1
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Li X, Groaz E, Herdewijn P, Lescrinier E. Impact of Single Acyclic Phosphonate Nucleotide (ZNA) Modifications on DNA Duplex Stability. Chemistry 2024:e202401254. [PMID: 38687344 DOI: 10.1002/chem.202401254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
An acyclic phosphonate-linked nucleic acid backbone (ZNA) demonstrated the capability to support duplex formation and propagate genetic information in vivo, unveiling its potential for evolution into a synthetic genetic system (XNA). To determine the structural impact of such modification, modified Dickerson Drew DNA dodecamers (DDDs) were prepared by solid phase synthesis, each containing either an (R) or (S) isomeric form of a cytosine ZNA nucleotide. While the DDD is known to adopt a stable duplex, both duplex and hairpin forms were simultaneously observed for both modified oligonucleotides by NMR spectroscopy over a broad temperature range (5-65 °C). Diffusion-ordered spectroscopy (DOSY) experiments allowed to separate duplex and hairpin signals based on the different diffusion constants of both conformational states. For the oligomer containing (R)-ZNA, only the duplex form occurred at 5 °C, while it was not possible to determine by NMR a single hairpin conformation at higher temperatures. In the case of the (S)-ZNA nucleoside modified oligomer, both hairpin and duplex forms were observable at 0 °C, while a single hairpin conformation was detected at 37 °C, suggesting a higher destabilizing effect on dsDNA.
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Affiliation(s)
- Xinlu Li
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, Leuven, B-3000, Belgium
| | - Elisabetta Groaz
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, Leuven, B-3000, Belgium
| | - Piet Herdewijn
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, Leuven, B-3000, Belgium
| | - Eveline Lescrinier
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, Leuven, B-3000, Belgium
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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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Pallan PS, Lybrand TP, Rozners E, Abramov M, Schepers G, Eremeeva E, Herdewijn P, Egli M. Conformational Morphing by a DNA Analogue Featuring 7-Deazapurines and 5-Halogenpyrimidines and the Origins of Adenine-Tract Geometry. Biochemistry 2023; 62:2854-2867. [PMID: 37694722 PMCID: PMC11062489 DOI: 10.1021/acs.biochem.3c00327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Several efforts are currently directed at the creation and cellular implementation of alternative genetic systems composed of pairing components that are orthogonal to the natural dA/dT and dG/dC base pairs. In an alternative approach, Watson-Crick-type pairing is conserved, but one or all of the four letters of the A, C, G, and T alphabet are substituted by modified components. Thus, all four nucleobases were altered to create halogenated deazanucleic acid (DZA): dA was replaced by 7-deaza-2'-deoxyadenosine (dzA), dG by 7-deaza-2'-deoxyguanosine (dzG), dC by 5-fluoro-2'-deoxycytidine (FdC), and dT by 5-chloro-2'-deoxyuridine (CldU). This base-pairing system was previously shown to retain function in Escherichia coli. Here, we analyze the stability, hydration, structure, and dynamics of a DZA Dickerson-Drew Dodecamer (DDD) of sequence 5'-FdC-dzG-FdC-dzG-dzA-dzA-CldU-CldU-FdC-dzG-FdC-dzG-3'. Contrary to similar stabilities of DDD and DZA-DDD, osmotic stressing revealed a dramatic loss of hydration for the DZA-DDD relative to that for the DDD. The parent DDD 5'-d(CGCGAATTCGCG)-3' features an A-tract, a run of adenosines uninterrupted by a TpA step, and exhibits a hallmark narrow minor groove. Crystal structures─in the presence of RNase H─and MD simulations show increased conformational plasticity ("morphing") of DZA-DDD relative to that of the DDD. The narrow dzA-tract minor groove in one structure widens to resemble that in canonical B-DNA in a second structure. These changes reflect an indirect consequence of altered DZA major groove electrostatics (less negatively polarized compared to that in DNA) and hydration (reduced compared to that in DNA). Therefore, chemical modifications outside the minor groove that lead to collapse of major groove electrostatics and hydration can modulate A-tract geometry.
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Affiliation(s)
- Pradeep S Pallan
- School of Medicine, Department of Biochemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Terry P Lybrand
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
| | - Mikhail Abramov
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Guy Schepers
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Elena Eremeeva
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Martin Egli
- School of Medicine, Department of Biochemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
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4
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Hoffmann SA, Diggans J, Densmore D, Dai J, Knight T, Leproust E, Boeke JD, Wheeler N, Cai Y. Safety by design: Biosafety and biosecurity in the age of synthetic genomics. iScience 2023; 26:106165. [PMID: 36895643 PMCID: PMC9988571 DOI: 10.1016/j.isci.2023.106165] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Technologies to profoundly engineer biology are becoming increasingly affordable, powerful, and accessible to a widening group of actors. While offering tremendous potential to fuel biological research and the bioeconomy, this development also increases the risk of inadvertent or deliberate creation and dissemination of pathogens. Effective regulatory and technological frameworks need to be developed and deployed to manage these emerging biosafety and biosecurity risks. Here, we review digital and biological approaches of a range of technology readiness levels suited to address these challenges. Digital sequence screening technologies already are used to control access to synthetic DNA of concern. We examine the current state of the art of sequence screening, challenges and future directions, and environmental surveillance for the presence of engineered organisms. As biosafety layer on the organism level, we discuss genetic biocontainment systems that can be used to created host organisms with an intrinsic barrier against unchecked environmental proliferation.
