940 Luxembourg
- TESSSI 81 Rue Réaumur Paris 75002 France
| | - Piet Herdewijn
- Laboratory for Medicinal Chemistry, Rega Institute Herestraat 49, KU Leuven Leuven Belgium
| | - Valérie Pezo
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay 2 Rue Gaston Crémieux 91057 Evry France
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3
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Gerecht K, Freund N, Liu W, Liu Y, Fürst MJLJ, Holliger P. The Expanded Central Dogma: Genome Resynthesis, Orthogonal Biosystems, Synthetic Genetics. Annu Rev Biophys 2023; 52:413-432. [PMID: 37159296 DOI: 10.1146/annurev-biophys-111622-091203] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Synthetic biology seeks to probe fundamental aspects of biological form and function by construction [i.e., (re)synthesis] rather than deconstruction (analysis). In this sense, biological sciences now follow the lead given by the chemical sciences. Synthesis can complement analytic studies but also allows novel approaches to answering fundamental biological questions and opens up vast opportunities for the exploitation of biological processes to provide solutions for global problems. In this review, we explore aspects of this synthesis paradigm as applied to the chemistry and function of nucleic acids in biological systems and beyond, specifically, in genome resynthesis, synthetic genetics (i.e., the expansion of the genetic alphabet, of the genetic code, and of the chemical make-up of genetic systems), and the elaboration of orthogonal biosystems and components.
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Affiliation(s)
- Karola Gerecht
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Niklas Freund
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Wei Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Yang Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Maximilian J L J Fürst
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
- Current address: Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
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4
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Hashimoto K, Fischer EC, Romesberg FE. Efforts toward Further Integration of an Unnatural Base Pair into the Biology of a Semisynthetic Organism. J Am Chem Soc 2021; 143:8603-8607. [PMID: 34096294 DOI: 10.1021/jacs.1c03860] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have developed semisynthetic organisms (SSOs) that by virtue of a family of synthetic, unnatural base pairs (UBPs), store and retrieve increased information. To date, transcription in the SSOs has relied on heterologous expression of the RNA polymerase from T7 bacteriophage; here, we explore placing transcription under the control of the endogenous host multisubunit RNA polymerase. The results demonstrate that the E. coli RNA polymerase is able to transcribe DNA containing a UBP and that with the most optimal UBP identified to date it should be possible to select for increased uptake of unnatural triphosphates. These advances should facilitate the creation of next generation SSOs.
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Affiliation(s)
- Koji Hashimoto
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Emil C Fischer
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E Romesberg
- Synthorx, a Sanofi Company, La Jolla, California 92037, United States
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5
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Espinasse A, Lembke HK, Cao AA, Carlson EE. Modified nucleoside triphosphates in bacterial research for in vitro and live-cell applications. RSC Chem Biol 2020; 1:333-351. [PMID: 33928252 PMCID: PMC8081287 DOI: 10.1039/d0cb00078g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022] Open
Abstract
Modified nucleoside triphosphates (NTPs) are invaluable tools to probe bacterial enzymatic mechanisms, develop novel genetic material, and engineer drugs and proteins with new functionalities. Although the impact of nucleobase alterations has predominantly been studied due to their importance for protein recognition, sugar and phosphate modifications have also been investigated. However, NTPs are cell impermeable due to their negatively charged phosphate tail, a major hurdle to achieving live bacterial studies. Herein, we review the recent advances made to investigate and evolve bacteria and their processes with the use of modified NTPs by exploring alterations in one of the three moieties: the nucleobase, the sugar and the phosphate tail. We also present the innovative methods that have been devised to internalize NTPs into bacteria for in vivo applications.
