1
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Mittal S, Nisler C, Szostak JW. Simulations predict preferred Mg 2+ coordination in a nonenzymatic primer-extension reaction center. Biophys J 2024; 123:1579-1591. [PMID: 38702884 PMCID: PMC11214020 DOI: 10.1016/j.bpj.2024.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
The mechanism by which genetic information was copied prior to the evolution of ribozymes is of great interest because of its importance to the origin of life. The most effective known process for the nonenzymatic copying of an RNA template is primer extension by a two-step pathway in which 2-aminoimidazole-activated nucleotides first react with each other to form an imidazolium-bridged intermediate that subsequently reacts with the primer. Reaction kinetics, structure-activity relationships, and X-ray crystallography have provided insight into the overall reaction mechanism, but many puzzles remain. In particular, high concentrations of Mg2+ are required for efficient primer extension, but the mechanism by which Mg2+ accelerates primer extension remains unknown. By analogy with the mechanism of DNA and RNA polymerases, a role for Mg2+ in facilitating the deprotonation of the primer 3'-hydroxyl is often assumed, but no catalytic metal ion is seen in crystal structures of the primer-extension complex. To explore the potential effects of Mg2+ binding in the reaction center, we performed atomistic molecular dynamics simulations of a series of modeled complexes in which a Mg2+ ion was placed in the reaction center with inner-sphere coordination with different sets of functional groups. Our simulations suggest that coordination of a Mg2+ ion with both O3' of the terminal primer nucleotide and the pro-Sp nonbridging oxygen of the reactive phosphate of an imidazolium-bridged dinucleotide would help to pre-organize the structure of the primer/template substrate complex to favor the primer-extension reaction. Our results suggest that the catalytic metal ion may play an important role in overcoming electrostatic repulsion between a deprotonated O3' and the reactive phosphate of the bridged dinucleotide and lead to testable predictions of the mode of Mg2+ binding that is most relevant to catalysis of primer extension.
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Affiliation(s)
- Shriyaa Mittal
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts; Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Collin Nisler
- Howard Hughes Medical Institute, Department of Chemistry, University of Chicago, Chicago, Illinois
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts; Department of Genetics, Harvard Medical School, Boston, Massachusetts; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts; Howard Hughes Medical Institute, Department of Chemistry, University of Chicago, Chicago, Illinois.
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2
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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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3
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Ding D, Zhou L, Giurgiu C, Szostak JW. Kinetic explanations for the sequence biases observed in the nonenzymatic copying of RNA templates. Nucleic Acids Res 2021; 50:35-45. [PMID: 34893864 PMCID: PMC8754633 DOI: 10.1093/nar/gkab1202] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/17/2021] [Accepted: 12/08/2021] [Indexed: 11/15/2022] Open
Abstract
The identification of nonenzymatic pathways for nucleic acid replication is a key challenge in understanding the origin of life. We have previously shown that nonenzymatic RNA primer extension using 2-aminoimidazole (2AI) activated nucleotides occurs primarily through an imidazolium-bridged dinucleotide intermediate. The reactive nature and preorganized structure of the intermediate increase the efficiency of primer extension but remain insufficient to drive extensive copying of RNA templates containing all four canonical nucleotides. To understand the factors that limit RNA copying, we synthesized all ten 2AI-bridged dinucleotide intermediates and measured the kinetics of primer extension in a model system. The affinities of the ten dinucleotides for the primer/template/helper complexes vary by over 7,000-fold, consistent with nearest neighbor energetic predictions. Surprisingly, the reaction rates at saturating intermediate concentrations still vary by over 15-fold, with the most weakly binding dinucleotides exhibiting a lower maximal reaction rate. Certain noncanonical nucleotides can decrease sequence dependent differences in affinity and primer extension rate, while monomers bridged to short oligonucleotides exhibit enhanced binding and reaction rates. We suggest that more uniform binding and reactivity of imidazolium-bridged intermediates may lead to the ability to copy arbitrary template sequences under prebiotically plausible conditions.
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Affiliation(s)
- Dian Ding
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA.,Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Constantin Giurgiu
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.,Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
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4
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Giurgiu C, Fang Z, Aitken HRM, Kim SC, Pazienza L, Mittal S, Szostak JW. Structure–Activity Relationships in Nonenzymatic Template‐Directed RNA Synthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Constantin Giurgiu
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Ziyuan Fang
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
| | - Harry R. M. Aitken
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
| | - Seohyun Chris Kim
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
| | - Lydia Pazienza
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Shriyaa Mittal
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Jack W. Szostak
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
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5
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Giurgiu C, Fang Z, Aitken HRM, Kim SC, Pazienza L, Mittal S, Szostak JW. Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis. Angew Chem Int Ed Engl 2021; 60:22925-22932. [PMID: 34428345 PMCID: PMC8490286 DOI: 10.1002/anie.202109714] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Indexed: 11/11/2022]
Abstract
The template-directed synthesis of RNA played an important role in the transition from prebiotic chemistry to the beginnings of RNA based life, but the mechanism of RNA copying chemistry is incompletely understood. We measured the kinetics of template copying with a set of primers with modified 3'-nucleotides and determined the crystal structures of these modified nucleotides in the context of a primer/template/substrate-analog complex. pH-rate profiles and solvent isotope effects show that deprotonation of the primer 3'-hydroxyl occurs prior to the rate limiting step, the attack of the alkoxide on the activated phosphate of the incoming nucleotide. The analogs with a 3 E ribose conformation show the fastest formation of 3'-5' phosphodiester bonds. Among those derivatives, the reaction rate is strongly correlated with the electronegativity of the 2'-substituent. We interpret our results in terms of differences in steric bulk and charge distribution in the ground vs. transition states.