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Affiliation(s)
- Stefan A Hoffmann
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - James Diggans
- Twist Bioscience, 681 Gateway Boulevard, South San Francisco, CA 9408, USA
| | - Douglas Densmore
- Department of Electrical and Computer Engineering, Boston University, 610 Commonwealth Avenue, Boston, MA 02215, USA
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Tom Knight
- Ginkgo Bioworks, 27 Drydock Avenue, Boston, MA 02210, USA
| | - Emily Leproust
- Twist Bioscience, 681 Gateway Boulevard, South San Francisco, CA 9408, USA
| | - Jef D Boeke
- Institute for Systems Genetics, and Department of Biochemistry & Molecular Pharmacology, NYU Langone Health, 435 East 30th Street, New York, NY 10016, USA.,Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Nicole Wheeler
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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5
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Sun L, Ma X, Zhang B, Qin Y, Ma J, Du Y, Chen T. From polymerase engineering to semi-synthetic life: artificial expansion of the central dogma. RSC Chem Biol 2022; 3:1173-1197. [PMID: 36320892 PMCID: PMC9533422 DOI: 10.1039/d2cb00116k] [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: 05/06/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
Nucleic acids have been extensively modified in different moieties to expand the scope of genetic materials in the past few decades. While the development of unnatural base pairs (UBPs) has expanded the genetic information capacity of nucleic acids, the production of synthetic alternatives of DNA and RNA has increased the types of genetic information carriers and introduced novel properties and functionalities into nucleic acids. Moreover, the efforts of tailoring DNA polymerases (DNAPs) and RNA polymerases (RNAPs) to be efficient unnatural nucleic acid polymerases have enabled broad application of these unnatural nucleic acids, ranging from production of stable aptamers to evolution of novel catalysts. The introduction of unnatural nucleic acids into living organisms has also started expanding the central dogma in vivo. In this article, we first summarize the development of unnatural nucleic acids with modifications or alterations in different moieties. The strategies for engineering DNAPs and RNAPs are then extensively reviewed, followed by summarization of predominant polymerase mutants with good activities for synthesizing, reverse transcribing, or even amplifying unnatural nucleic acids. Some recent application examples of unnatural nucleic acids with their polymerases are then introduced. At the end, the approaches of introducing UBPs and synthetic genetic polymers into living organisms for the creation of semi-synthetic organisms are reviewed and discussed.
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Affiliation(s)
- Leping Sun
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Xingyun Ma
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Binliang Zhang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Yanjia Qin
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Jiezhao Ma
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
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6
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Saito-Tarashima N, Murai A, Minakawa N. Rewriting the Central Dogma with Synthetic Genetic Polymers. Chem Pharm Bull (Tokyo) 2022; 70:310-315. [DOI: 10.1248/cpb.c21-00960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Akiho Murai
- Graduate School of Pharmaceutical Science, Tokushima University
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7
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Nguyen H, Abramov M, Rozenski J, Eremeeva E, Herdewijn P. In vivo assembly and expression of DNA containing non-canonical bases in the yeast Saccharomyces cerevisiae. Chembiochem 2022; 23:e202200060. [PMID: 35322918 DOI: 10.1002/cbic.202200060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/16/2022] [Indexed: 11/10/2022]
Abstract
Chemically modified nucleic acids are of utmost interest in synthetic biology to create a regulable and sophisticated synthetic system with tailor-made properties. Implanting chemically modified nucleic acids in microorganisms might serve biotechnological applications, while using them in human cells might lead to new advanced medicines. Previously, we reported that a fully modified DNA sequence (called DZA) composed of the four base-modified nucleotides - 7-deaza-adenine, 5-chlorouracil, 7-deaza-guanine and 5-fluorocytosine - could function as a genetic template in prokaryotic cells, Escherichia coli . Here, we report the synthesis of long, partially or fully modified DZA fragments that encode the yeast-enhanced red fluorescence protein (yEmRFP). The DZA sequences were directly introduced in the genome of the eukaryotic cells, Saccharomyces cerevisiae , via the yeast natural homologous recombination. The simple and straightforward DZA cloning strategy reported herein might be of interest to scientists working in the field of xenobiology in yeast.
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Affiliation(s)
- Hoai Nguyen
- KU Leuven Rega Institute for Medical Research.: Katholieke Universiteit Leuven Rega Institute for Medical Research, Medicinal Chemistry, BELGIUM
| | - Mikhail Abramov
- KU Leuven Rega Institute for Medical Research: Katholieke Universiteit Leuven Rega Institute for Medical Research, Medicinal Chemistry, BELGIUM
| | - Jef Rozenski
- KU Leuven Rega Institute for Medical Research.: Katholieke Universiteit Leuven Rega Institute for Medical Research, Medicinal Chemistry, BELGIUM
| | - Elena Eremeeva
- KU Leuven Rega Institute for Medical Research.: Katholieke Universiteit Leuven Rega Institute for Medical Research, Medicinal Chemistry, BELGIUM
| | - Piet Herdewijn
- Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - box 1030, 3000, Leuven, BELGIUM
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8
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Yang H, Eremeeva E, Abramov M, Herdewijn P. The Network of Replication, Transcription, and Reverse Transcription of a Synthetic Genetic Cassette. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hui Yang
- Medicinal Chemistry Rega Institute for Medical Research KU Leuven Herestraat 49, Box-1041 3000 Leuven Belgium
| | - Elena Eremeeva
- Medicinal Chemistry Rega Institute for Medical Research KU Leuven Herestraat 49, Box-1041 3000 Leuven Belgium
| | - Mikhail Abramov
- Medicinal Chemistry Rega Institute for Medical Research KU Leuven Herestraat 49, Box-1041 3000 Leuven Belgium
| | - Piet Herdewijn
- Medicinal Chemistry Rega Institute for Medical Research KU Leuven Herestraat 49, Box-1041 3000 Leuven Belgium
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9
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Nguyen H, Abramov M, Eremeeva E, Herdewijn P. In Vivo Expression of Genetic Information from Phosphoramidate-DNA. Chembiochem 2021; 21:272-278. [PMID: 31868979 DOI: 10.1002/cbic.201900712] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Indexed: 12/31/2022]
Abstract
Chemically modified genes and genomes with customized properties will become a valuable tool in numerous fields, including synthetic biology, biotechnology, and medicine. These genetic materials are meant to store and exchange information with DNA and RNA while tuning their functionality. Herein, we outline the development of an alternative genetic system carrying phosphoramidate linkages that successfully propagates genetic information in bacteria and at the same time is labile to acidic conditions. The P3'→N5' phosphoramidate-containing DNA (PN-DNA) was enzymatically synthesized by using 5'-amino-2',5'-deoxycytidine 5'-N-triphosphates (NH-dCTPs) as substrates for DNA polymerases and employed to encode antibiotic resistance in Escherichia coli. The resulting PN-DNA can be efficiently destroyed by mild acidic conditions, whereas an unmodified counterpart remains intact. A cloning strategy was proposed for assembling modified fragments into a genome. This method can be of interest to scientists working in the field of orthogonal nucleic acid genes and genomes.
