1
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Gerecht K, Freund N, Liu W, Liu Y, Fürst MJLJ, Holliger P. The Expanded Central Dogma: Genome Resynthesis, Orthogonal Biosystems, Synthetic Genetics. Annu Rev Biophys 2023; 52:413-432. [PMID: 37159296 DOI: 10.1146/annurev-biophys-111622-091203] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Synthetic biology seeks to probe fundamental aspects of biological form and function by construction [i.e., (re)synthesis] rather than deconstruction (analysis). In this sense, biological sciences now follow the lead given by the chemical sciences. Synthesis can complement analytic studies but also allows novel approaches to answering fundamental biological questions and opens up vast opportunities for the exploitation of biological processes to provide solutions for global problems. In this review, we explore aspects of this synthesis paradigm as applied to the chemistry and function of nucleic acids in biological systems and beyond, specifically, in genome resynthesis, synthetic genetics (i.e., the expansion of the genetic alphabet, of the genetic code, and of the chemical make-up of genetic systems), and the elaboration of orthogonal biosystems and components.
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Affiliation(s)
- Karola Gerecht
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Niklas Freund
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Wei Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Yang Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Maximilian J L J Fürst
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
- Current address: Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
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2
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Pinna S, Kunz C, Halpern A, Harrison SA, Jordan SF, Ward J, Werner F, Lane N. A prebiotic basis for ATP as the universal energy currency. PLoS Biol 2022; 20:e3001437. [PMID: 36194581 PMCID: PMC9531788 DOI: 10.1371/journal.pbio.3001437] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 08/30/2022] [Indexed: 11/07/2022] Open
Abstract
ATP is universally conserved as the principal energy currency in cells, driving metabolism through phosphorylation and condensation reactions. Such deep conservation suggests that ATP arose at an early stage of biochemical evolution. Yet purine synthesis requires 6 phosphorylation steps linked to ATP hydrolysis. This autocatalytic requirement for ATP to synthesize ATP implies the need for an earlier prebiotic ATP equivalent, which could drive protometabolism before purine synthesis. Why this early phosphorylating agent was replaced, and specifically with ATP rather than other nucleoside triphosphates, remains a mystery. Here, we show that the deep conservation of ATP might reflect its prebiotic chemistry in relation to another universally conserved intermediate, acetyl phosphate (AcP), which bridges between thioester and phosphate metabolism by linking acetyl CoA to the substrate-level phosphorylation of ADP. We confirm earlier results showing that AcP can phosphorylate ADP to ATP at nearly 20% yield in water in the presence of Fe3+ ions. We then show that Fe3+ and AcP are surprisingly favoured. A wide range of prebiotically relevant ions and minerals failed to catalyse ADP phosphorylation. From a panel of prebiotic phosphorylating agents, only AcP, and to a lesser extent carbamoyl phosphate, showed any significant phosphorylating potential. Critically, AcP did not phosphorylate any other nucleoside diphosphate. We use these data, reaction kinetics, and molecular dynamic simulations to infer a possible mechanism. Our findings might suggest that the reason ATP is universally conserved across life is that its formation is chemically favoured in aqueous solution under mild prebiotic conditions.
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Affiliation(s)
- Silvana Pinna
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
| | - Cäcilia Kunz
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
| | - Aaron Halpern
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
| | - Stuart A. Harrison
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
| | - Sean F. Jordan
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
| | - John Ward
- Department of Biochemical Engineering, University College London, London, United Kingdom
| | - Finn Werner
- Institute for Structural and Molecular Biology, University College London, Darwin Building, London, United Kingdom
| | - Nick Lane
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
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3
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Copper complex of a thienyl-hydrazone rhodamine derivative is a highly selective colorimetric sensor for pyrophosphate. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2021.153606] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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4
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Calabrese C, Uriarte I, Insausti A, Vallejo-López M, Basterretxea FJ, Cochrane SA, Davis BG, Corzana F, Cocinero EJ. Observation of the Unbiased Conformers of Putative DNA-Scaffold Ribosugars. ACS CENTRAL SCIENCE 2020; 6:293-303. [PMID: 32123748 PMCID: PMC7047431 DOI: 10.1021/acscentsci.9b01277] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Indexed: 06/10/2023]