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Affiliation(s)
- Constantin Giurgiu
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Ziyuan Fang
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Harry R M Aitken
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Seohyun Chris Kim
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lydia Pazienza
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Shriyaa Mittal
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
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6
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Kim SC, O'Flaherty DK, Giurgiu C, Zhou L, Szostak JW. The Emergence of RNA from the Heterogeneous Products of Prebiotic Nucleotide Synthesis. J Am Chem Soc 2021; 143:3267-3279. [PMID: 33636080 DOI: 10.1021/jacs.0c12955] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances in prebiotic chemistry are beginning to outline plausible pathways for the synthesis of the canonical ribonucleotides and their assembly into oligoribonucleotides. However, these reaction pathways suggest that many noncanonical nucleotides are likely to have been generated alongside the standard ribonucleotides. Thus, the oligomerization of prebiotically synthesized nucleotides is likely to have led to a highly heterogeneous collection of oligonucleotides comprised of a wide range of types of nucleotides connected by a variety of backbone linkages. How then did relatively homogeneous RNA emerge from this primordial heterogeneity? Here we focus on nonenzymatic template-directed primer extension as a process that would have strongly enriched for homogeneous RNA over the course of multiple cycles of replication. We review the effects on copying the kinetics of nucleotides with altered nucleobase and sugar moieties, when they are present as activated monomers and when they are incorporated into primer and template oligonucleotides. We also discuss three variations in backbone connectivity, all of which are nonheritable and regenerate native RNA upon being copied. The kinetic superiority of RNA synthesis suggests that nonenzymatic copying served as a chemical selection mechanism that allowed relatively homogeneous RNA to emerge from a complex mixture of prebiotically synthesized nucleotides and oligonucleotides.
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Affiliation(s)
- Seohyun Chris Kim
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Derek K O'Flaherty
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Constantin Giurgiu
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
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7
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Walton T, DasGupta S, Duzdevich D, Oh SS, Szostak JW. In vitro selection of ribozyme ligases that use prebiotically plausible 2-aminoimidazole-activated substrates. Proc Natl Acad Sci U S A 2020; 117:5741-5748. [PMID: 32123094 PMCID: PMC7084097 DOI: 10.1073/pnas.1914367117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The hypothesized central role of RNA in the origin of life suggests that RNA propagation predated the advent of complex protein enzymes. A critical step of RNA replication is the template-directed synthesis of a complementary strand. Two experimental approaches have been extensively explored in the pursuit of demonstrating protein-free RNA synthesis: template-directed nonenzymatic RNA polymerization using intrinsically reactive monomers and ribozyme-catalyzed polymerization using more stable substrates such as biological 5'-triphosphates. Despite significant progress in both approaches in recent years, the assembly and copying of functional RNA sequences under prebiotic conditions remains a challenge. Here, we explore an alternative approach to RNA-templated RNA copying that combines ribozyme catalysis with RNA substrates activated with a prebiotically plausible leaving group, 2-aminoimidazole (2AI). We applied in vitro selection to identify ligase ribozymes that catalyze phosphodiester bond formation between a template-bound primer and a phosphor-imidazolide-activated oligomer. Sequencing revealed the progressive enrichment of 10 abundant sequences from a random sequence pool. Ligase activity was detected in all 10 RNA sequences; all required activation of the ligator with 2AI and generated a 3'-5' phosphodiester bond. We propose that ribozyme catalysis of phosphodiester bond formation using intrinsically reactive RNA substrates, such as imidazolides, could have been an evolutionary step connecting purely nonenzymatic to ribozyme-catalyzed RNA template copying during the origin of life.
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Affiliation(s)
- Travis Walton
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Saurja DasGupta
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Daniel Duzdevich
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology, 37673 Pohang, Gyeongbuk, South Korea
| | - Jack W Szostak
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114;
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
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8
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Kim SC, Zhou L, Zhang W, O'Flaherty DK, Rondo-Brovetto V, Szostak JW. A Model for the Emergence of RNA from a Prebiotically Plausible Mixture of Ribonucleotides, Arabinonucleotides, and 2'-Deoxynucleotides. J Am Chem Soc 2020; 142:2317-2326. [PMID: 31913615 PMCID: PMC7577264 DOI: 10.1021/jacs.9b11239] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
The abiotic synthesis of ribonucleotides
is thought to have been
an essential step toward the emergence of the RNA world. However,
it is likely that the prebiotic synthesis of ribonucleotides was accompanied
by the simultaneous synthesis of arabinonucleotides, 2′-deoxyribonucleotides,
and other variations on the canonical nucleotides. In order to understand
how relatively homogeneous RNA could have emerged from such complex
mixtures, we have examined the properties of arabinonucleotides and
2′-deoxyribonucleotides in nonenzymatic template-directed primer
extension reactions. We show that nonenzymatic primer extension with
activated arabinonucleotides is much less efficient than with activated
ribonucleotides, and furthermore that once an arabinonucleotide is
incorporated, continued primer extension is strongly inhibited. As
previously shown, 2′-deoxyribonucleotides are also less efficiently
incorporated in primer extension reactions, but the difference is
more modest. Experiments with mixtures of nucleotides suggest that
the coexistence of ribo- and arabinonucleotides does not impede the
copying of RNA templates. Moreover, chimeric oligoribonucleotides
containing 2′-deoxy- or arabinonucleotides are effective templates
for RNA synthesis. We propose that the initial genetic polymers were
random sequence chimeric oligonucleotides formed by untemplated polymerization,
but that template copying chemistry favored RNA synthesis; multiple
rounds of replication may have led to pools of oligomers composed
mainly of RNA.
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Affiliation(s)
- Seohyun Chris Kim
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Wen Zhang
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Derek K O'Flaherty
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Valeria Rondo-Brovetto
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
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9
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Abstract
The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an 'RNA world', notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pK a values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.
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10
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Tupper AS, Shi K, Higgs PG. The Role of Templating in the Emergence of RNA from the Prebiotic Chemical Mixture. Life (Basel) 2017; 7:life7040041. [PMID: 29088116 PMCID: PMC5745554 DOI: 10.3390/life7040041] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/25/2017] [Accepted: 10/26/2017] [Indexed: 01/11/2023] Open
Abstract
Biological RNA is a uniform polymer in three senses: it uses nucleotides of a single chirality; it uses only ribose sugars and four nucleobases rather than a mixture of other sugars and bases; and it uses only 3'-5' bonds rather than a mixture of different bond types. We suppose that prebiotic chemistry would generate a diverse mixture of potential monomers, and that random polymerization would generate non-uniform strands of mixed chirality, monomer composition, and bond type. We ask what factors lead to the emergence of RNA from this mixture. We show that template-directed replication can lead to the emergence of all the uniform properties of RNA by the same mechanism. We study a computational model in which nucleotides react via polymerization, hydrolysis, and template-directed ligation. Uniform strands act as templates for ligation of shorter oligomers of the same type, whereas mixed strands do not act as templates. The three uniform properties emerge naturally when the ligation rate is high. If there is an exact symmetry, as with the chase of chirality, the uniform property arises via a symmetry-breaking phase transition. If there is no exact symmetry, as with monomer selection and backbone regioselectivity, the uniform property emerges gradually as the rate of template-directed ligation is increased.