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Affiliation(s)
- Hoai Nguyen
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Mikhail Abramov
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Elena Eremeeva
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000, Leuven, Belgium
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10
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Yang H, Eremeeva E, Abramov M, Herdewijn P. The Network of Replication, Transcription, and Reverse Transcription of a Synthetic Genetic Cassette. Angew Chem Int Ed Engl 2020; 60:4175-4182. [PMID: 33142013 DOI: 10.1002/anie.202011887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/27/2020] [Indexed: 11/07/2022]
Abstract
Synthetic nucleic acids, with four non-canonical nucleobases, can function as genetic materials. A comprehensive analysis of PCR amplification, transcription, reverse transcription, and cloning was done to screen for alternative genetic monomers. A small library of six modified nucleobases was selected: the modified 2'-deoxyribonucleoside (dZTPs) and ribonucleoside (rZTPs) triphosphates of 7-deaza-adenine, 5-chlorouracil, 7-deaza-guanine or inosine together with 5-fluorocytosine or 5-bromocytosine. The fragments composed of one to four modified nucleotides (denoted as DZA) have been successfully recognized and transcribed to natural or modified RNA (denoted as RZA) by T7 RNA polymerase. The fully modified RZA fragment could be reverse transcribed and then amplified in the presence of various dZTPs. Noticeably, modified fragments could function as genetic templates in vivo by encoding the 678 base pair gene of a fluorescent protein in bacteria. These results demonstrate the existence of a fully simulated genetic circuit that uses synthetic materials.
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Affiliation(s)
- Hui Yang
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, Box-1041, 3000, Leuven, Belgium
| | - Elena Eremeeva
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, Box-1041, 3000, Leuven, Belgium
| | - Mikhail Abramov
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, Box-1041, 3000, Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, Box-1041, 3000, Leuven, Belgium
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11
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Tarashima NS, Matsuo A, Minakawa N. Gene Expression of 4'-Thioguanine DNA via 4'-Thiocytosine RNA. J Am Chem Soc 2020; 142:17255-17259. [PMID: 33016701 DOI: 10.1021/jacs.0c07145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
DNA and RNA nucleotides are ubiquitous molecules that store and transmit genetic information. The emergence of synthetic elements that fulfill the function of DNA and RNA provides an alternative gene expression system. Herein, we demonstrate the gene expression of 4'-thioguanine DNA (dSG DNA) via 4'-thiocytosine RNA (dSC RNA) to give green fluorescent protein (GFPuv) in a single test tube. In replication, transcription, and translation, DNA/RNA polymerases and Escherichia coli (E. coli) ribosome can tolerate the replacement of O4' with S4' in the nucleotide, despite the fact that sulfur has a larger atomic radius than oxygen. Additionally, dSG DNA and dSC RNA acted as alternative genetic polymers to natural DNA and RNA for protein synthesis in artificial cells comprising a reconstituted E. coli gene expression machinery. This work involved simple experiments that are widely used in molecular biology, but which underscore the feasibility of life control by substances other than DNA/RNA nucleotides.
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Affiliation(s)
- Noriko S Tarashima
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima, 770-8505, Japan
| | - Ayako Matsuo
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima, 770-8505, Japan
| | - Noriaki Minakawa
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima, 770-8505, Japan
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12
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Takahashi S, Herdwijn P, Sugimoto N. Effect of Molecular Crowding on DNA Polymerase Reactions along Unnatural DNA Templates. Molecules 2020; 25:E4120. [PMID: 32927591 PMCID: PMC7571040 DOI: 10.3390/molecules25184120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 11/17/2022] Open
Abstract
Unnatural nucleic acids are promising materials to expand genetic information beyond the natural bases. During replication, substrate nucleotide incorporation should be strictly controlled for optimal base pairing with template strand bases. Base-pairing interactions occur via hydrogen bonding and base stacking, which could be perturbed by the chemical environment. Although unnatural nucleobases and sugar moieties have undergone extensive structural improvement for intended polymerization, the chemical environmental effect on the reaction is less understood. In this study, we investigated how molecular crowding could affect native DNA polymerization along various templates comprising unnatural nucleobases and sugars. Under non-crowding conditions, the preferred incorporation efficiency of pyrimidine deoxynucleotide triphosphates (dNTPs) by the Klenow fragment (KF) was generally high with low fidelity, whereas that of purine dNTPs was the opposite. However, under crowding conditions, the efficiency remained almost unchanged with varying preferences in each case. These results suggest that hydrogen bonding and base-stacking interactions could be perturbed by crowding conditions in the bulk solution and polymerase active center during transient base pairing before polymerization. This study highlights that unintended dNTP incorporation against unnatural nucleosides could be differentiated in cases of intracellular reactions.
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Affiliation(s)
- Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan;
| | - Piet Herdwijn
- Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Herestraat 49-box 1041, 3000 Leuven, Belgium;
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan;
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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13
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Nie P, Bai Y, Mei H. Synthetic Life with Alternative Nucleic Acids as Genetic Materials. Molecules 2020; 25:molecules25153483. [PMID: 32751873 PMCID: PMC7435384 DOI: 10.3390/molecules25153483] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022] Open
Abstract
DNA, the fundamental genetic polymer of all living organisms on Earth, can be chemically modified to embrace novel functions that do not exist in nature. The key chemical and structural parameters for genetic information storage, heredity, and evolution have been elucidated, and many xenobiotic nucleic acids (XNAs) with non-canonical structures are developed as alternative genetic materials in vitro. However, it is still particularly challenging to replace DNAs with XNAs in living cells. This review outlines some recent studies in which the storage and propagation of genetic information are achieved in vivo by expanding genetic systems with XNAs.
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14
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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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15
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Renders M, Dumbre S, Abramov M, Kestemont D, Margamuljana L, Largy E, Cozens C, Vandenameele J, Pinheiro VB, Toye D, Frère JM, Herdewijn P. Kinetic analysis of N-alkylaryl carboxamide hexitol nucleotides as substrates for evolved polymerases. Nucleic Acids Res 2019; 47:2160-2168. [PMID: 30698800 PMCID: PMC6412122 DOI: 10.1093/nar/gkz008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/21/2018] [Accepted: 01/21/2019] [Indexed: 11/20/2022] Open
Abstract
Six 1′,5′-anhydrohexitol uridine triphosphates were synthesized with aromatic substitutions appended via a carboxamide linker to the 5-position of their bases. An improved method for obtaining such 5-substituted hexitol nucleosides and nucleotides is described. The incorporation profile of the nucleotide analogues into a DNA duplex overhang using recently evolved XNA polymerases is compared. Long, mixed HNA sequences featuring the base modifications are generated. The apparent binding affinity of four of the nucleotides to the enzyme, the rate of the chemical step and of product release, plus the specificity constant for the incorporation of these modified nucleotides into a DNA duplex overhang using the HNA polymerase T6G12_I521L are determined via pre-steady-state kinetics. HNA polymers displaying aromatic functional groups could have significant impact on the isolation of stable and high-affinity binders and catalysts, or on the design of nanomaterials.
