1
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Moody ER, Obexer R, Nickl F, Spiess R, Lovelock SL. An enzyme cascade enables production of therapeutic oligonucleotides in a single operation. Science 2023; 380:1150-1154. [PMID: 37319201 DOI: 10.1126/science.add5892] [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] [Received: 06/21/2022] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
Therapeutic oligonucleotides have emerged as a powerful drug modality with the potential to treat a wide range of diseases; however, the rising number of therapies poses a manufacturing challenge. Existing synthetic methods use stepwise extension of sequences immobilized on solid supports and are limited by their scalability and sustainability. We report a biocatalytic approach to efficiently produce oligonucleotides in a single operation where polymerases and endonucleases work in synergy to amplify complementary sequences embedded within catalytic self-priming templates. This approach uses unprotected building blocks and aqueous conditions. We demonstrate the versatility of this methodology through the synthesis of clinically relevant oligonucleotide sequences containing diverse modifications.
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Affiliation(s)
- E R Moody
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - R Obexer
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - F Nickl
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - R Spiess
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - S L Lovelock
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
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2
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Wu KB, Skrodzki CJA, Su Q, Lin J, Niu J. "Click handle"-modified 2'-deoxy-2'-fluoroarabino nucleic acid as a synthetic genetic polymer capable of post-polymerization functionalization. Chem Sci 2022; 13:6873-6881. [PMID: 35774169 PMCID: PMC9200136 DOI: 10.1039/d2sc00679k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/16/2022] [Indexed: 01/01/2023] Open
Abstract
The functions of natural nucleic acids such as DNA and RNA have transcended genetic information carriers and now encompass affinity reagents, molecular catalysts, nanostructures, data storage, and many others. However, the vulnerability of natural nucleic acids to nuclease degradation and the lack of chemical functionality have imposed a significant constraint on their ever-expanding applications. Herein, we report the synthesis and polymerase recognition of a 5-(octa-1,7-diynyl)uracil 2′-deoxy-2′-fluoroarabinonucleic acid (FANA) triphosphate. The DNA-templated, polymerase-mediated primer extension using this “click handle”-modified FANA (cmFANA) triphosphate and other FANA nucleotide triphosphates consisting of canonical nucleobases efficiently generated full-length products. The resulting cmFANA polymers exhibited excellent nuclease resistance and the ability to undergo efficient click conjugation with azide-functionalized molecules, thereby becoming a promising platform for serving as a programmable and evolvable synthetic genetic polymer capable of post-polymerization functionalization. Polymerase-mediated incorporation of a “click handle”-modified fluoroarabinonucleic acid (cmFANA) triphosphate produces a new class of nuclease-resistant, evolvable genetic polymers that can be functionalized with azide-containing molecules.![]()
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Affiliation(s)
- Kevin B Wu
- Department of Chemistry, Boston College 2609 Beacon Street, Chestnut Hill MA 20467 USA
| | | | - Qiwen Su
- Department of Chemistry, Boston College 2609 Beacon Street, Chestnut Hill MA 20467 USA
| | - Jennifer Lin
- Department of Chemistry, Boston College 2609 Beacon Street, Chestnut Hill MA 20467 USA
| | - Jia Niu
- Department of Chemistry, Boston College 2609 Beacon Street, Chestnut Hill MA 20467 USA
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3
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Hans S, Kumar N, Gohil N, Khambhati K, Bhattacharjee G, Deb SS, Maurya R, Kumar V, Reshamwala SMS, Singh V. Rebooting life: engineering non-natural nucleic acids, proteins and metabolites in microorganisms. Microb Cell Fact 2022; 21:100. [PMID: 35643549 PMCID: PMC9148472 DOI: 10.1186/s12934-022-01828-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/15/2022] [Indexed: 12/01/2022] Open
Abstract
The surging demand of value-added products has steered the transition of laboratory microbes to microbial cell factories (MCFs) for facilitating production of large quantities of important native and non-native biomolecules. This shift has been possible through rewiring and optimizing different biosynthetic pathways in microbes by exercising frameworks of metabolic engineering and synthetic biology principles. Advances in genome and metabolic engineering have provided a fillip to create novel biomolecules and produce non-natural molecules with multitude of applications. To this end, numerous MCFs have been developed and employed for production of non-natural nucleic acids, proteins and different metabolites to meet various therapeutic, biotechnological and industrial applications. The present review describes recent advances in production of non-natural amino acids, nucleic acids, biofuel candidates and platform chemicals.
