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Weigel RK, Rangamani A, Alabi CA. Synthetically encoded complementary oligomers. Nat Rev Chem 2023; 7:875-888. [PMID: 37973830 DOI: 10.1038/s41570-023-00556-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2023] [Indexed: 11/19/2023]
Abstract
Creating the next generation of advanced materials will require controlling molecular architecture to a degree typically achieved only in biopolymers. Sequence-defined polymers take inspiration from biology by using chain length and monomer sequence as handles for tuning structure and function. These sequence-defined polymers can assemble into discrete structures, such as molecular duplexes, via reversible interactions between functional groups. Selectivity can be attained by tuning the monomer sequence, thereby creating the need for chemical platforms that can produce sequence-defined polymers at scale. Developing sequence-defined polymers that are specific for their complementary sequence and achieve their desired binding strengths is critical for producing increasingly complex structures for new functional materials. In this Review Article, we discuss synthetic platforms that produce sequence-defined, duplex-forming oligomers of varying length, strength and association mode, and highlight several analytical techniques used to characterize their hybridization.
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Affiliation(s)
- R Kenton Weigel
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Adithya Rangamani
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Christopher A Alabi
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA.
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Hu W, Liu Y, Zhang X, Zheng P, Yang F, Guo G, Xie X, Huang J, Chen W. Small change for big improvement in the preparation of the key intermediate N 1, N 3-disubstituted 1,3,5-triazone of ensitrelvir. RSC Adv 2023; 13:3688-3693. [PMID: 36756552 PMCID: PMC9890673 DOI: 10.1039/d2ra07844a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/14/2023] [Indexed: 01/26/2023] Open
Abstract
In this study, the key intermediate N 1, N 3-disubstituted 1,3,5-triazone of ensitrelvir fumaric acid, approved in Japan for the treatment of SARS-CoV-2 infection under the emergency regulatory approval system, was produced from S-ethylisothiourea hydrobromide and aminomethyl triazole with CDI by four-step telescoped strategy including CDI-activated, condensation, CDI-cyclization, and N 1-alkylation. The strategy with simple conditions and operations had a total yield of 53% on a gram scale. The strategy for synthesizing the key N 1, N 3-disubstituted 1,3,5-triazone intermediate of ensitrelvir might provide a new avenue for further research and development of ensitrelvir analogs.
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Affiliation(s)
- Wei Hu
- School of Pharmaceutical Sciences, Gannan Medical University Ganzhou 341000 P. R. China
| | - Yuanchang Liu
- School of Pharmaceutical Sciences, Gannan Medical University Ganzhou 341000 P. R. China
| | - Xiang Zhang
- School of Pharmaceutical Sciences, Gannan Medical University Ganzhou 341000 P. R. China
| | - Panpan Zheng
- School of Pharmaceutical Sciences, Gannan Medical University Ganzhou 341000 P. R. China
| | - Feifei Yang
- School of Pharmaceutical Sciences, Gannan Medical University Ganzhou 341000 P. R. China
| | - Guangyang Guo
- School of Pharmaceutical Sciences, Gannan Medical University Ganzhou 341000 P. R. China
| | - Xin Xie
- School of Pharmaceutical Sciences, Gannan Medical University Ganzhou 341000 P. R. China .,Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University Ganzhou 341000 P. R. China
| | - Jiuzhong Huang
- School of Pharmaceutical Sciences, Gannan Medical University Ganzhou 341000 P. R. China .,Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University Ganzhou 341000 P. R. China
| | - Weiming Chen
- School of Pharmaceutical Sciences, Gannan Medical University Ganzhou 341000 P. R. China .,Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University Ganzhou 341000 P. R. China
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Journot G, Neier R, Gualandi A. Hydrogenation of Calix[4]pyrrole: From the Formation to the Synthesis of Calix[4]pyrrolidine. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
| | - Reinhard Neier
- Department of Chemistry University of Neuchâtel Avenue Bellevaux 51 2000 Neuchâtel Switzerland
| | - Andrea Gualandi
- Dipartimento di Chimica “G. Ciamician” Alma Mater Studiorum – Università di Bologna Via Selmi 2 I-40126 Bologna Italy
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Kim EK, Martin V, Krishnamurthy R. Orotidine-Containing RNA: Implications for the Hierarchical Selection (Systems Chemistry Emergence) of RNA. Chemistry 2017; 23:12668-12675. [PMID: 28708927 DOI: 10.1002/chem.201702912] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Indexed: 02/05/2023]
Abstract
The prebiotic synthesis of canonical nucleobases from HCN is a cornerstone for the RNA world hypothesis. However, their role in the primordial pathways to RNA is still debated. The very same process starting from HCN also gives rise to orotic acid, which (via orotidine) plays a crucial role in extant biology in the de novo synthesis of uridine and cytidine, the informational base-pairs in RNA. However, orotidine itself is absent in RNA. Given the prebiotic and biological relevance of orotic acid vis-à-vis uracil, we investigated orotidine-containing RNA oligonucleotides and show that they have severely compromised base-pairing properties. While not unexpected, these results suggest that the emergence of extant RNA cannot just be a consequence of the plausible prebiotic formation of its chemical constituents/building blocks. In combination with other investigations on alternative prebiotic nucleobases, sugars, and linkers, these findings imply that the selection of the components of extant RNA occurred at a higher hierarchical level of an oligomer/polymer based on its functional properties-pointing to a systems chemistry emergence of RNA from a library of precursors.