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Affiliation(s)
- Marleen Renders
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Rega, Herestraat 49 box 1041, 3000 Leuven, Belgium
| | - Shrinivas Dumbre
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Rega, Herestraat 49 box 1041, 3000 Leuven, Belgium
| | - Mikhail Abramov
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Rega, Herestraat 49 box 1041, 3000 Leuven, Belgium
| | - Donaat Kestemont
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Rega, Herestraat 49 box 1041, 3000 Leuven, Belgium
| | - Lia Margamuljana
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Rega, Herestraat 49 box 1041, 3000 Leuven, Belgium
| | - Eric Largy
- ARNA laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR5320, IECB, 2 rue Robert Escarpit, 33600 Pessac, France
| | - Christopher Cozens
- Structural and Molecular Biology Department, University College London, Gower Street, London WC1E B6T, UK.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, United Kingdom
| | - Julie Vandenameele
- Laboratory of Enzymology and Protein Folding/Robotein Platform, Centre for Protein Engineering (CIP), Department of Life Sciences, University of Liège, Quartier Agora, Allée du six Août 13, Bât. B6a, 4000 Liège, Belgium
| | - Vitor B Pinheiro
- Structural and Molecular Biology Department, University College London, Gower Street, London WC1E B6T, UK.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, United Kingdom
| | - Dominique Toye
- Chemical engineering laboratory, University of Liège, Allée de la chimie, 3, Bât B6c, 4000 Liège, Belgium
| | - Jean-Marie Frère
- Laboratory of Enzymology and Protein Folding/Robotein Platform, Centre for Protein Engineering (CIP), Department of Life Sciences, University of Liège, Quartier Agora, Allée du six Août 13, Bât. B6a, 4000 Liège, Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Rega, Herestraat 49 box 1041, 3000 Leuven, Belgium.,Université d'Evry, CNRS-UMR8030/Laboratoire iSSB, CEA, DRF, IG, Genoscope, Université Paris-Saclay, Evry 91000, France
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16
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Affiliation(s)
- John C. Chaput
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry University of California, Irvine CA USA
| | - Piet Herdewijn
- Medicinal Chemistry Rega Institute for Medical Research KU Leuven Leuven Belgien
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17
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Affiliation(s)
- John C. Chaput
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry University of California, Irvine CA USA
| | - Piet Herdewijn
- Medicinal Chemistry Rega Institute for Medical Research KU Leuven Leuven Belgium
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18
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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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19
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Li X, Dumbre SG, Lescrinier E, Groaz E, Herdewijn P. Synthesis and Conformation of Pentopyranoside Nucleoside Phosphonates. J Org Chem 2019; 84:6589-6603. [PMID: 31046278 DOI: 10.1021/acs.joc.8b03178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In contrast to natural nucleosides, where the nucleobase is positioned at the anomeric center, we report the synthesis of pentopyranoside nucleosides with a phosphonate functionality at the 1'-anomeric oxygen. Starting from l-arabinose, key functionalized l- glycero- and l- erythro-pentopyranose carbohydrate synthons were prepared and further elaborated into the final six-membered ring nucleosides via nucleobase incorporation and phosphonomethylation reactions. NMR analysis demonstrated that these nucleoside phosphonates exist in solution as conformers predominantly adopting a chair structure in which the base moiety is equatorially positioned. Such conformation prevents unfavorable 1,3-diaxial steric and electronic interactions. Notably, the stereochemical outcome of the Vorbrüggen glycosylation step utilized en route to the thymine analogue clearly suggests the absence of anchimeric assistance, as opposed to what is usually observed during nucleoside synthesis using protected furanose precursors. The finding that the diphosphates of the compounds developed in this study are recognized by DNA polymerases is important in view of the future selection of artificial genetic systems and dedicated polymerases as well as applications in therapy.
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Affiliation(s)
- Xiaochen Li
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Shrinivas G Dumbre
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Eveline Lescrinier
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Elisabetta Groaz
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
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20
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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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21
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Efthymiou T, Gavette J, Stoop M, De Riccardis F, Froeyen M, Herdewijn P, Krishnamurthy R. Chimeric XNA: An Unconventional Design for Orthogonal Informational Systems. Chemistry 2018; 24:12811-12819. [PMID: 29901248 DOI: 10.1002/chem.201802287] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/12/2018] [Indexed: 10/14/2022]
Abstract
The paradigm of homogenous-sugar-backbone of RNA and DNA has reliably guided the construction of many functional and useful xeno nucleic acid (XNA) systems to date. Deviations from this monotonous and canonical design, in many cases, results in oligonucleotide systems that lack base pairing with themselves, or with RNA or DNA. Here we show that nucleotides of two such compromised XNA systems can be combined with RNA and DNA in specific patterns to produce chimeric-backbone oligonucleotides, which in certain cases demonstrate base pairing properties comparable to-or stronger than-canonical systems, while also altering the conventional Watson-Crick pairing behavior. The unorthodox pairing properties generated from these chimeric sugar-backbone oligonucleotides suggest a counterintuitive approach of creating modules consisting of non-base pairing XNAs with RNA/DNA in a set pattern. This strategy has the potential to increase the diversity of unconventional nucleic acids leading to orthogonal backbone-sequence-controlled informational systems.