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Affiliation(s)
- Adeline Espinasse
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Hannah K. Lembke
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Angela A. Cao
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
- Department of Medicinal Chemistry, University of Minnesota208 Harvard Street SEMinneapolisMinnesota 55454USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota321 Church St SEMinneapolisMinnesota 55454USA
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6
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Csibra E, Renders M, Pinheiro VB. Bacterial Cell Display as a Robust and Versatile Platform for Engineering Low-Affinity Ligands and Enzymes. Chembiochem 2020; 21:2844-2853. [PMID: 32413179 PMCID: PMC7586821 DOI: 10.1002/cbic.202000203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/11/2020] [Indexed: 12/31/2022]
Abstract
Directed evolution has been remarkably successful at expanding the chemical and functional boundaries of biology. That progress is heavily dependent on the robustness and flexibility of the available selection platforms, given the significant cost to (re)develop a given platform to target a new desired function. Bacterial cell display has a significant track record as a viable strategy for the engineering of mesophilic enzymes, as enzyme activity can be probed directly and free from interference from the cellular milieu, but its adoption has lagged behind other display-based methods. Herein, we report the development of SNAP as a quantitative reporter for bacterial cell display, which enables fast troubleshooting and the systematic development of the display-based selection platform, thus improving its robustness. In addition, we demonstrate that even weak interactions between displayed proteins and nucleic acids can be harnessed for the specific labelling of bacterial cells, allowing functional characterisation of DNA binding proteins and enzymes, thus making it a highly flexible platform for these biochemical functions. Together, this establishes bacterial display as a robust and flexible platform, ideally suited for the systematic engineering of ligands and enzymes needed for XNA molecular biology.
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Affiliation(s)
- Eszter Csibra
- University College LondonDepartment of Structural and Molecular BiologyGower StreetLondonWC1E 6BTUK
- Current address: Imperial College LondonExhibition RoadLondonSW7 2AZUK
| | - Marleen Renders
- Rega Institute for Medical ResearchKU LeuvenHerestraat, 49 box 10413000LeuvenBelgium
- Current address: Touchlight Genetics Ltd. Morelands & Riverdale BuildingsLower Sunbury RoadHamptonTW12 2ERUK
| | - Vitor B. Pinheiro
- University College LondonDepartment of Structural and Molecular BiologyGower StreetLondonWC1E 6BTUK
- Rega Institute for Medical ResearchKU LeuvenHerestraat, 49 box 10413000LeuvenBelgium
- Institute of Structural and Molecular BiologyBirkbeck CollegeUniversity of LondonMalet StreetLondonWC1E 7HXUK
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7
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Duffy K, Arangundy-Franklin S, Holliger P. Modified nucleic acids: replication, evolution, and next-generation therapeutics. BMC Biol 2020; 18:112. [PMID: 32878624 PMCID: PMC7469316 DOI: 10.1186/s12915-020-00803-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Modified nucleic acids, also called xeno nucleic acids (XNAs), offer a variety of advantages for biotechnological applications and address some of the limitations of first-generation nucleic acid therapeutics. Indeed, several therapeutics based on modified nucleic acids have recently been approved and many more are under clinical evaluation. XNAs can provide increased biostability and furthermore are now increasingly amenable to in vitro evolution, accelerating lead discovery. Here, we review the most recent discoveries in this dynamic field with a focus on progress in the enzymatic replication and functional exploration of XNAs.
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Affiliation(s)
- Karen Duffy
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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8
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Gruber A, Haferkamp I. Nucleotide Transport and Metabolism in Diatoms. Biomolecules 2019; 9:E761. [PMID: 31766535 PMCID: PMC6995639 DOI: 10.3390/biom9120761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/11/2019] [Accepted: 11/18/2019] [Indexed: 01/01/2023] Open
Abstract
Plastids, organelles that evolved from cyanobacteria via endosymbiosis in eukaryotes, provide carbohydrates for the formation of biomass and for mitochondrial energy production to the cell. They generate their own energy in the form of the nucleotide adenosine triphosphate (ATP). However, plastids of non-photosynthetic tissues, or during the dark, depend on external supply of ATP. A dedicated antiporter that exchanges ATP against adenosine diphosphate (ADP) plus inorganic phosphate (Pi) takes over this function in most photosynthetic eukaryotes. Additional forms of such nucleotide transporters (NTTs), with deviating activities, are found in intracellular bacteria, and, surprisingly, also in diatoms, a group of algae that acquired their plastids from other eukaryotes via one (or even several) additional endosymbioses compared to algae with primary plastids and higher plants. In this review, we summarize what is known about the nucleotide synthesis and transport pathways in diatom cells, and discuss the evolutionary implications of the presence of the additional NTTs in diatoms, as well as their applications in biotechnology.