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Affiliation(s)
- Eun-Kyong Kim
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines Rd, La Jolla, Ca, 92037, USA
| | - Vincent Martin
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines Rd, La Jolla, Ca, 92037, USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines Rd, La Jolla, Ca, 92037, USA
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Xia X, Piao X, Bong D. Bifacial PNA complexation inhibits enzymatic access to DNA and RNA. Chembiochem 2014; 15:31-6. [PMID: 24259287 PMCID: PMC3896088 DOI: 10.1002/cbic.201300536] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Indexed: 02/02/2023]
Abstract
FULL STOP: Herein we report the effective in vitro inhibition of transcription, reverse-transcription and exonuclease function by formation of synthetic bPNA-nucleic acid triplex structures. Selective bPNA targeting of both DNA and RNA substrates suggests possible application of bPNAs as synthetic regulators of nucleic acid function.
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Affiliation(s)
- Xin Xia
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18 Avenue, Columbus, OH 43210 (USA)
| | - Xijun Piao
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18 Avenue, Columbus, OH 43210 (USA)
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18 Avenue, Columbus, OH 43210 (USA)
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Karri P, Punna V, Kim K, Krishnamurthy R. Base-Pairing Properties of a Structural Isomer of Glycerol Nucleic Acid. Angew Chem Int Ed Engl 2013; 52:5840-4. [DOI: 10.1002/anie.201300795] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 03/19/2013] [Indexed: 11/09/2022]
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Karri P, Punna V, Kim K, Krishnamurthy R. Base-Pairing Properties of a Structural Isomer of Glycerol Nucleic Acid. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300795] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kuruvilla E, Schuster GB, Hud NV. Enhanced nonenzymatic ligation of homopurine miniduplexes: support for greater base stacking in a pre-RNA world. Chembiochem 2012; 14:45-8. [PMID: 23225671 DOI: 10.1002/cbic.201200601] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Indexed: 11/07/2022]
Abstract
The ancestors of RNA? There is a long-standing proposal that contemporary nucleic acids might have evolved from RNA-like polymers that utilized only purine-purine base pairs. Here we demonstrate the great advantage that increased nucleobase stacking area provides for nonenzymatic ligation.
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Affiliation(s)
- Elizabeth Kuruvilla
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
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Menor-Salván C, Marín-Yaseli MR. Prebiotic chemistry in eutectic solutions at the water-ice matrix. Chem Soc Rev 2012; 41:5404-15. [PMID: 22660387 DOI: 10.1039/c2cs35060b] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A crystalline ice matrix at subzero temperatures can maintain a liquid phase where organic solutes and salts concentrate to form eutectic solutions. This concentration effect converts the confined reactant solutions in the ice matrix, sometimes making condensation and polymerisation reactions occur more favourably. These reactions occur at significantly high rates from a prebiotic chemistry standpoint, and the labile products can be protected from degradation. The experimental study of the synthesis of nitrogen heterocycles at the ice-water system showed the efficiency of this scenario and could explain the origin of nucleobases in the inner Solar System bodies, including meteorites and extra-terrestrial ices, and on the early Earth. The same conditions can also favour the condensation of monomers to form ribonucleic acid and peptides. Together with the synthesis of these monomers, the ice world (i.e., the chemical evolution in the range between the freezing point of water and the limit of stability of liquid brines, 273 to 210 K) is an under-explored experimental model in prebiotic chemistry.
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Affiliation(s)
- César Menor-Salván
- Centro de Astrobiología (INTA-CSIC), INTA, E-28850 Torrejón de Ardoz, Spain.