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Affiliation(s)
- Tim Efthymiou
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.,NSF/NASA Center for Chemical Evolution, Atlanta, GA, 30332, USA
| | - Jesse Gavette
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.,NSF/NASA Center for Chemical Evolution, Atlanta, GA, 30332, USA
| | - Matthias Stoop
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.,NSF/NASA Center for Chemical Evolution, Atlanta, GA, 30332, USA
| | - Francesco De Riccardis
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.,NSF/NASA Center for Chemical Evolution, Atlanta, GA, 30332, USA.,Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, Salerno, Italy
| | - Mathy Froeyen
- Department of Medicinal Chemistry, Institute for Medical Research, KU Leuven, Herestraat, 49, Leuven, 3000, Belgium
| | - Piet Herdewijn
- Department of Medicinal Chemistry, Institute for Medical Research, KU Leuven, Herestraat, 49, Leuven, 3000, Belgium
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.,NSF/NASA Center for Chemical Evolution, Atlanta, GA, 30332, USA
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22
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Jabgunde AM, Jaziri F, Bande O, Froeyen M, Abramov M, Nguyen H, Schepers G, Lescrinier E, Pinheiro VB, Pezo V, Marlière P, Herdewijn P. Methylated Nucleobases: Synthesis and Evaluation for Base Pairing In Vitro and In Vivo. Chemistry 2018; 24:12695-12707. [DOI: 10.1002/chem.201802304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/07/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Amit M. Jabgunde
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Faten Jaziri
- Génomique Métabolique, Genoscope; Institut François Jacob; CEA; CNRS; Univ Evry, Université Paris-Saclay; 91057 Evry France
| | - Omprakash Bande
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Matheus Froeyen
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Mikhail Abramov
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Hoai Nguyen
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Guy Schepers
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Eveline Lescrinier
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Vitor B. Pinheiro
- Institute of Structural and Molecular Biology; University College London; Darwin Building, Gower Street London WC1E 6BT United Kingdom
| | - Valérie Pezo
- Génomique Métabolique, Genoscope; Institut François Jacob; CEA; CNRS; Univ Evry, Université Paris-Saclay; 91057 Evry France
| | - Philippe Marlière
- Génomique Métabolique, Genoscope; Institut François Jacob; CEA; CNRS; Univ Evry, Université Paris-Saclay; 91057 Evry France
| | - Piet Herdewijn
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
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23
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Kestemont D, Renders M, Leonczak P, Abramov M, Schepers G, Pinheiro VB, Rozenski J, Herdewijn P. XNA ligation using T4 DNA ligase in crowding conditions. Chem Commun (Camb) 2018; 54:6408-6411. [PMID: 29872779 DOI: 10.1039/c8cc02414f] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
T4 DNA ligase is capable of ligating 2'OMe-RNA duplexes, HNA, LNA and FANA mixed sequences in the presence of 10% w/v PEG8000 and 3 M betaine. The enzymatic joining of oligonucleotides containing multiple consecutive XNA nucleotides at the ligation site has not been reported before.
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Affiliation(s)
- Donaat Kestemont
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49 box 1041, 3000 Leuven, Belgium.
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24
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Liu C, Cozens C, Jaziri F, Rozenski J, Maréchal A, Dumbre S, Pezo V, Marlière P, Pinheiro VB, Groaz E, Herdewijn P. Phosphonomethyl Oligonucleotides as Backbone-Modified Artificial Genetic Polymers. J Am Chem Soc 2018; 140:6690-6699. [DOI: 10.1021/jacs.8b03447] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Chao Liu
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | | | - Faten Jaziri
- iSSB, Genopole, CNRS, UEVE, Université Paris-Saclay, 5 rue Henri Desbruères, 91030 Evry Cedex, France
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | | | - Shrinivas Dumbre
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Valérie Pezo
- iSSB, Genopole, CNRS, UEVE, Université Paris-Saclay, 5 rue Henri Desbruères, 91030 Evry Cedex, France
| | - Philippe Marlière
- iSSB, Genopole, CNRS, UEVE, Université Paris-Saclay, 5 rue Henri Desbruères, 91030 Evry Cedex, France
| | - Vitor B. Pinheiro
- University College London, Gower Street, London WC1E 6BT, U.K
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, U.K
| | - Elisabetta Groaz
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
- iSSB, Genopole, CNRS, UEVE, Université Paris-Saclay, 5 rue Henri Desbruères, 91030 Evry Cedex, France
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25
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Röthlisberger P, Levi-Acobas F, Sarac I, Marlière P, Herdewijn P, Hollenstein M. On the enzymatic incorporation of an imidazole nucleotide into DNA. Org Biomol Chem 2018; 15:4449-4455. [PMID: 28485736 DOI: 10.1039/c7ob00858a] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The expansion of the genetic alphabet with an additional, artificial base pair is of high relevance for numerous applications in synthetic biology. The enzymatic construction of metal base pairs is an alluring strategy that would ensure orthogonality to canonical nucleic acids. So far, very little is known on the enzymatic fabrication of metal base pairs. Here, we report on the synthesis and the enzymatic incorporation of an imidazole nucleotide into DNA. The imidazole nucleotide dIm is known to form highly stable dIm-Ag+-dIm artificial base pairs that cause minimal structural perturbation of DNA duplexes and was considered to be an ideal candidate for the enzymatic construction of metal base pairs. We demonstrate that dImTP is incorporated with high efficiency and selectivity opposite a templating dIm nucleotide by the Kf exo-. The presence of Mn2+, and to a smaller extent Ag+, enhances the efficiency of this polymerization reaction, however, without being strictly required. In addition, multiple incorporation events could be observed, albeit with modest efficiency. We demonstrate that the dIm-Mn+-dIm cannot be constructed by DNA polymerases and suggest that parameters other than stability of a metal base pair and its impact on the structure of DNA duplexes govern the enzymatic formation of artificial metal base pairs.
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Affiliation(s)
- Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.
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26
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Feldman AW, Fischer EC, Ledbetter MP, Liao JY, Chaput JC, Romesberg FE. A Tool for the Import of Natural and Unnatural Nucleoside Triphosphates into Bacteria. J Am Chem Soc 2018; 140:1447-1454. [PMID: 29338214 DOI: 10.1021/jacs.7b11404] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Nucleoside triphosphates play a central role in biology, but efforts to study these roles have proven difficult because the levels of triphosphates are tightly regulated in a cell and because individual triphosphates can be difficult to label or modify. In addition, many synthetic biology efforts are focused on the development of unnatural nucleoside triphosphates that perform specific functions in the cellular environment. In general, both of these efforts would be facilitated by a general means to directly introduce desired triphosphates into cells. Previously, we demonstrated that recombinant expression of a nucleoside triphosphate transporter from Phaeodactylum tricornutum (PtNTT2) in Escherichia coli functions to import triphosphates that are added to the media. Here, to explore the generality and utility of this approach, we report a structure-activity relationship study of PtNTT2. Using a conventional competitive uptake inhibition assay, we characterize the effects of nucleobase, sugar, and triphosphate modification, and then develop an LC-MS/MS assay to directly measure the effects of the modifications on import. Lastly, we use the transporter to import radiolabeled or 2'-fluoro-modified triphosphates and quantify their incorporation into DNA and RNA. The results demonstrate the general utility of the PtNTT2-mediated import of natural or modified nucleoside triphosphates for different molecular or synthetic biology applications.