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4
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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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5
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Veale CGL, Talukdar A, Vauzeilles B. ICBS 2021: Looking Toward the Next Decade of Chemical Biology. ACS Chem Biol 2022; 17:728-743. [PMID: 35293726 DOI: 10.1021/acschembio.2c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Clinton G. L. Veale
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Boris Vauzeilles
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
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6
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Abstract
The maturation of chemical synthesis during the 20th century has elevated the discipline from a largely empirical into a rational science. This ability to purposefully craft matter at the molecular level has put chemists in a privileged position to contribute to progress in neighboring natural sciences. Recently, we have witnessed another major advance in the field in which chemists use chemical and biological "synthetic" methods together to alter the structures and properties of biological macromolecules in ways heretofore unimagined. This interdisciplinary approach to synthesis has even allowed us to expand upon the defining characteristics of living organisms at the molecular level. In this perspective, we present a case study for the successful addition of new chemistries to the fundamental processes of the central dogma of molecular biology, exemplified by the expansion of the genetic code.
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Affiliation(s)
- Christian S. Diercks
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- These authors contributed equally
| | - David A. Dik
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- These authors contributed equally
| | - Peter G. Schultz
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Lead contact
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7
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Pezo V, Jaziri F, Bourguignon PY, Louis D, Jacobs-Sera D, Rozenski J, Pochet S, Herdewijn P, Hatfull GF, Kaminski PA, Marliere P. Noncanonical DNA polymerization by aminoadenine-based siphoviruses. Science 2021; 372:520-524. [PMID: 33926956 DOI: 10.1126/science.abe6542] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/25/2021] [Indexed: 01/05/2023]
Abstract
Bacteriophage genomes harbor the broadest chemical diversity of nucleobases across all life forms. Certain DNA viruses that infect hosts as diverse as cyanobacteria, proteobacteria, and actinobacteria exhibit wholesale substitution of aminoadenine for adenine, thereby forming three hydrogen bonds with thymine and violating Watson-Crick pairing rules. Aminoadenine-encoded DNA polymerases, homologous to the Klenow fragment of bacterial DNA polymerase I that includes 3'-exonuclease but lacks 5'-exonuclease, were found to preferentially select for aminoadenine instead of adenine in deoxynucleoside triphosphate incorporation templated by thymine. Polymerase genes occur in synteny with genes for a biosynthesis enzyme that produces aminoadenine deoxynucleotides in a wide array of Siphoviridae bacteriophages. Congruent phylogenetic clustering of the polymerases and biosynthesis enzymes suggests that aminoadenine has propagated in DNA alongside adenine since archaic stages of evolution.
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Affiliation(s)
- Valerie 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
| | - Pierre-Yves Bourguignon
- Werkstatt fuer Potenzielle Genetik, Naunynstrasse 30, 10997 Berlin, Germany.,TESSSI, 81 Rue Réaumur, 75002 Paris, France
| | | | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260 USA
| | - Jef Rozenski
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Sylvie Pochet
- Organic Chemistry, CNRS UMR3523, Department of Chemistry and Biocatalysis, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260 USA
| | - Pierre-Alexandre Kaminski
- Biology of Gram-Positive Pathogens, CNRS URL3526, Department of Microbiology, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Philippe Marliere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France. .,TESSSI, 81 Rue Réaumur, 75002 Paris, France
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8
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Abstract
Collectively, the dsDNA tailed bacteriophages (Caudovirales) contain the largest chemical diversity of naturally occurring deoxynucleotides in DNA observed to date. The continuing discovery of new modifications in phages suggest many more are waiting to be found. Thus, methods for the observation and characterization of noncanonical nucleosides are timely. We present here protocols for extraction of genomic DNA from bacteriophage particles, enzymatic hydrolysis of DNA to free nucleosides, and examination of nucleoside composition by HPLC and mass spectrometry.
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Affiliation(s)
- Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, MA, USA
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9
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Espinasse A, Lembke HK, Cao AA, Carlson EE. Modified nucleoside triphosphates in bacterial research for in vitro and live-cell applications. RSC Chem Biol 2020; 1:333-351. [PMID: 33928252 PMCID: PMC8081287 DOI: 10.1039/d0cb00078g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022] Open
Abstract
Modified nucleoside triphosphates (NTPs) are invaluable tools to probe bacterial enzymatic mechanisms, develop novel genetic material, and engineer drugs and proteins with new functionalities. Although the impact of nucleobase alterations has predominantly been studied due to their importance for protein recognition, sugar and phosphate modifications have also been investigated. However, NTPs are cell impermeable due to their negatively charged phosphate tail, a major hurdle to achieving live bacterial studies. Herein, we review the recent advances made to investigate and evolve bacteria and their processes with the use of modified NTPs by exploring alterations in one of the three moieties: the nucleobase, the sugar and the phosphate tail. We also present the innovative methods that have been devised to internalize NTPs into bacteria for in vivo applications.