Abstract
The constitution, configuration, and flexibility of the core sugars of DNA molecules alter their function in diverse roles. Conformational itineraries of the ribofuranosides (fs) have long been known to finely determine rates of processing, yet we also know that, strikingly, semifunctional DNAs containing pyranosides (ps) or other configurations can be created, suggesting sufficient but incompletely understood plasticity. The multiple conformers involved in such processes are necessarily influenced by context and environment: solvent, hosts, ligands. Notably, however, to date the unbiased, "naked" conformers have not been experimentally determined. Here, the inherent conformational biases of DNA scaffold deoxyribosides in unsolvated and solvated forms have now been defined using gas-phase microwave and solution-phase NMR spectroscopies coupled with computational analyses and exploitation of critical differences between natural-abundance isotopologues. Serial determination of precise, individual spectra for conformers of these 25 isotopologues in alpha (α-d) and beta (β-d); pyrano (p) and furano (f) methyl 2-deoxy-d-ribosides gave not only unprecedented atomic-level resolution structures of associated conformers but also their quantitative populations. Together these experiments revealed that typical 2E and 3E conformations of the sugar found in complex DNA structures are not inherently populated. Moreover, while both OH-5' and OH-3' are constrained by intramolecular hydrogen bonding in the unnatural αf scaffold, OH-3' is "born free" in the "naked" lowest lying energy conformer of natural βf. Consequently, upon solvation, unnatural αf is strikingly less perturbable (retaining 2T1 conformation in vacuo and water) than natural βf. Unnatural αp and βp ribosides also display low conformational perturbability. These first experimental data on inherent, unbiased conformers therefore suggest that it is the background of conformational flexibility of βf that may have led to its emergence out of multiple possibilities as the sugar scaffold for "life's code" and suggest a mechanism by which the resulting freedom of OH-3' (and hence accessibility as a nucleophile) in βf may drive preferential processing and complex structure formation, such as replicative propagation of DNA from 5'-to-3'.
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Affiliation(s)
- Camilla Calabrese
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
- Instituto
Biofisika (CSIC, UPV/EHU), 48080 Bilbao, Spain
| | - Iciar Uriarte
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
- Instituto
Biofisika (CSIC, UPV/EHU), 48080 Bilbao, Spain
| | - Aran Insausti
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
- Instituto
Biofisika (CSIC, UPV/EHU), 48080 Bilbao, Spain
| | - Montserrat Vallejo-López
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
| | - Francisco J. Basterretxea
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
| | - Stephen A. Cochrane
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Benjamin G. Davis
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom
- The
Rosalind Franklin Institute, Oxfordshire, OX11 0FA, United Kingdom
| | - Francisco Corzana
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La
Rioja, 26006 Logroño, Spain
| | - Emilio J. Cocinero
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
- Instituto
Biofisika (CSIC, UPV/EHU), 48080 Bilbao, Spain
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5
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Bauwens B, Rozenski J, Herdewijn P, Robben J. A Single Amino Acid Substitution in Therminator DNA Polymerase Increases Incorporation Efficiency of Deoxyxylonucleotides. Chembiochem 2018; 19:2410-2420. [PMID: 30204290 DOI: 10.1002/cbic.201800411] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Indexed: 11/11/2022]
Abstract
Deoxyxylonucleic acid (dxNA) is a synthetic polymer that might have potential for heredity and evolution. Because of dxNA's unusual backbone geometry, sequence information stored in it is presumed to be inaccessible to natural nucleic acids or proteins. Despite a large structural similarity with natural nucleotides, incorporation of 2'-deoxyxylonucleotides (dxNTs) through the action of polymerases is limited. We present the identification of a mutant of the DNA polymerase Therminator with increased tolerance to deoxyxylose-induced backbone distortions. Whereas the original polymerase stops after incorporation of two consecutive dxNTs, the mutant is able to catalyse the extension of incorporated dxNTs with 2'-deoxyribonucleotides (dNTs) and the incorporation of up to four dxNTs alternates with dNTs, thereby translocating a highly distorted double helix throughout the entire polymerase. A single His-to-Arg substitution very close to the catalytic site residues is held to be responsible for interaction with the primer phosphate groups and for stabilizing nucleotide sugar-induced distortions during incorporation and translocation.