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Affiliation(s)
- Andrew S Tupper
- Origins Institute and Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, ON L8S 4L8, Canada.
| | - Kevin Shi
- Origins Institute and Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Paul G Higgs
- Origins Institute and Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4K1, Canada.
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11
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Izgu EC, Oh SS, Szostak JW. Synthesis of activated 3'-amino-3'-deoxy-2-thio-thymidine, a superior substrate for the nonenzymatic copying of nucleic acid templates. Chem Commun (Camb) 2016; 52:3684-6. [PMID: 26857159 DOI: 10.1039/c5cc10317g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a scalable synthesis of 3'-amino-3'-deoxy-2-thio-thymidine-5'-phosphoro-2-methylimidazolide, an activated monomer that can copy adenosine residues in nucleic acid templates rapidly without a polymerase. The sulfur atom substitution enhances the rate of template copying by 5-fold compared with the 3'-amino-3'-deoxy-T monomer, while the 3'-amino monomers exhibit a 2- to 30-fold enhancement compared with their ribonucleotide counterparts.
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Affiliation(s)
- Enver Cagri Izgu
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA. and Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Seung Soo Oh
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA. and Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA. and Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA and Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138, USA
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12
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Maiti M, Maiti M, Knies C, Dumbre S, Lescrinier E, Rosemeyer H, Ceulemans A, Herdewijn P. Xylonucleic acid: synthesis, structure, and orthogonal pairing properties. Nucleic Acids Res 2015; 43:7189-200. [PMID: 26175047 PMCID: PMC4551940 DOI: 10.1093/nar/gkv719] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 06/29/2015] [Accepted: 07/01/2015] [Indexed: 11/22/2022] Open
Abstract
There is a common interest for studying xeno-nucleic acid systems in the fields of synthetic biology and the origin of life, in particular, those with an engineered backbone and possessing novel properties. Along this line, we have investigated xylonucleic acid (XyloNA) containing a potentially prebiotic xylose sugar (a 3'-epimer of ribose) in its backbone. Herein, we report for the first time the synthesis of four XyloNA nucleotide building blocks and the assembly of XyloNA oligonucleotides containing all the natural nucleobases. A detailed investigation of pairing and structural properties of XyloNAs in comparison to DNA/RNA has been performed by thermal UV-melting, CD, and solution state NMR spectroscopic studies. XyloNA has been shown to be an orthogonal self-pairing system which adopts a slightly right-handed extended helical geometry. Our study on one hand, provides understanding for superior structure-function (-pairing) properties of DNA/RNA over XyloNA for selection as an informational polymer in the prebiotic context, while on the other hand, finds potential of XyloNA as an orthogonal genetic system for application in synthetic biology.
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Affiliation(s)
- Mohitosh Maiti
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Munmun Maiti
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Christine Knies
- Organic Materials Chemistry and Bioorganic Chemistry, Institute of Chemistry of New Materials, University of Osnabrück, Barbarastrasse. 7, D-49069 Osnabrück, Germany
| | - Shrinivas Dumbre
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Eveline Lescrinier
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Helmut Rosemeyer
- Organic Materials Chemistry and Bioorganic Chemistry, Institute of Chemistry of New Materials, University of Osnabrück, Barbarastrasse. 7, D-49069 Osnabrück, Germany
| | - Arnout Ceulemans
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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13
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Cleaves HJ, Meringer M, Goodwin J. 227 Views of RNA: Is RNA Unique in Its Chemical Isomer Space? ASTROBIOLOGY 2015; 15. [PMID: 26200431 PMCID: PMC4523004 DOI: 10.1089/ast.2014.1213] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Ribonucleic acid (RNA) is one of the two nucleic acids used by extant biochemistry and plays a central role as the intermediary carrier of genetic information in transcription and translation. If RNA was involved in the origin of life, it should have a facile prebiotic synthesis. A wide variety of such syntheses have been explored. However, to date no one-pot reaction has been shown capable of yielding RNA monomers from likely prebiotically abundant starting materials, though this does not rule out the possibility that simpler, more easily prebiotically accessible nucleic acids may have preceded RNA. Given structural constraints, such as the ability to form complementary base pairs and a linear covalent polymer, a variety of structural isomers of RNA could potentially function as genetic platforms. By using structure-generation software, all the potential structural isomers of the ribosides (BC5H9O4, where B is nucleobase), as well as a set of simpler minimal analogues derived from them, that can potentially serve as monomeric building blocks of nucleic acid-like molecules are enumerated. Molecules are selected based on their likely stability under biochemically relevant conditions (e.g., moderate pH and temperature) and the presence of at least two functional groups allowing the monomers to be incorporated into linear polymers. The resulting structures are then evaluated by using molecular descriptors typically applied in quantitative structure-property relationship (QSPR) studies and predicted physicochemical properties. Several databases have been queried to determine whether any of the computed isomers had been synthesized previously. Very few of the molecules that emerge from this structure set have been previously described. We conclude that ribonucleosides may have competed with a multitude of alternative structures whose potential proto-biochemical roles and abiotic syntheses remain to be explored.
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Affiliation(s)
- H. James Cleaves
- Earth-Life Science Institute (ELSI), Tokyo Institute of Technology, Tokyo, Japan
- Institute for Advanced Study, Princeton, New Jersey, USA
- Blue Marble Space Institute of Science, Washington, DC, USA
- Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Markus Meringer
- German Aerospace Center (DLR), Earth Observation Center (EOC), Oberpfaffenhofen-Wessling, Germany
| | - Jay Goodwin
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
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14
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Abstract
This review discusses the template-directed preparation of sequence-defined polymers.