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Affiliation(s)
- Aaron W Feldman
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Emil C Fischer
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael P Ledbetter
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jen-Yu Liao
- Department of Pharmaceutical Sciences, University of California , Irvine, California 92697, United States
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California , Irvine, California 92697, United States
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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27
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Eremeeva E, Abramov M, Margamuljana L, Herdewijn P. Base-Modified Nucleic Acids as a Powerful Tool for Synthetic Biology and Biotechnology. Chemistry 2017; 23:9560-9576. [PMID: 28513881 DOI: 10.1002/chem.201700679] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 11/10/2022]
Abstract
The ability of various nucleoside triphosphate analogues of deoxyguanosine and deoxycytidine with 7-deazadeoxyadenosine (A1 ) and 5-chlorodeoxyuridine (T1 ) to serve as substrates for Taq DNA polymerase was evaluated. The triphosphate set composed of A1 , T1 , and 7-deazadeoxyguanosine with either 5-methyldeoxycytidine or 5-fluorodeoxycytidine was successfully employed in the polymerase chain reaction (PCR) of 1.5 kb fragments as well as random oligonucleotide libraries. Another effective combination of triphosphates for the synthesis of a 1 kb PCR product was A1 , T1 , deoxyinosine, and 5-bromodeoxycytidine. In vivo experiments using an antibiotic-resistant gene containing the latter set demonstrated that the bacterial machinery accepts fully modified sequences as genetic templates. Moreover, the ability of the base-modified segments to selectively protect DNA from cleavage by restriction endonucleases was shown. This approach can be used to regulate the endonuclease cleavage pattern.
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Affiliation(s)
- Elena Eremeeva
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 box 1041, 3000, Leuven, Belgium
| | - Michail Abramov
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 box 1041, 3000, Leuven, Belgium
| | - Lia Margamuljana
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 box 1041, 3000, Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 box 1041, 3000, Leuven, Belgium.,Université d'évry, CNRS-UMR8030/ Laboratoire iSSB, CEA, DRF, IG, Genoscope, Université Paris-Saclay, évry, 91000, Paris, France
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28
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Diafa S, Evéquoz D, Leumann CJ, Hollenstein M. Enzymatic Synthesis of 7',5'-Bicyclo-DNA Oligonucleotides. Chem Asian J 2017; 12:1347-1352. [PMID: 28371464 DOI: 10.1002/asia.201700374] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 03/30/2017] [Indexed: 01/06/2023]
Abstract
The selection of artificial genetic polymers with tailor-made properties for their application in synthetic biology requires the exploration of new nucleosidic scaffolds that can be used in selection experiments. Herein, we describe the synthesis of a bicyclo-DNA triphosphate (i.e., 7',5'-bc-TTP) and show its potential to serve for the generation of new xenonucleic acids (XNAs) based on this scaffold. 7',5'-bc-TTP is a good substrate for Therminator DNA polymerase, and up to seven modified units can be incorporated into a growing DNA chain. In addition, this scaffold sustains XNA-dependent DNA synthesis and potentially also XNA-dependent XNA synthesis. However, DNA-dependent XNA synthesis on longer templates is hampered by competitive misincorporation of deoxyadenosine triphosphate (dATP) caused by the slow rate of incorporation of 7',5'-bc-TTP.
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Affiliation(s)
- Stella Diafa
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Damien Evéquoz
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Marcel Hollenstein
- Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
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29
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Röthlisberger P, Levi-Acobas F, Hollenstein M. New synthetic route to ethynyl-dUTP: A means to avoid formation of acetyl and chloro vinyl base-modified triphosphates that could poison SELEX experiments. Bioorg Med Chem Lett 2017; 27:897-900. [PMID: 28089700 DOI: 10.1016/j.bmcl.2017.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/04/2017] [Accepted: 01/05/2017] [Indexed: 01/10/2023]
Abstract
5-Ethynyl-2'-deoxyuridine is a common base-modified nucleoside analogue that has served in various applications including selection experiments for potent aptamers and in biosensing. The synthesis of the corresponding triphosphates involves a mild acidic deprotection step. Herein, we show that this deprotection leads to the formation of other nucleoside analogs which are easily converted to triphosphates. The modified nucleoside triphosphates are excellent substrates for numerous DNA polymerases under both primer extension and PCR conditions and could thus poison selection experiments by blocking sites that need to be further modified. The formation of these nucleoside analogs can be circumvented by application of a new synthetic route that is described herein.
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Affiliation(s)
- Pascal Röthlisberger
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France; CNRS UMR3523 Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Fabienne Levi-Acobas
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France; CNRS UMR3523 Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Marcel Hollenstein
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France; CNRS UMR3523 Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
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Chen T, Hongdilokkul N, Liu Z, Thirunavukarasu D, Romesberg FE. The expanding world of DNA and RNA. Curr Opin Chem Biol 2016; 34:80-87. [PMID: 27565457 DOI: 10.1016/j.cbpa.2016.08.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/04/2016] [Indexed: 01/07/2023]
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.
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Affiliation(s)
- Tingjian Chen
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA
| | - Narupat Hongdilokkul
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA
| | - Zhixia Liu
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA
| | - Deepak Thirunavukarasu
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA.
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31
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Eremeeva E, Abramov M, Margamuljana L, Rozenski J, Pezo V, Marlière P, Herdewijn P. Chemical Morphing of DNA Containing Four Noncanonical Bases. Angew Chem Int Ed Engl 2016; 55:7515-9. [PMID: 27159019 DOI: 10.1002/anie.201601529] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 01/04/2023]
Abstract
The ability of alternative nucleic acids, in which all four nucleobases are substituted, to replicate in vitro and to serve as genetic templates in vivo was evaluated. A nucleotide triphosphate set of 5-chloro-2'-deoxyuridine, 7-deaza-2'-deoxyadenosine, 5-fluoro-2'-deoxycytidine, and 7-deaza-2'deoxyguanosine successfully underwent polymerase chain reaction (PCR) amplification using templates of different lengths (57 or 525mer) and Taq or Vent (exo-) DNA polymerases as catalysts. Furthermore, a fully morphed gene encoding a dihydrofolate reductase was generated by PCR using these fully substituted nucleotides and was shown to transform and confer trimethoprim resistance to E. coli. These results demonstrated that fully modified templates were accurately read by the bacterial replication machinery and provide the first example of a long fully modified DNA molecule being functional in vivo.
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Affiliation(s)
- Elena Eremeeva
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Michail Abramov
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Lia Margamuljana
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Jef Rozenski
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Valerie Pezo
- ISSB, Génopole, Genavenir 6, Equipe Xénome, 5 rue Henri Desbruères, 91030, Evry Cedex, France
| | - Philippe Marlière
- ISSB, Génopole, Genavenir 6, Equipe Xénome, 5 rue Henri Desbruères, 91030, Evry Cedex, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium. .,ISSB, Génopole, Genavenir 6, Equipe Xénome, 5 rue Henri Desbruères, 91030, Evry Cedex, France.