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Affiliation(s)
- Boris Bauwens
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001, Heverlee, Belgium
| | - Jef Rozenski
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1030, 3000, Leuven, Belgium
| | - Piet Herdewijn
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1030, 3000, Leuven, Belgium
| | - Johan Robben
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001, Heverlee, Belgium
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6
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Depaix A, Peyrottes S, Roy B. One-Pot Synthesis of Nucleotides and Conjugates in Aqueous Medium. European J Org Chem 2016. [DOI: 10.1002/ejoc.201601299] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anaïs Depaix
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; ENSCM, Université de Montpellier; Campus Triolet, cc 1705, Place Eugène Bataillon 34095 Montpellier cedex 5 France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; ENSCM, Université de Montpellier; Campus Triolet, cc 1705, Place Eugène Bataillon 34095 Montpellier cedex 5 France
| | - Béatrice Roy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; ENSCM, Université de Montpellier; Campus Triolet, cc 1705, Place Eugène Bataillon 34095 Montpellier cedex 5 France
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7
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Torres L, Krüger A, Csibra E, Gianni E, Pinheiro VB. Synthetic biology approaches to biological containment: pre-emptively tackling potential risks. Essays Biochem 2016; 60:393-410. [PMID: 27903826 PMCID: PMC5264511 DOI: 10.1042/ebc20160013] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/29/2022]
Abstract
Biocontainment comprises any strategy applied to ensure that harmful organisms are confined to controlled laboratory conditions and not allowed to escape into the environment. Genetically engineered microorganisms (GEMs), regardless of the nature of the modification and how it was established, have potential human or ecological impact if accidentally leaked or voluntarily released into a natural setting. Although all evidence to date is that GEMs are unable to compete in the environment, the power of synthetic biology to rewrite life requires a pre-emptive strategy to tackle possible unknown risks. Physical containment barriers have proven effective but a number of strategies have been developed to further strengthen biocontainment. Research on complex genetic circuits, lethal genes, alternative nucleic acids, genome recoding and synthetic auxotrophies aim to design more effective routes towards biocontainment. Here, we describe recent advances in synthetic biology that contribute to the ongoing efforts to develop new and improved genetic, semantic, metabolic and mechanistic plans for the containment of GEMs.
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Affiliation(s)
- Leticia Torres
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K.
| | - Antje Krüger
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Eszter Csibra
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Edoardo Gianni
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Vitor B Pinheiro
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K.
- Birkbeck, Department of Biological Sciences, University of London, Malet Street, WC1E 7HX, U.K
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8
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Kervio E, Sosson M, Richert C. The effect of leaving groups on binding and reactivity in enzyme-free copying of DNA and RNA. Nucleic Acids Res 2016; 44:5504-14. [PMID: 27235418 PMCID: PMC4937335 DOI: 10.1093/nar/gkw476] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 05/06/2016] [Accepted: 05/09/2016] [Indexed: 01/29/2023] Open
Abstract
The template-directed incorporation of nucleotides at the terminus of a growing primer is the basis of the transmission of genetic information. Nature uses polymerases-catalyzed reactions, but enzyme-free versions exist that employ nucleotides with organic leaving groups. The leaving group affects yields, but it was not clear whether inefficient extensions are due to poor binding, low reactivity toward the primer, or rapid hydrolysis. We have measured the binding of a total of 15 different activated nucleotides to DNA or RNA sequences. Further, we determined rate constants for the chemical step of primer extension involving methylimidazolides or oxyazabenzotriazolides of deoxynucleotides or ribonucleotides. Binding constants range from 10 to >500 mM and rate constants from 0.1 to 370 M(-1) h(-1) For aminoterminal primers, a fast covalent step and slow hydrolysis are the main factors leading to high yields. For monomers with weakly pairing bases, the leaving group can improve binding significantly. A detailed mechanistic picture emerges that explains why some enzyme-free primer extensions occur in high yield, while others remain recalcitrant to copying without enzymatic catalysis. A combination of tight binding and rapid extension, coupled with slow hydrolysis induces efficient enzyme-free copying.
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Affiliation(s)
- Eric Kervio
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Marilyne Sosson
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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9
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De S, Groaz E, Margamuljana L, Herdewijn P. Syntheses of 5'-Nucleoside Monophosphate Derivatives with Unique Aminal, Hemiaminal, and Hemithioaminal Functionalities: A New Class of 5'-Peptidyl Nucleotides. Chemistry 2016; 22:8167-80. [PMID: 27136602 DOI: 10.1002/chem.201600721] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Indexed: 11/07/2022]
Abstract
A number of synthetically useful transformations have been developed to generate novel 5'-peptidyl nucleoside monophosphate analogues that incorporate sensitive phosphoaminal, -hemiaminal or -hemithioaminal functionalities. The strategies adopted entailed the coupling between dipeptides, which enclose a reactive Cα-functionalized glycine residue and phosphate or phosphorothioate moieties. These developments led to potentially powerful and general methodologies for the preparation of α-phosphorylated pseudopeptides as well as nucleoside monophosphate mimics. The resulting conjugates are of interest for a variety of important applications, which range from drug development to synthetic biology, as pronucleotides or artificial building blocks for the enzymatic synthesis of xenobiotic information systems. The potential of all dipeptide-TMP conjugates as pyrophosphate mimics in the DNA polymerization reaction was tested, and the influence of the nature of the linker was evaluated by in vitro chain elongation assay in the presence of wild-type microbial DNA polymerases.