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15
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Blain JC, Ricardo A, Szostak JW. Synthesis and nonenzymatic template-directed polymerization of 2'-amino-2'-deoxythreose nucleotides. J Am Chem Soc 2014; 136:2033-9. [PMID: 24409991 PMCID: PMC4105081 DOI: 10.1021/ja411950n] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
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Threose nucleic acid (TNA) is a potential
alternative genetic material
that may have played a role in the early evolution of life. We have
developed a novel synthesis of 2′-amino modified TNA nucleosides
(2′-NH2-TNA) based on a cycloaddition reaction between
a glycal and an azodicarboxylate, followed by direct nucleosidation
of the cycloadduct. Using this route, we synthesized the thymine and
guanine 2′-NH2-TNA nucleosides in seven steps with
24% and 12% overall yield, respectively. We then phosphorylated the
guanine nucleoside on the 3′-hydroxyl, activated the phosphate
as the 2-methylimidazolide, and tested the ability of the activated
nucleotide to copy C4 RNA, DNA, and TNA templates by nonenzymatic
primer extension. We measured pseudo-first-order rate constants for
the first nucleotide addition step of 1.5, 0.97, and 0.57 h–1 on RNA, DNA, and TNA templates, respectively, at pH 7.5 and 4 °C
with 150 mM NaCl, 100 mM N-(hydroxylethyl)imidazole
catalyst, and 5 mM activated nucleotide. The activated nucleotide
hydrolyzed with a rate constant of 0.39 h–1, causing
the polymerization reaction to stall before complete template copying
could be achieved. These extension rates are more than 1 order of
magnitude slower than those for amino-sugar ribonucleotides under
the same conditions, and copying of the TNA template, which best represented
a true self-copying reaction, was the slowest of all. The poor kinetics
of 2′-NH2-TNA template copying could give insight
into why TNA was ultimately not used as a genetic material by biological
systems.
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Affiliation(s)
- J Craig Blain
- Howard Hughes Medical Institute and Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
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16
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Kaiser A, Richert C. Nucleotide-based copying of nucleic acid sequences without enzymes. J Org Chem 2013; 78:793-9. [PMID: 23327991 DOI: 10.1021/jo3025779] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chemical primer extension is the enzyme-free incorporation of nucleotides at the end of an oligonucleotide, directed by a template. The reaction mimics the copying of sequences during replication but relies on recognition and reactivity of nucleic acids alone. Copying is low-yielding, particularly for long RNA. Hydrolysis of active esters and inhibition through hydrolysis products have been identified as factors that prevent high yields, and approaches to overcoming them have culminated in successful template-directed solid-phase syntheses for RNA and phosphoramidate DNA.
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Affiliation(s)
- Andreas Kaiser
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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17
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Zhang S, Zhang N, Blain JC, Szostak JW. Synthesis of N3'-P5'-linked phosphoramidate DNA by nonenzymatic template-directed primer extension. J Am Chem Soc 2013; 135:924-32. [PMID: 23252395 PMCID: PMC3548433 DOI: 10.1021/ja311164j] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
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A fast and accurate pathway for nonenzymatic RNA replication
would
simplify models for the emergence of the RNA world from the prebiotic
chemistry of the early earth. However, numerous difficulties stand
in the way of an experimental demonstration of effective nonenzymatic
RNA replication. To gain insight into the necessary properties of
potentially self-replicating informational polymers, we have studied
several model systems based on amino–sugar nucleotides. Here
we describe the synthesis of N3′–P5′-linked phosphoramidate
DNA (3′-NP-DNA) by the template-directed polymerization of
activated 3′-amino-2′,3′-dideoxyribonucleotides.
3′-NP-DNA is an interesting model because of its very RNA-like
A-type duplex conformation and because activated 3′-amino-2′,3′-dideoxyribonucleotides
are much more reactive than the corresponding activated ribonucleotides.
In contrast to our previous studies with 2′-amino-2′,3′-dideoxyribonucleotides
(for which G and C but not A and T exhibit efficient template copying),
we have found that all four canonical 3′-amino-2′,3′-dideoxyribonucleotides
(G, C, A, and T) polymerize efficiently on RNA templates. RNA templates
are generally superior to DNA templates, and oligo-ribo-T templates
are superior to oligo-ribo-U templates, which are the least efficient
of the RNA homopolymer templates. We have also found that activation
of 3′-aminonucleotides with 2-methylimidazole results in a
ca. 10-fold higher polymerization rate relative to activation with
imidazole, an observation that parallels earlier findings with ribonucleotides.
We discuss the implications of our experiments for the possibility
of self-replication in the 3′-NP-DNA and RNA systems.
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Affiliation(s)
- Shenglong Zhang
- Howard Hughes Medical Institute and Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
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18
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Cape JL, Edson JB, Spencer LP, DeClue MS, Ziock HJ, Maurer S, Rasmussen S, Monnard PA, Boncella JM. Phototriggered DNA phosphoramidate ligation in a tandem 5'-amine deprotection/3'-imidazole activated phosphate coupling reaction. Bioconjug Chem 2012; 23:2014-9. [PMID: 22985338 DOI: 10.1021/bc300093y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the preparation and use of an N-methyl picolinium carbamate protecting group for applications in a phototriggered nonenzymatic DNA phosphoramidate ligation reaction. Selective 5'-amino protection of a modified 13-mer oligonucleotide is achieved in aqueous solution by reaction with an N-methyl-4-picolinium carbonyl imidazole triflate protecting group precursor. Deprotection is carried out by photoinduced electron transfer from Ru(bpy)(3)(2+) using visible light photolysis and ascorbic acid as a sacrificial electron donor. Phototriggered 5'- amino oligonucleotide deprotection is used to initiate a nonenzymatic ligation of the 13-mer to an imidazole activated 3'-phospho-hairpin template to generate a ligated product with a phosphoramidate linkage. We demonstrate that this methodology offers a simple way to exert control over reaction initiation and rates in nonenzymatic DNA ligation for potential applications in the study of model protocellular systems and prebiotic nucleic acid synthesis.
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Affiliation(s)
- Jonathan L Cape
- Material, Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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19
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Kaiser A, Spies S, Lommel T, Richert C. Template-Directed Synthesis in 3′- and 5′-Direction with Reversible Termination. Angew Chem Int Ed Engl 2012; 51:8299-303. [DOI: 10.1002/anie.201203859] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Indexed: 01/21/2023]
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20
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Kaiser A, Spies S, Lommel T, Richert C. Template-Directed Synthesis in 3′- and 5′-Direction with Reversible Termination. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203859] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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21
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Abstract
The general notion of an "RNA World" is that, in the early development of life on the Earth, genetic continuity was assured by the replication of RNA and genetically encoded proteins were not involved as catalysts. There is now strong evidence indicating that an RNA World did indeed exist before DNA- and protein-based life. However, arguments regarding whether life on Earth began with RNA are more tenuous. It might be imagined that all of the components of RNA were available in some prebiotic pool, and that these components assembled into replicating, evolving polynucleotides without the prior existence of any evolved macromolecules. A thorough consideration of this "RNA-first" view of the origin of life must reconcile concerns regarding the intractable mixtures that are obtained in experiments designed to simulate the chemistry of the primitive Earth. Perhaps these concerns will eventually be resolved, and recent experimental findings provide some reason for optimism. However, the problem of the origin of the RNA World is far from being solved, and it is fruitful to consider the alternative possibility that RNA was preceded by some other replicating, evolving molecule, just as DNA and proteins were preceded by RNA.