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32
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Eremeeva E, Abramov M, Margamuljana L, Rozenski J, Pezo V, Marlière P, Herdewijn P. Chemical Morphing of DNA Containing Four Noncanonical Bases. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601529] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Elena Eremeeva
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
| | - Michail Abramov
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
| | - Lia Margamuljana
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
| | - Jef Rozenski
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
| | - Valerie Pezo
- ISSB; Génopole; Genavenir 6; Equipe Xénome; 5 rue Henri Desbruères 91030 Evry Cedex France
| | - Philippe Marlière
- ISSB; Génopole; Genavenir 6; Equipe Xénome; 5 rue Henri Desbruères 91030 Evry Cedex France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
- ISSB; Génopole; Genavenir 6; Equipe Xénome; 5 rue Henri Desbruères 91030 Evry Cedex France
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33
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Froeyen M, Abu el Asrar R, Abramov M, Herdewijn P. Molecular simulation of cyclohexanyl nucleic acid (CNA) duplexes with CNA, DNA and RNA and CNA triloop and tetraloop hairpin structures. Bioorg Med Chem 2016; 24:1778-85. [PMID: 26968651 DOI: 10.1016/j.bmc.2016.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/29/2016] [Accepted: 03/02/2016] [Indexed: 01/09/2023]
Abstract
As part of a selection strategy for artificial nucleic acids (XNA) (to be considered as potential new information systems in vivo), we have carried out a modelling study on cyclohexanyl nucleic acids (CNA) duplexes and hairpins. CNA may form a duplex as well as hairpin structures, having the carbocyclic nucleosides in the (4)C1 conformation (with equatorial basis). The geometry of ds CNA is close to that of a HNA:RNA duplex. We demonstrated that CNA triphosphates function as a substrate for polymerases. Modelling experiments indicate that the monomers are probably presented to the polymerase in the (1)C4 conformation.
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Affiliation(s)
- Matheus Froeyen
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Rania Abu el Asrar
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Mikhail Abramov
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium.
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Schmidt M, de Lorenzo V. Synthetic bugs on the loose: containment options for deeply engineered (micro)organisms. Curr Opin Biotechnol 2016; 38:90-6. [PMID: 26874261 DOI: 10.1016/j.copbio.2016.01.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 12/14/2022]
Abstract
Synthetic Biology (SynBio) has brought up again questions on the environmental fate of microorganisms carrying genetic modifications. The growing capacity of editing genomes for deployment of man-made programs opens unprecedented biotechnological opportunities. But the same exacerbate concerns regarding fortuitous or deliberate releases to the natural medium. Most approaches to tackle these worries involve endowing SynBio agents with containment devices for halting horizontal gene transfer and survival of the live agents only at given times and places. Genetic circuits and trophic restraint schemes have been proposed to this end in the pursuit of complete containment. The most promising include adoption of alternative genetic codes and/or dependency on xenobiotic amino acids and nucleotides. But the field has to still overcome serious bottlenecks.
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Affiliation(s)
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain.
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35
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Bande O, Braddick D, Agnello S, Jang M, Pezo V, Schepers G, Rozenski J, Lescrinier E, Marlière P, Herdewijn P. Base pairing involving artificial bases in vitro and in vivo. Chem Sci 2015; 7:995-1010. [PMID: 29896368 PMCID: PMC5954848 DOI: 10.1039/c5sc03474d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/28/2015] [Indexed: 01/09/2023] Open
Abstract
Herein we report the synthesis, base pairing properties and in vivo transliteration of N8-glycosylated 8-aza-deoxyguanosine and 8-aza-9-deaza-deoxyguanosine nucleotides with 8-amino-deoxyinosine, 1-N-methyl-8-amino-deoxyinosine and 7,8-dihydro-8-oxo-deoxy-inosine/adenosine/guanosine as pairing partners.
Herein we report the synthesis of N8-glycosylated 8-aza-deoxyguanosine (N8-8-aza-dG) and 8-aza-9-deaza-deoxyguanosine (N8-8-aza-9-deaza-dG) nucleotides and their base pairing properties with 5-methyl-isocytosine (d-isoCMe), 8-amino-deoxyinosine (8-NH2-dI), 1-N-methyl-8-amino-deoxyinosine (1-Me-8-NH2-dI), 7,8-dihydro-8-oxo-deoxyinosine (8-Oxo-dI), 7,8-dihydro-8-oxo-deoxyadenosine (8-Oxo-dA), and 7,8-dihydro-8-oxo-deoxyguanosine (8-Oxo-dG), in comparison with the d-isoCMe:d-isoG artificial genetic system. As demonstrated by Tm measurements, the N8-8-aza-dG:d-isoCMe base pair formed less stable duplexes as the C:G and d-isoCMe:d-isoG pairs. Incorporation of 8-NH2-dI versus the N8-8-aza-dG nucleoside resulted in a greater reduction in Tm stability, compared to d-isoCMe:d-isoG. Insertion of the methyl group at the N1 position of 8-NH2-dI did not affect duplex stability with N8-8-aza-dG, thus suggesting that the base paring takes place through Hoogsteen base pairing. The cellular interpretation of the nucleosides was studied, whereby a lack of recognition or mispairing of the incorporated nucleotides with the canonical DNA bases indicated the extent of orthogonality in vivo. The most biologically orthogonal nucleosides identified included the 8-amino-deoxyinosines (1-Me-8-NH2-dI and 8-NH2-dI) and N8-8-aza-9-deaza-dG. The 8-oxo modifications mimic oxidative damage ahead of cancer development, and the impact of the MutM mediated recognition of these 8-oxo-deoxynucleosides was studied, finding no significant impact in their in vivo assay.
