1
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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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2
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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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3
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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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4
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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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5
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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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6
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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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7
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Whitfield CJ, Little RC, Khan K, Ijiro K, Connolly BA, Tuite EM, Pike AR. Self-Priming Enzymatic Fabrication of Multiply Modified DNA. Chemistry 2018; 24:15267-15274. [PMID: 29931815 DOI: 10.1002/chem.201801976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/19/2018] [Indexed: 12/15/2022]
Abstract
The self-priming synthesis of multiply modified DNA by the extension of repeating unit duplex "oligoseeds" provides a source of versatile DNA. Sterically-demanding nucleotides 5-Br-dUTP, 7-deaza-7-I-dATP, 6-S-dGTP, 5-I-dCTP as well as 5-(octadiynyl)-dCTP were incorporated into two extending oligoseeds; [GATC]5 /[GATC]5 and [A4 G]4 /[CT4 ]4 . The products contained modifications on one or both strands of DNA, demonstrating their recognition by the polymerase as both template (reading) and substrate (writing). Nucleobase modifications that lie in the major groove were reliably read and written by the polymerase during the extension reaction, even when bulky or in contiguous sequences. Repeat sequence DNA over 500 bp long, bearing four different modified units was produced by this method. The number, position and type of modification, as well as the overall length of the DNA can be controlled to yield designer DNA that offers sequence-determined sites for further chemical adaptations, targeted small molecule binding studies, or sensing and sequencing applications.
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Affiliation(s)
- Colette J Whitfield
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Rachel C Little
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Kasid Khan
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Kuniharu Ijiro
- Research Institute for Electronic Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Bernard A Connolly
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Eimer M Tuite
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Andrew R Pike
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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8
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Gasse C, Zaarour M, Noppen S, Abramov M, Marlière P, Liekens S, De Strooper B, Herdewijn P. Modulation of BACE1 Activity by Chemically Modified Aptamers. Chembiochem 2018; 19:754-763. [PMID: 29327496 DOI: 10.1002/cbic.201700461] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/10/2018] [Indexed: 11/10/2022]
Abstract
A modified DNA aptamer that binds BACE1, a therapeutic target involved in Alzheimer's disease has been developed. This ssXNA not only tightly binds to BACE1 but also inhibits its protease activity in vitro in the same range as a previously described unmodified aptamer. We report the in vitro selection of functional oligonucleotides incorporating two nucleobase modifications: 5-chlorouracil and 7-deazaadenine. The nucleoside analogue 5-chloro-2'-deoxyuridine has already been explored as a replacement for thymidine in a chemically modified genome of a bacterium. Thus, 5-chlorouracil modification is a good candidate to support genetic transfer in vivo as well as functional activity.
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Affiliation(s)
- Cécile Gasse
- Univ Evry, CNRS-UMR8030-Laboratoire iSSB, CEA, DRF, IG, Genoscope, Université Paris-Saclay, 5 rue Henri Desbruères, Évry, 91030, France
| | - Marwa Zaarour
- Univ Evry, CNRS-UMR8030-Laboratoire iSSB, CEA, DRF, IG, Genoscope, Université Paris-Saclay, 5 rue Henri Desbruères, Évry, 91030, France
| | - Sam Noppen
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Postbus 1043, 3000, Leuven, Belgium
| | - Mikhail Abramov
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Philippe Marlière
- The European Syndicate of Synthetic Scientists and Industrialists (TESSI), 81 rue Réaumur, 75002, Paris, France
| | - Sandra Liekens
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Postbus 1043, 3000, Leuven, Belgium
| | - Bart De Strooper
- VIB, Center for Brain & Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Department of Neurosciences, Leuven Institute for Neuroscience and Disease, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.,Dementia Research Institute (UK), University College London, Gower Street, WC1E 6BT, London, UK
| | - Piet Herdewijn
- Univ Evry, CNRS-UMR8030-Laboratoire iSSB, CEA, DRF, IG, Genoscope, Université Paris-Saclay, 5 rue Henri Desbruères, Évry, 91030, France.,Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
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9
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Chen T, Romesberg FE. Enzymatic Synthesis, Amplification, and Application of DNA with a Functionalized Backbone. Angew Chem Int Ed Engl 2017; 56:14046-14051. [PMID: 28914996 DOI: 10.1002/anie.201707367] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/04/2017] [Indexed: 12/29/2022]
Abstract
The ability to amplify DNA along with its unprecedented sequence control has led to its use for different applications, but all are limited by the properties available to natural nucleotides. We previously reported the evolution of polymerase SFM4-3, which better tolerates 2'-modified substrates. To explore the utility of SFM4-3, we now report the characterization of its recognition of substrates with 2'-azido, 2'-chloro, 2'-amino, or arabinose sugars. We find that SFM4-3 can efficiently synthesize polymers composed of these nucleotides, and most interestingly, that SFM4-3 can also PCR amplify these modified oligonucleotides. When combined with post-amplification modification, the latter allows for the exponential amplification of polymers that may be functionalized with desired moieties arrayed in a controlled fashion, the utility of which we demonstrate with extensive small molecule functionalization and the production and initial characterization of a novel DNA hydrogel.
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Affiliation(s)
- Tingjian Chen
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
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10
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Chen T, Romesberg FE. Enzymatic Synthesis, Amplification, and Application of DNA with a Functionalized Backbone. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Tingjian Chen
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Floyd E. Romesberg
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
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11
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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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