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Affiliation(s)
- Michael P Robertson
- Departments of Chemistry and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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22
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Zhang N, Zhang S, Szostak JW. Activated ribonucleotides undergo a sugar pucker switch upon binding to a single-stranded RNA template. J Am Chem Soc 2012; 134:3691-4. [PMID: 22296305 PMCID: PMC3448298 DOI: 10.1021/ja212027q] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Indexed: 12/02/2022]
Abstract
Template-directed polymerization of chemically activated ribonucleotide monomers, such as nucleotide 5'-phosphorimidazolides, has been studied as a model for nonenzymatic RNA replication during the origin of life. Kinetic studies of the polymerization of various nucleotide monomers on oligonucleotide templates have suggested that the A-form (C3'-endo sugar pucker) conformation is optimal for both monomers and templates for efficient copying. However, RNA monomers are predominantly in the C2'-endo conformation when free in solution, except for cytidine, which is approximately equally distributed between the C2'-endo and C3'-endo conformations. We hypothesized that ribonucleotides undergo a switch in sugar pucker upon binding to an A-type template and that this conformational switch allows or enhances subsequent polymerization. We used transferred nuclear Overhauser effect spectroscopy (TrNOESY), which can be used for specific detection of the bound conformation of small-molecule ligands with relatively weak affinity to receptors, to study the interactions between nucleotide 5'-phosphorimidazolides and single-stranded oligonucleotide templates. We found that the sugar pucker of activated ribonucleotides switches from C2'-endo in the free state to C3'-endo upon binding to an RNA template. This switch occurs only on RNA and not on DNA templates. Furthermore, activated 2'-deoxyribonucleotides maintain a C2'-endo sugar pucker in both the free and template-bound states. Our results provide a structural explanation for the observations that activated ribonucleotides are superior to activated deoxyribonucleotides and that RNA templates are superior to DNA templates in template-directed nonenzymatic primer-extension reactions.
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Affiliation(s)
- Na Zhang
- Howard Hughes
Medical Institute and Department of Molecular
Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street,
Boston, Massachusetts 02114, United States
| | - Shenglong Zhang
- Howard Hughes
Medical Institute and Department of Molecular
Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street,
Boston, Massachusetts 02114, United States
| | - Jack W. Szostak
- Howard Hughes
Medical Institute and Department of Molecular
Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street,
Boston, Massachusetts 02114, United States
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23
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D'Alonzo D, Guaragna A, Palumbo G. Exploring the role of chirality in nucleic acid recognition. Chem Biodivers 2012; 8:373-413. [PMID: 21404424 DOI: 10.1002/cbdv.201000303] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The study of the base-pairing properties of nucleic acids with sugar moieties in the backbone belonging to the L-series (β-L-DNA, β-L-RNA, and their analogs) are reviewed. The major structural factors underlying the formation of stable heterochiral complexes obtained by incorporation of modified nucleotides into natural duplexes, or by hybridization between homochiral strands of opposite sense of chirality are highlighted. In addition, the perspective use of L-nucleic acids as candidates for various therapeutic applications, or as tools for both synthetic biology and etiology-oriented investigations on the structure and stereochemistry of natural nucleic acids is discussed.
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Affiliation(s)
- Daniele D'Alonzo
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, via Cinthia, 4, I-80126 Napoli.
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24
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Efficient enzyme-free copying of all four nucleobases templated by immobilized RNA. Nat Chem 2011; 3:603-8. [PMID: 21778979 DOI: 10.1038/nchem.1086] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 06/06/2011] [Indexed: 11/08/2022]
Abstract
The transition from inanimate materials to the earliest forms of life must have involved multiplication of a catalytically active polymer that is able to replicate. The semiconservative replication that is characteristic of genetic information transfer requires strands that contain more than one type of nucleobase. Short strands of RNA can act as catalysts, but attempts to induce efficient self-copying of mixed sequences (containing four different nucleobases) have been unsuccessful with ribonucleotides. Here we show that inhibition by spent monomers, formed by the hydrolysis of the activated nucleotides, is the cause for incomplete extension of growing daughter strands on RNA templates. Immobilization of strands and periodic displacement of the solution containing the activated monomers overcome this inhibition. Any of the four nucleobases (A/C/G/U) is successfully copied in the absence of enzymes. We conclude therefore that in a prebiotic world, oligoribonucleotides may have formed and undergone self-copying on surfaces.
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25
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Bell NM, Wong R, Micklefield J. A non-enzymatic, DNA template-directed morpholino primer extension approach. Chemistry 2010; 16:2026-30. [PMID: 20087911 DOI: 10.1002/chem.200902237] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Neil M Bell
- School of Chemistry, The University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7ND, UK
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26
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Abstract
Starting from pyranose nucleic acids, several series of modified nucleic acids with a six-membered carbohydrate moiety (mimic) have been synthesized and analyzed over a period of 20 years, and this work is summarized here. The process starts with structural and conformational considerations, followed by synthetic efforts and a structural analysis, and ends up with a biological confirmation of the concept, demonstrating that these modified nucleic acids represent very valuable tools in chemistry and biology.
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Affiliation(s)
- Piet Herdewijn
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven.
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27
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Brudno Y, Liu DR. Recent progress toward the templated synthesis and directed evolution of sequence-defined synthetic polymers. ACTA ACUST UNITED AC 2009; 16:265-76. [PMID: 19318208 DOI: 10.1016/j.chembiol.2009.02.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 01/20/2009] [Accepted: 02/16/2009] [Indexed: 12/21/2022]
Abstract
Biological polymers such as nucleic acids and proteins are ubiquitous in living systems, but their ability to address problems beyond those found in nature is constrained by factors such as chemical or biological instability, limited building-block functionality, bioavailability, and immunogenicity. In principle, sequence-defined synthetic polymers based on nonbiological monomers and backbones might overcome these constraints; however, identifying the sequence of a synthetic polymer that possesses a specific desired functional property remains a major challenge. Molecular evolution can rapidly generate functional polymers but requires a means of translating amplifiable templates such as nucleic acids into the polymer being evolved. This review covers recent advances in the enzymatic and nonenzymatic templated polymerization of nonnatural polymers and their potential applications in the directed evolution of sequence-defined synthetic polymers.