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Affiliation(s)
- Adeline Espinasse
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Hannah K. Lembke
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Angela A. Cao
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
- Department of Medicinal Chemistry, University of Minnesota208 Harvard Street SEMinneapolisMinnesota 55454USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota321 Church St SEMinneapolisMinnesota 55454USA
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10
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Discovery of an Unnatural DNA Modification Derived from a Natural Secondary Metabolite. Cell Chem Biol 2020; 28:97-104.e4. [PMID: 33053370 DOI: 10.1016/j.chembiol.2020.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/19/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023]
Abstract
Despite widespread interest for understanding how modified bases have evolved their contemporary functions, limited experimental evidence exists for measuring how close an organism is to accidentally creating a new, modified base within the framework of its existing genome. Here, we describe the biochemical and structural basis for how a single-point mutation in E. coli's naturally occurring cytosine methyltransferase can surprisingly endow a neomorphic ability to create the unnatural DNA base, 5-carboxymethylcytosine (5cxmC), in vivo. Mass spectrometry, bacterial genetics, and structure-guided biochemistry reveal this base to be exclusively derived from the natural but sparse secondary metabolite carboxy-S-adenosyl-L-methionine (CxSAM). Our discovery of a new, unnatural DNA modification reveals insights into the substrate selectivity of DNA methyltransferase enzymes, offers a promising new biotechnological tool for the characterization of the mammalian epigenome, and provides an unexpected model for how neomorphic bases could arise in nature from repurposed host metabolites.
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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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Duffy K, Arangundy-Franklin S, Holliger P. Modified nucleic acids: replication, evolution, and next-generation therapeutics. BMC Biol 2020; 18:112. [PMID: 32878624 PMCID: PMC7469316 DOI: 10.1186/s12915-020-00803-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Modified nucleic acids, also called xeno nucleic acids (XNAs), offer a variety of advantages for biotechnological applications and address some of the limitations of first-generation nucleic acid therapeutics. Indeed, several therapeutics based on modified nucleic acids have recently been approved and many more are under clinical evaluation. XNAs can provide increased biostability and furthermore are now increasingly amenable to in vitro evolution, accelerating lead discovery. Here, we review the most recent discoveries in this dynamic field with a focus on progress in the enzymatic replication and functional exploration of XNAs.
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Affiliation(s)
- Karen Duffy
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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13
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Nie P, Bai Y, Mei H. Synthetic Life with Alternative Nucleic Acids as Genetic Materials. Molecules 2020; 25:E3483. [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] [Grants] [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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Affiliation(s)
| | | | - Hui Mei
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (P.N.); (Y.B.)
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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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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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16
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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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17
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Mehta AP, Wang Y, Reed SA, Supekova L, Javahishvili T, Chaput JC, Schultz PG. Bacterial Genome Containing Chimeric DNA–RNA Sequences. J Am Chem Soc 2018; 140:11464-11473. [DOI: 10.1021/jacs.8b07046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Angad P. Mehta
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yiyang Wang
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sean A. Reed
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lubica Supekova
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tsotne Javahishvili
- Bay Area Innovation Center, Corteva Agriscience, 4010 Point Eden Way, Hayward, California 94545, United States
| | | | - Peter G. Schultz
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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18
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Li D, Bheemanaboina RRY, Battini N, Tangadanchu VKR, Fang XF, Zhou CH. Novel organophosphorus aminopyrimidines as unique structural DNA-targeting membrane active inhibitors towards drug-resistant methicillin-resistant Staphylococcus aureus. MEDCHEMCOMM 2018; 9:1529-1537. [PMID: 30288226 DOI: 10.1039/c8md00301g] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 07/29/2018] [Indexed: 12/18/2022]
Abstract
A series of novel unique structural organophosphorus aminopyrimidines were developed as potential DNA-targeting membrane active inhibitors through an efficient one-pot procedure from aldehydes, phosphonate and aminopyrimidine. The biological assay revealed that some of the prepared compounds displayed antibacterial activities. In particular, imidazole derivative 2c exhibited more potent inhibitory activity against MRSA with an MIC value of 4 μg mL-1 in comparison with the clinical drugs chloromycin and norfloxacin. Experiments revealed that the active molecule 2c had the ability to rapidly kill the tested strains without obviously triggering the development of bacterial resistance, showed low toxicity to L929 cells and could disturb the cell membrane. The molecular docking study discovered that compound 2c could bind with DNA gyrase via hydrogen bonds and other weak interactions. Further exploration disclosed that the active molecule 2c could also effectively intercalate into MRSA DNA and form a steady 2c-DNA supramolecular complex, which might further block DNA replication to exert powerful antibacterial effects.
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Affiliation(s)
- Di Li
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
| | - Rammohan R Yadav Bheemanaboina
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
| | - Narsaiah Battini
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
| | - Vijai Kumar Reddy Tangadanchu
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
| | - Xian-Fu Fang
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
| | - Cheng-He Zhou
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
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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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20
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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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