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Affiliation(s)
- Ansgar Gruber
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Ilka Haferkamp
- Pflanzenphysiologie, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany;
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9
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Abstract
To increase the scope of natural biosystem, nucleic acids have been intensively modified. One direction includes the development of a synthetic alternative to the native DNA and RNA, denoted Xenobiotic nucleic acids (XNAs) that are able to store and transfer genetic information either by base-modification or backbone-modification. Another line of research aims to develop alternative third base pair additional to natural A:T and G:C. These unnatural base pairs (UBPs) can store increased information content encoded in three base pairs. This review outlines the recent progress made towards XNA and UBP applications as new components of the genomic DNA as well as biostable aptamers. New achievements in the replacement of a bacterial genome by unnatural non-canonical nucleotides are also described.
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Affiliation(s)
- Elena Eremeeva
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, 3000 Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, 3000 Leuven, Belgium.
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10
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Kick-starting evolution efficiency with an autonomous evolution mutation system. Metab Eng 2019; 54:127-136. [DOI: 10.1016/j.ymben.2019.03.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/19/2019] [Accepted: 03/30/2019] [Indexed: 01/25/2023]
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11
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Luo M, Groaz E, Froeyen M, Pezo V, Jaziri F, Leonczak P, Schepers G, Rozenski J, Marlière P, Herdewijn P. Invading Escherichia coli Genetics with a Xenobiotic Nucleic Acid Carrying an Acyclic Phosphonate Backbone (ZNA). J Am Chem Soc 2019; 141:10844-10851. [PMID: 31251601 DOI: 10.1021/jacs.9b04714] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A synthetic orthogonal polymer embracing a chiral acyclic-phosphonate backbone [(S)-ZNA] is presented that uniquely adds to the emerging family of xenobiotic nucleic acids (XNAs). (S)-ZNA consists of reiterating six-atom structural units and can be accessed in few synthetic steps from readily available phophonomethylglycerol nucleoside (PMGN) precursors. Comparative thermal stability experiments conducted on homo- and heteroduplexes made of (S)-ZNA are described that evince its high self-hybridization efficiency in contrast to poor binding of natural complements. Although preliminary and not conclusive, circular dichroism data and dynamic modeling computations provide support to a left-handed geometry of double-stranded (S)-ZNA. Nonetheless, PMGN diphosphate monomers were recognized as substrates by Escherichia coli (E. coli) polymerase I as well as being imported into E. coli cells equipped with an algal nucleotide transporter. A further investigation into the in vivo propagation of (S)-ZNA culminated with the demonstration of the first synthetic nucleic acid with an acyclic backbone that can be transliterated to DNA by the E. coli cellular machinery.
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Affiliation(s)
- Min Luo
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Elisabetta Groaz
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Mathy Froeyen
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Valérie Pezo
- Génomique Métabolique, Genoscope, Institut François Jacob , CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux 91057 Evry , France
| | - Faten Jaziri
- Génomique Métabolique, Genoscope, Institut François Jacob , CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux 91057 Evry , France
| | - Piotr Leonczak
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Guy Schepers
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Jef Rozenski
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Philippe Marlière
- Génomique Métabolique, Genoscope, Institut François Jacob , CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux 91057 Evry , France
| | - Piet Herdewijn
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
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12
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Non canonical genetic material. Curr Opin Biotechnol 2018; 57:25-33. [PMID: 30554069 DOI: 10.1016/j.copbio.2018.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 11/13/2018] [Accepted: 12/03/2018] [Indexed: 01/20/2023]
Abstract
To increase the scope of natural biosystem, nucleic acids have been intensively modified. One direction includes the development of a synthetic alternative to the native DNA and RNA, denoted Xenobiotic nucleic acids (XNAs) that are able to store and transfer genetic information either by base-modification or backbone-modification. Another line of research aims to develop alternative third base pair additional to natural A:T and G:C. These unnatural base pairs (UBPs) can store increased information content encoded in three base pairs. This review outlines the recent progress made towards XNA and UBP applications as new components of the genomic DNA as well as biostable aptamers. New achievements in the replacement of a bacterial genome by unnatural non-canonical nucleotides are also described.
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