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Affiliation(s)
- Yevgeny Brudno
- Department of Chemistry and Chemical Biology and the Howard Hughes Medical Institute, 12 Oxford Street, Harvard University, Cambridge, MA 02138, USA
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28
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Loakes D, Holliger P. Darwinian chemistry: towards the synthesis of a simple cell. MOLECULAR BIOSYSTEMS 2009; 5:686-94. [PMID: 19562107 DOI: 10.1039/b904024b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The total synthesis of a simple cell is in many ways the ultimate challenge in synthetic biology. Outlined eight years ago in a visionary article by Szostak et al. (J. W. Szostak, D. P. Bartel and P. L. Luisi, Nature, 2001, 409, 387), the chances of success seemed remote. However, recent progress in nucleic acid chemistry, directed evolution and membrane biophysics have brought the prospect of a simple synthetic cell with life-like properties such as growth, division, heredity and evolution within reach. Success in this area will not only revolutionize our understanding of abiogenesis but provide a fertile test-bed for models of prebiotic chemistry and early evolution. Last but not least, a robust "living" protocell may provide a versatile and safe chassis for embedding synthetic devices and systems.
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Affiliation(s)
- David Loakes
- Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
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29
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Monnard PA, Ziock H. Eutectic Phase in Water-Ice: A Self-Assembled Environment Conducive to Metal-Catalyzed Non-Enzymatic RNA Polymerization. Chem Biodivers 2008; 5:1521-1539. [DOI: 10.1002/cbdv.200890141] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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Kleiner RE, Brudno Y, Birnbaum ME, Liu DR. DNA-templated polymerization of side-chain-functionalized peptide nucleic acid aldehydes. J Am Chem Soc 2008; 130:4646-59. [PMID: 18341334 PMCID: PMC2748799 DOI: 10.1021/ja0753997] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DNA-templated polymerization of synthetic building blocks provides a potential route to the laboratory evolution of sequence-defined polymers with structures and properties not necessarily limited to those of natural biopolymers. We previously reported the efficient and sequence-specific DNA-templated polymerization of peptide nucleic acid (PNA) aldehydes. Here, we report the enzyme-free, DNA-templated polymerization of side-chain-functionalized PNA tetramer and pentamer aldehydes. We observed that polymerization of tetramer and pentamer PNA building blocks with a single lysine-based side chain at various positions in the building block could proceed efficiently and sequence specifically. In addition, DNA-templated polymerization also proceeded efficiently and in a sequence-specific manner with pentamer PNA aldehydes containing two or three lysine side chains in a single building block to generate more densely functionalized polymers. To further our understanding of side-chain compatibility and expand the capabilities of this system, we also examined the polymerization efficiencies of 20 pentamer building blocks each containing one of five different side-chain groups and four different side-chain regio- and stereochemistries. Polymerization reactions were efficient for all five different side-chain groups and for three of the four combinations of side-chain regio- and stereochemistries. Differences in the efficiency and initial rate of polymerization correlate with the apparent melting temperature of each building block, which is dependent on side-chain regio- and stereochemistry but relatively insensitive to side-chain structure among the substrates tested. Our findings represent a significant step toward the evolution of sequence-defined synthetic polymers and also demonstrate that enzyme-free nucleic acid-templated polymerization can occur efficiently using substrates with a wide range of side-chain structures, functionalization positions within each building block, and functionalization densities.
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Affiliation(s)
- Ralph E. Kleiner
- Contribution from the Howard Hughes Medical Institute and the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Yevgeny Brudno
- Contribution from the Howard Hughes Medical Institute and the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Michael E. Birnbaum
- Contribution from the Howard Hughes Medical Institute and the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - David R. Liu
- Contribution from the Howard Hughes Medical Institute and the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
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31
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Monnard PA, Szostak JW. Metal-ion catalyzed polymerization in the eutectic phase in water-ice: a possible approach to template-directed RNA polymerization. J Inorg Biochem 2008; 102:1104-11. [PMID: 18329104 DOI: 10.1016/j.jinorgbio.2008.01.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Revised: 01/17/2008] [Accepted: 01/18/2008] [Indexed: 10/22/2022]
Abstract
The emergence of an RNA world requires among other processes the non-enzymatic, template-directed replication of genetic polymers such as RNA or related nucleic acids, possibly catalyzed by metal-ions. The absence of uridilate derivative polymerization on adenine containing templates has been the main issue preventing an efficient template-directed RNA polymerization. We report here the investigation of template-directed RNA polymerization in the eutectic phase in water-ice. In particular, it was found that activated uridilate monomers in the presence of metal-ion catalysts could efficiently elongate RNA hairpins whose 5'-overhangs served as the templating sequence. The same applies for every other pyrimidine and purine nucleobase. Moreover, the initial elongation rates were always higher in the presence of a template complementary to the nucleotide than in systems without proper base-pairing opportunities. These results suggest that a template-directed RNA polymerization catalyzed by metal-ions could be carried out under eutectic phase in water-ice conditions.
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Affiliation(s)
- Pierre-Alain Monnard
- Los Alamos National Laboratory, EES-6, PO Box 1663, MS-D462, Los Alamos, NM 87545, USA.
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32
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33
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Vogel SR, Richert C. Adenosine residues in the template do not block spontaneous replication steps of RNA. Chem Commun (Camb) 2007:1896-8. [PMID: 17695221 DOI: 10.1039/b702768k] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sub-freezing temperatures, azabenzotriazolide activation, multiple monomer addition, and helper displacement help to overcome what seemed like an intrinsic block of adenine-templated RNA replication steps in the absence of enzymes.
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Affiliation(s)
- Stephanie R Vogel
- Institute for Organic Chemistry, University of Karlsruhe (TH), 76131 Karlsruhe, Germany
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34
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Affiliation(s)
- Adam P Silverman
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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35
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Adelfinskaya O, Terrazas M, Froeyen M, Marlière P, Nauwelaerts K, Herdewijn P. Polymerase-catalyzed synthesis of DNA from phosphoramidate conjugates of deoxynucleotides and amino acids. Nucleic Acids Res 2007; 35:5060-72. [PMID: 17652326 PMCID: PMC1976459 DOI: 10.1093/nar/gkm498] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 06/06/2007] [Accepted: 06/07/2007] [Indexed: 11/20/2022] Open
Abstract
Some selected amino acids, in particular L-aspartic acid (L-Asp) and L-histidine (L-His), can function as leaving group during polymerase-catalyzed incorporation of deoxyadenosine monophosphate (dAMP) in DNA. Although L-Asp-dAMP and L-His-dAMP bind, most probably, in a different way in the active site of the enzyme, aspartic acid and histidine can be considered as mimics of the pyrophosphate moiety of deoxyadenosine triphosphate. L-Aspartic acid is more efficient than D-aspartic acid as leaving group. Such P-N conjugates of amino acids and deoxynucleotides provide a novel experimental ground for diversifying nucleic acid metabolism in the field of synthetic biology.