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Affiliation(s)
- Swarup De
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Elisabetta Groaz
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Lia Margamuljana
- 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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10
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Zlatev I, Foster DJ, Liu J, Charisse K, Brigham B, Parmar RG, Jadhav V, Maier MA, Rajeev KG, Egli M, Manoharan M. 5'-C-Malonyl RNA: Small Interfering RNAs Modified with 5'-Monophosphate Bioisostere Demonstrate Gene Silencing Activity. ACS Chem Biol 2016; 11:953-60. [PMID: 26675211 DOI: 10.1021/acschembio.5b00654] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
5'-Phosphorylation is a critical step in the cascade of events that leads to loading of small interfering RNAs (siRNAs) into the RNA-induced silencing complex (RISC) to elicit gene silencing. 5'-Phosphorylation of exogenous siRNAs is generally accomplished by a cytosolic Clp1 kinase, and in most cases, the presence of a 5'-monophosphate on synthetic siRNAs is not a prerequisite for activity. Chemically introduced, metabolically stable 5'-phosphate mimics can lead to higher metabolic stability, increased RISC loading, and higher gene silencing activities of chemically modified siRNAs. In this study, we report the synthesis of 5'-C-malonyl RNA, a 5'-monophosphate bioisostere. A 5'-C-malonyl-modified nucleotide was incorporated at the 5'-terminus of chemically modified RNA oligonucleotides using solid-phase synthesis. In vitro silencing activity, in vitro metabolic stability, and in vitro RISC loading of 5'-C-malonyl siRNA was compared to corresponding 5'-phosphorylated and 5'-nonphosphorylated siRNAs. The 5'-C-malonyl siRNAs showed sustained or improved in vitro gene silencing and high levels of Ago2 loading and conferred dramatically improved metabolic stability to the antisense strand of the siRNA duplexes. In silico modeling studies indicate a favorable fit of the 5'-C-malonyl group within the 5'-phosphate binding pocket of human Ago2MID domain.
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Affiliation(s)
- Ivan Zlatev
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Donald J. Foster
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Jingxuan Liu
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Klaus Charisse
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Benjamin Brigham
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Rubina G. Parmar
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Vasant Jadhav
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Martin A. Maier
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | | | - Martin Egli
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
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11
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De S, Groaz E, Margamuljana L, Abramov M, Marlière P, Herdewijn P. Sulfonate derived phosphoramidates as active intermediates in the enzymatic primer-extension of DNA. Org Biomol Chem 2015; 13:3950-62. [PMID: 25719514 DOI: 10.1039/c5ob00157a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel unnatural 5'-phosphoramidate nucleosides, capable of being processed as substrates by DNA polymerases for multiple nucleotide incorporations, have been designed. The mimics feature metabolites such as taurine and a broad range of aliphatic sulfonates coupled through a P-N bond to the 5'-phosphate position of deoxynucleotides, to allow binding interactions in the enzyme active site. The utility of all of the analogues as pyrophosphate mimics was demonstrated for the chain elongation of DNA, using both thermophilic and mesophilic microbial polymerases.
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Affiliation(s)
- S De
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
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12
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Hwang C, Kashemirov BA, McKenna CE. On the observation of discrete fluorine NMR spectra for uridine 5'-β,γ-fluoromethylenetriphosphate diastereomers at basic pH. J Org Chem 2014; 79:5315-9. [PMID: 24819695 PMCID: PMC4059216 DOI: 10.1021/jo500452b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Indexed: 11/28/2022]
Abstract
Jakeman et al. recently reported the inability to distinguish the diastereomers of uridine 5'-β,γ-fluoromethylenetriphosphate (β,γ-CHF-UTP, 1) by (19)F NMR under conditions we previously prescribed for the resolution of the corresponding β,γ-CHF-dGTP spectra, stating further that 1 decomposed under these basic conditions. Here we show that the (19)F NMR spectra of 1 (~1:1 diastereomer mixture prepared by coupling of UMP-morpholidate with fluoromethylenebis(phosphonic acid)) in D2O at pH 10 are indeed readily distinguishable. 1 in this solution was stable for 24 h at rt.