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Affiliation(s)
- Omprakash Bande
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Darren Braddick
- iSSB - CNRS FRE3561 , University of Evry-Val-d'Essonne , 5 rue Henri Desbruères, Genopole Campus 1, Bât. 6 , F-91030 Évry Cedex , France
| | - Stefano Agnello
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Miyeon Jang
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Valérie Pezo
- iSSB - CNRS FRE3561 , University of Evry-Val-d'Essonne , 5 rue Henri Desbruères, Genopole Campus 1, Bât. 6 , F-91030 Évry Cedex , France
| | - Guy Schepers
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Jef Rozenski
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Eveline Lescrinier
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Philippe Marlière
- iSSB - CNRS FRE3561 , University of Evry-Val-d'Essonne , 5 rue Henri Desbruères, Genopole Campus 1, Bât. 6 , F-91030 Évry Cedex , France
| | - Piet Herdewijn
- iSSB - CNRS FRE3561 , University of Evry-Val-d'Essonne , 5 rue Henri Desbruères, Genopole Campus 1, Bât. 6 , F-91030 Évry Cedex , France.,Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
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36
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D'Alonzo D, Froeyen M, Schepers G, Di Fabio G, Van Aerschot A, Herdewijn P, Palumbo G, Guaragna A. 1',5'-Anhydro-L-ribo-hexitol Adenine Nucleic Acids (α-L-HNA-A): Synthesis and Chiral Selection Properties in the Mirror Image World. J Org Chem 2015; 80:5014-22. [PMID: 25853790 DOI: 10.1021/acs.joc.5b00406] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis and a preliminary investigation of the base pairing properties of (6' → 4')-linked 1',5'-anhydro-L-ribo-hexitol nucleic acids (α-L-HNA) have herein been reported through the study of a model oligoadenylate system in the mirror image world. Despite its considerable preorganization due to the rigidity of the "all equatorial" pyranyl sugar backbone, α-L-HNA represents a versatile informational biopolymer, in view of its capability to cross-communicate with natural and unnatural complements in both enantiomeric forms. This seems the result of an inherent flexibility of the oligonucleotide system, as witnessed by the singular formation of iso- and heterochiral associations composed of regular, enantiomorphic helical structures. The peculiar properties of α-L-HNA (and most generally of the α-HNA system) provide new elements in our understanding of the structural prerequisites ruling the stereoselectivity of the hybridization processes of nucleic acids.
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Affiliation(s)
- Daniele D'Alonzo
- †Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, 80126 Napoli, Italy
| | - Mathy Froeyen
- ‡Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Guy Schepers
- ‡Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Giovanni Di Fabio
- †Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, 80126 Napoli, Italy
| | - Arthur Van Aerschot
- ‡Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Piet Herdewijn
- ‡Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Giovanni Palumbo
- †Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, 80126 Napoli, Italy
| | - Annalisa Guaragna
- †Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, 80126 Napoli, Italy
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37
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Bande O, Abu El Asrar R, Braddick D, Dumbre S, Pezo V, Schepers G, Pinheiro VB, Lescrinier E, Holliger P, Marlière P, Herdewijn P. Isoguanine and 5-methyl-isocytosine bases, in vitro and in vivo. Chemistry 2015; 21:5009-22. [PMID: 25684598 PMCID: PMC4531829 DOI: 10.1002/chem.201406392] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Indexed: 11/10/2022]
Abstract
The synthesis, base-pairing properties and in vitro and in vivo characteristics of 5-methyl-isocytosine (isoCMe) and isoguanine (isoG) nucleosides, incorporated in an HNA(h) (hexitol nucleic acid)–DNA(d) mosaic backbone, are described. The required h-isoG phosphoramidite was prepared by a selective deamination as a key step. As demonstrated by Tm measurements the hexitol sugar showed slightly better mismatch discrimination against dT. The d-isoG base mispairing follows the order T>G>C while the h-isoG base mispairing follows the order G>C>T. The h- and d-isoCMe bases mainly mispair with G. Enzymatic incorporation experiments show that the hexitol backbone has a variable effect on selectivity. In the enzymatic assays, isoG misincorporates mainly with T, and isoCMe misincorporates mainly with A. Further analysis in vivo confirmed the patterns of base-pair interpretation for the deoxyribose and hexitol isoCMe/isoG bases in a cellular context, through incorporation of the bases into plasmidic DNA. Results in vivo demonstrated that mispairing and misincorporation was dependent on the backbone scaffold of the base, which indicates rational advances towards orthogonality.
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Affiliation(s)
- Omprakash Bande
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven (Belgium)
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Maruyama H, Furukawa K, Kamiya H, Minakawa N, Matsuda A. Transcription of 4′-thioDNA templates to natural RNA in vitro and in mammalian cells. Chem Commun (Camb) 2015; 51:7887-90. [DOI: 10.1039/c4cc08862j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Synthetic chemically modified nucleic acids, which are compatible with DNA/RNA polymerases, have great potential as a genetic material for synthetic biological studies.
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Affiliation(s)
- Hideto Maruyama
- Faculty of Pharmaceutical Sciences
- Hokkaido University
- Sapporo 060-0812
- Japan
| | - Kazuhiro Furukawa
- Graduate School of Pharmaceutical Sciences
- The University of Tokushima
- Tokushima 770-8505
- Japan
| | - Hiroyuki Kamiya
- Graduate School of Biomedical & Health Sciences
- Hiroshima University
- Hiroshima 734-8553
- Japan
| | - Noriaki Minakawa
- Graduate School of Pharmaceutical Sciences
- The University of Tokushima
- Tokushima 770-8505
- Japan
| | - Akira Matsuda
- Faculty of Pharmaceutical Sciences
- Hokkaido University
- Sapporo 060-0812
- Japan
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39
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Synthesis of new biocarrier–nucleotide systems for cellular delivery in bacterial auxotrophic strains. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.09.096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Pezo V, Schepers G, Lambertucci C, Marlière P, Herdewijn P. Probing ambiguous base-pairs by genetic transformation with XNA templates. Chembiochem 2014; 15:2255-8. [PMID: 25158283 DOI: 10.1002/cbic.201402226] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Indexed: 11/11/2022]
Abstract
The templating potential of anhydrohexitol oligonucleotides bearing ambiguous bases was studied in vivo, by using a selection screen for mosaic heteroduplex plasmids in Escherichia coli. 1,5-Anhydro-2,3-dideoxy-2-(5-nitroindazol-1-yl)-D-arabino-hexitol showed the greatest ambiguity among the three nucleosides tested. At most two successive ambiguous bases could be tolerated on hexitol templates read in bacterial cells. Hexitol nucleosides bearing simplified heterocycles thus stand as promising monomers for generating random DNA sequences in vivo from defined synthetic oligonucleotides.
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Affiliation(s)
- Valérie Pezo
- CEA, DSV, IG, Genoscope, 2 rue Gaston Crémieux 91057 Evry Cedex (France); ISSB, Génopole genavenir6, Equipe Xénome, 5 rue Henri Desbruères 91030 Evry Cedex (France)
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41
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De S, Groaz E, Herdewijn P. Tailoring Peptide-Nucleotide Conjugates (PNCs) for Nucleotide Delivery in Bacterial Cells. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301781] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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