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Affiliation(s)
- O. Adelfinskaya
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Department of Pharmaceutical Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium and Genoscope - Centre National de Séquençage, 2 rue Gaston Crémieux CP5706, 91057 Evry cedex, France
| | - M. Terrazas
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Department of Pharmaceutical Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium and Genoscope - Centre National de Séquençage, 2 rue Gaston Crémieux CP5706, 91057 Evry cedex, France
| | - M. Froeyen
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Department of Pharmaceutical Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium and Genoscope - Centre National de Séquençage, 2 rue Gaston Crémieux CP5706, 91057 Evry cedex, France
| | - P. Marlière
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Department of Pharmaceutical Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium and Genoscope - Centre National de Séquençage, 2 rue Gaston Crémieux CP5706, 91057 Evry cedex, France
| | - K. Nauwelaerts
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Department of Pharmaceutical Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium and Genoscope - Centre National de Séquençage, 2 rue Gaston Crémieux CP5706, 91057 Evry cedex, France
| | - P. Herdewijn
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Department of Pharmaceutical Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium and Genoscope - Centre National de Séquençage, 2 rue Gaston Crémieux CP5706, 91057 Evry cedex, France
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36
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Lin NT, Lin SY, Lee SL, Chen CH, Hsu CH, Hwang LP, Xie ZY, Chen CH, Huang SL, Luh TY. From Polynorbornene to the Complementary Polynorbornene by Replication. Angew Chem Int Ed Engl 2007; 46:4481-5. [PMID: 17455179 DOI: 10.1002/anie.200700472] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nai-Ti Lin
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
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37
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Lin NT, Lin SY, Lee SL, Chen CH, Hsu CH, Hwang LP, Xie ZY, Chen CH, Huang SL, Luh TY. From Polynorbornene to the Complementary Polynorbornene by Replication. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700472] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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38
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Dose C, Seitz O. Single nucleotide specific detection of DNA by native chemical ligation of fluorescence labeled PNA-probes. Bioorg Med Chem 2007; 16:65-77. [PMID: 17499998 DOI: 10.1016/j.bmc.2007.04.059] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 04/05/2007] [Accepted: 04/27/2007] [Indexed: 10/23/2022]
Abstract
DNA-directed chemical ligations provide the opportunity to diagnose DNA sequences with very high sequence specificity. Fluorescent labels have been attached to reactive probes to enable the homogeneous detection of DNA and RNA. However, it has frequently been found that the attachment of fluorescent labels results in decreases of ligation fidelity. Herein we describe the development of a fluorogenic ligation reaction that provides for 10(2)-fold to perfect sequence selectivity. The reaction is based on the isocysteine-mediated native chemical PNA ligation. It is shown that DNA-induced rate accelerations of approximately 43.000-fold can be obtained through subtle variations of the ligation conditions. PNA-thioesters and isocysteine-PNA conjugates were labeled with FAM and TMR fluorophores, respectively. For gaining rapid synthetic access, a convenient on-resin labeling approach was developed. A new PNA monomer featuring an Alloc-protected lysine side chain was synthesized and coupled in solid-phase PNA synthesis. In the event of a ligation reaction the two fluorophores are brought into proximity. It is shown that fluorescence resonance energy transfer provides a positive fluorescence signal which is specific for product formation rather than for loss of starting materials. Single base mutations can be detected within minutes and with very high sequence selectivity at optimized conditions.
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Affiliation(s)
- Christian Dose
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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39
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Dmochowska B, Skorupa E, Pellowska-Januszek L, Czarkowska M, Sikorski A, Wiśniewski A. Preparation, single-crystal X-ray diffraction and high-resolution NMR spectroscopic analyses of N-[(1,4-anhydro-5-deoxy-2,3-O-isopropylidene-d,l-ribitol)-5-yl]trimethylammonium iodide. Carbohydr Res 2006; 341:1916-21. [PMID: 16729990 DOI: 10.1016/j.carres.2006.04.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Revised: 04/13/2006] [Accepted: 04/18/2006] [Indexed: 11/20/2022]
Abstract
The synthesis and isolation of 1,4-anhydro-5-deoxy-5-iodo-2,3-O-isopropylidene-D,L-ribitol and N-[(1,4-anhydro-5-deoxy-2,3-O-isopropylidene-D,L-ribitol)-5-yl]trimethylammonium iodide are described. The products were examined by (1)H, (13)C NMR spectroscopy, and N-[(1,4-anhydro-5-deoxy-2,3-O-isopropylidene-D,L-ribitol)-5-yl]trimethylammonium iodide was additionally analyzed by X-ray crystallography.
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40
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Maier T, Przylas I, Strater N, Herdewijn P, Saenger W. Reinforced HNA backbone hydration in the crystal structure of a decameric HNA/RNA hybrid. J Am Chem Soc 2005; 127:2937-43. [PMID: 15740130 DOI: 10.1021/ja045843v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The crystal structure of a decameric HNA/RNA (HNA = 2',3'-dideoxy-1',5'-anhydro-d-arabinohexitol nucleic acid) hybrid with the RNA sequence 5'-GGCAUUACGG-3' is the first crystal structure of a hybrid duplex between a naturally occurring nucleic acid and a strand, which is fully modified to contain a six-membered ring instead of ribose. The presence of four duplex helices in the asymmetric unit allows for a detailed discussion of hydration, which revealed a tighter spinelike backbone hydration for the HNA- than for the RNA-strands. The reinforced backbone hydration is suggested to contribute significantly to the exceptional stability of HNA-containing duplexes and might be one of the causes for the evolutionary preference for ribose-derived nucleic acids.