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Affiliation(s)
- Candy
S. Hwang
- Department of Chemistry, University of
Southern California, Los Angeles, California 90089, United States
| | - Boris A. Kashemirov
- Department of Chemistry, University of
Southern California, Los Angeles, California 90089, United States
| | - Charles E. McKenna
- Department of Chemistry, University of
Southern California, Los Angeles, California 90089, United States
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13
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Sun Q, Gong S, Sun J, Wang C, Liu S, Liu G, Ma C. Efficient synthesis of nucleoside 5′-triphosphates and their β,γ-bridging oxygen-modified analogs from nucleoside 5′-phosphates. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.02.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Kimoto M, Hikida Y, Hirao I. Site-Specific Functional Labeling of Nucleic Acids by In Vitro Replication and Transcription using Unnatural Base Pair Systems. Isr J Chem 2013. [DOI: 10.1002/ijch.201300013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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15
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Abstract
For over 20 years, laboratories around the world have been applying the principles of Darwinian evolution to isolate DNA and RNA molecules with specific ligand-binding or catalytic activities. This area of synthetic biology, commonly referred to as in vitro genetics, is made possible by the availability of natural polymerases that can replicate genetic information in the laboratory. Moving beyond natural nucleic acids requires organic chemistry to synthesize unnatural analogues and polymerase engineering to create enzymes that recognize artificial substrates. Progress in both of these areas has led to the emerging field of synthetic genetics, which explores the structural and functional properties of synthetic genetic polymers by in vitro evolution. This review examines recent advances in the Darwinian evolution of artificial genetic polymers and their potential downstream applications in exobiology, molecular medicine, and synthetic biology.
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Affiliation(s)
- John C Chaput
- Center for Evolutionary Medicine and Informatics in the Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-5301, USA.
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16
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Hollenstein M. Nucleoside triphosphates--building blocks for the modification of nucleic acids. Molecules 2012; 17:13569-91. [PMID: 23154273 PMCID: PMC6268876 DOI: 10.3390/molecules171113569] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 11/07/2012] [Accepted: 11/09/2012] [Indexed: 11/16/2022] Open
Abstract
Nucleoside triphosphates are moldable entities that can easily be functionalized at various locations. The enzymatic polymerization of these modified triphosphate analogues represents a versatile platform for the facile and mild generation of (highly) functionalized nucleic acids. Numerous modified triphosphates have been utilized in a broad palette of applications spanning from DNA-tagging and -labeling to the generation of catalytic nucleic acids. This review will focus on the recent progress made in the synthesis of modified nucleoside triphosphates as well as on the understanding of the mechanisms underlying their polymerase acceptance. In addition, the usefulness of chemically altered dNTPs in SELEX and related methods of in vitro selection will be highlighted, with a particular emphasis on the generation of modified DNA enzymes (DNAzymes) and DNA-based aptamers.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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Giraut A, Abu El-Asrar R, Marlière P, Delarue M, Herdewijn P. 2'-Deoxyribonucleoside phosphoramidate triphosphate analogues as alternative substrates for E. coli polymerase III. Chembiochem 2012; 13:2439-44. [PMID: 23023962 DOI: 10.1002/cbic.201200413] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Indexed: 01/27/2023]
Abstract
Thermostable bacterial polymerases like Taq, Therminator and Vent exo(-) are able to perform DNA synthesis by using modified DNA precursors, a property that is exploited in several therapeutic and biotechnological applications. Viral polymerases are also known to accept modified substrates, and this has proven crucial in the development of antiviral therapies. However, non-thermostable polymerases of bacterial origin, or engineered variants, that have similar substrate tolerance and could be used for synthetic biology purposes remain to be identified. We have identified the α subunit of Escherichia coli polymerase III (Pol III α) as a bacterial polymerase that is able to recognise and process as substrates several pyrophosphate-modified dATP analogues in place of its natural substrate dATP for template-directed DNA synthesis. A number of dATP analogues featuring a modified pyrophosphate group were able to serve as substrates during enzymatic DNA synthesis by Pol III α. Features such as the presence of potentially chelating chemical groups and the size and spatial flexibility of the chemical structure seem to be of major importance for the modified leaving group to play its role during the enzymatic reaction. In addition, we could establish that if the pyrophosphate group is altered, deoxynucleotide incorporation proceeds with an efficiency varying with the nature of the nucleobase. Our results represent a great step towards the achievement of a system of artificial DNA synthesis hosted by E. coli and involving the use of altered nucleotide precursors for nucleic acid synthesis.
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Affiliation(s)
- Anne Giraut
- Katholieke Universiteit Leuven, Rega Institute, Laboratory for Medicinal Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium
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