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Affiliation(s)
- Timm Maier
- Institut für Chemie der Freien Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
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41
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Skorupa E, Dmochowska B, Pellowska-Januszek L, Wojnowski W, Chojnacki J, Wiśniewski A. Synthesis and structure of selected quaternary N-(1,4-anhydro-5-deoxy-2,3-O-isopropylidene-D,L-ribitol-5-yl)ammonium salts. Carbohydr Res 2005; 339:2355-62. [PMID: 15388350 DOI: 10.1016/j.carres.2004.06.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2003] [Accepted: 06/25/2004] [Indexed: 10/26/2022]
Abstract
The syntheses have been developed for quaternary N-(1,4-anhydro-5-deoxy-2,3-O-isopropylidene-D,L-ribitol-5-yl)ammonium salts derived from five aromatic amines, pyridine, 2-methylpyridine, 3-carbamoylpyridine, 4-(N,N-dimethylamino)pyridine, and quinoline, as well as two tertiary aliphatic amines, trimethylamine and triethylamine. Reactions of 1,4-anhydro-2,3-O-isopropylidene-5-O-tosyl-D,L-ribitol with tri-n-propylamine and tri-n-butylamine were unsuccessful. The products were identified on the basis of their 1H and 13C NMR spectra. The structure of N-(1,4-anhydro-5-deoxy-2,3-O-isopropylidene-D,L-ribitol-5-yl)trimethylammonium tosylate was additionally elucidated by X-ray diffractometry.
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Affiliation(s)
- Eugenia Skorupa
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, PL-80-952 Gdańsk, Poland
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42
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Abstract
The demonstration that ribosomal peptide synthesis is a ribozyme-catalyzed reaction makes it almost certain that there was once an RNA World. The central problem for origin-of-life studies, therefore, is to understand how a protein-free RNA World became established on the primitive Earth. We first review the literature on the prebiotic synthesis of the nucleotides, the nonenzymatic synthesis and copying of polynucleotides, and the selection of ribozyme catalysts of a kind that might have facilitated polynucleotide replication. This leads to a brief outline of the Molecular Biologists' Dream, an optimistic scenario for the origin of the RNA World. In the second part of the review we point out the many unresolved problems presented by the Molecular Biologists' Dream. This in turn leads to a discussion of genetic systems simpler than RNA that might have "invented" RNA. Finally, we review studies of prebiotic membrane formation.
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Lescrinier E, Froeyen M, Herdewijn P. Difference in conformational diversity between nucleic acids with a six-membered 'sugar' unit and natural 'furanose' nucleic acids. Nucleic Acids Res 2003; 31:2975-89. [PMID: 12799423 PMCID: PMC162241 DOI: 10.1093/nar/gkg407] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Natural nucleic acids duplexes formed by Watson-Crick base pairing fold into right-handed helices that are classified in two families of secondary structures, i.e. the A- and B-form. For a long time, these A and B allomorphic nucleic acids have been considered as the 'non plus ultra' of double-stranded nucleic acids geometries with the only exception of Z-DNA, a left-handed helix that can be adopted by some DNA sequences. The five-membered furanose ring in the sugar-phosphate backbone of DNA and RNA is the underlying cause of this restriction in conformational diversity. A collection of new Watson-Crick duplexes have joined the 'original' nucleic acid double helixes at the moment the furanose sugar was replaced by different types of six-membered ring systems. The increase in this structural and conformational diversity originates from the rigid chair conformation of a saturated six-membered ring that determines the orientation of the ring substituents with respect to each other. The original A- and B-form oligonucleotide duplexes have expanded into a whole family of new structures with the potential for selective cross-communication in a parallel or antiparallel orientation, opening up a new world for information storage and for molecular recognition-directed self-organization.
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Affiliation(s)
- Eveline Lescrinier
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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Lescrinier E, Esnouf R, Schraml J, Busson R, Heus H, Hilbers C, Herdewijn P. Solution structure of a HNA-RNA hybrid. CHEMISTRY & BIOLOGY 2000; 7:719-31. [PMID: 10980452 DOI: 10.1016/s1074-5521(00)00017-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Synthetic nucleic acid analogues with a conformationally restricted sugar-phosphate backbone are widely used in antisense strategies for biomedical and biochemical applications. The modified backbone protects the oligonucleotides against degradation within the living cell, which allows them to form stable duplexes with sequences in target mRNAs with the aim of arresting their translation. The biologically most active antisense oligonucleotides also trigger cleavage of the target RNA through activation of endogenous RNase H. Systematic studies of synthetic oligonucleotides have also been conducted to delineate the origin of the chirality of DNA and RNA that are both composed of D-nucleosides. RESULTS Hexitol nucleic acids (HNA) are the first example of oligonucleotides with a six-membered carbohydrate moiety that can bind strongly and selectively to complementary RNA oligomers. We present the first high resolution nuclear magnetic resonance structure of a HNA oligomer bound to a complementary RNA strand. The HNA-RNA complex forms an anti-parallel heteroduplex and adopts a helical conformation that belongs to the A-type family. Possibly, due to the rigidity of the rigid chair conformation of the six-membered ring both the HNA and RNA strand in the duplex are well defined. The observed absence of end-fraying effects also indicate a reduced conformational flexibility of the HNA-RNA duplex compared to canonical dsRNA or an RNA-DNA duplex. CONCLUSIONS The P-P distance across the minor groove, which is close to A-form, and the rigid conformation of the HNA-RNA complex, explain its resistance towards degradation by Rnase H. The A-form character of the HNA-RNA duplex and the reduced flexibility of the HNA strand is possibly responsible for the stereoselectivity of HNA templates in non-enzymatic replication of oligonucleotides, supporting the theory that nucleosides with six-membered rings could have existed at some stage in molecular evolution.
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Affiliation(s)
- E Lescrinier
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
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Kozlov IA, Orgel LE. Oligomerization of deoxyguanosine 5'-phosphoro-2-methylimidazolide on a polycytidylate template. ORIGINS LIFE EVOL B 1999; 29:593-5. [PMID: 10666742 DOI: 10.1023/a:1006666926870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The oligomerization of deoxyguanosine 5'-phosphoro-2-methylimidazolide on a polycytidylate template is much less efficient than the oligomerization of the corresponding activated ribonucleotide. Nonetheless oligomers containing up to eight nucleotide residues are detected. The products are 3'-5'-linked oligodeoxyribonucleotides capped at the 5'-terminus with a pyrophosphate-linked monomer.
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Affiliation(s)
- I A Kozlov
- Salk Institute for Biological Studies, San Diego, CA 92186, USA
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