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Eschenmoser A. Ätiologie potentiell primordialer Biomolekül-Strukturen: Vom Vitamin B12 zu den Nukleinsäuren und der Frage nach der Chemie der Entstehung des Lebens - ein Rückblick. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103672] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Eschenmoser A. Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective. Angew Chem Int Ed Engl 2011; 50:12412-72. [PMID: 22162284 DOI: 10.1002/anie.201103672] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Indexed: 11/10/2022]
Abstract
"We'll never be able to know" is a truism that leads to resignation with respect to any experimental effort to search for the chemistry of life's origin. But such resignation runs radically counter to the challenge imposed upon chemistry as a natural science. Notwithstanding the prognosis according to which the shortest path to understanding the metamorphosis of the chemical into the biological is by way of experimental modeling of "artificial chemical life", the scientific search for the route nature adopted in creating the life we know will arguably never truly end. It is, after all, part of the search for our own origin.
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Affiliation(s)
- Albert Eschenmoser
- Organisch-chemisches Laboratorium der ETH Zürich, Hönggerberg, Wolfgang-Pauli-Str. 10, CHI H309, CH-8093 Zürich, Switzerland
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Buckley R, Enekwa CD, Williams LD, Hud NV. Molecular Recognition of Watson-Crick-Like Purine-Purine Base Pairs. Chembiochem 2011; 12:2155-8. [DOI: 10.1002/cbic.201100375] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Indexed: 12/12/2022]
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Hernández-Rodríguez M, Xie J, Osornio YM, Krishnamurthy R. Mapping the landscape of potentially primordial informational oligomers: (3'→2')-D-phosphoglyceric acid linked acyclic oligonucleotides tagged with 2,4-disubstituted 5-aminopyrimidines as recognition elements. Chem Asian J 2011; 6:1252-62. [PMID: 21387563 DOI: 10.1002/asia.201000828] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Indexed: 11/09/2022]
Abstract
The (3'→2')-phosphodiester glyceric acid backbone containing an acyclic oligomer tagged with 2,4-disubstituted pyrimidines as alternative recognition elements have been synthesized. Strong cross-pairing of a 2,4-dioxo-5-aminopyrimidine hexamer, rivaling locked nucleic acid (LNA) and peptide nucleic acid (PNA), with complementary adenine-containing DNA and RNA sequences was observed. The corresponding 2,4-diamino- and 2-amino-4-oxo-5-aminopyrimidine-tagged oligomers were synthesized, but difficulties in deprotection, purification, and isolation thwarted further investigations. The acyclic phosphate backbone structure of the protected oligomer seems to be prone to an eliminative degradation owing to the acidic hydrogen at the 2'-position--an arrangement that renders the oligomer vulnerable to the conditions used for the removal of the protecting groups on the heterocyclic recognition element. However, the free oligomers seem to be stable under the conditions investigated.
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Affiliation(s)
- Marcos Hernández-Rodríguez
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA-92037, USA
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Vitamin-B12-Mimetika mit einem Peptidrückgrat und einstellbaren Koordinations- und Redoxeigenschaften. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001928] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Zhou K, Zelder F. Vitamin B12 Mimics Having a Peptide Backbone and Tuneable Coordination and Redox Properties. Angew Chem Int Ed Engl 2010; 49:5178-80. [DOI: 10.1002/anie.201001928] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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16
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Šponer J, Vázquez-Mayagoitia Á, Sumpter B, Leszczynski J, Šponer J, Otyepka M, Banáš P, Fuentes-Cabrera M. Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues. Chemistry 2010; 16:3057-65. [DOI: 10.1002/chem.200902068] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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17
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Diederichsen U. Dynamic sequence modification: a design principle for synthetic informational oligomers. Chembiochem 2010; 10:2717-9. [PMID: 19830762 DOI: 10.1002/cbic.200900543] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ulf Diederichsen
- Georg-August-Universität Göttingen, Institut für Organische und Biomolekulare Chemie, Tammannstrasse 2, 37077 Göttingen, Germany.
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Zhang X, Krishnamurthy R. Mapping the landscape of potentially primordial informational oligomers: oligo-dipeptides tagged with orotic acid derivatives as recognition elements. Angew Chem Int Ed Engl 2010; 48:8124-8. [PMID: 19768828 DOI: 10.1002/anie.200904188] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xuejun Zhang
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Zhang X, Krishnamurthy R. Mapping the Landscape of Potentially Primordial Informational Oligomers: Oligo-dipeptides Tagged with Orotic Acid Derivatives as Recognition Elements. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Menor-Salván C, Ruiz-Bermejo DM, Guzmán MI, Osuna-Esteban S, Veintemillas-Verdaguer S. Synthesis of pyrimidines and triazines in ice: implications for the prebiotic chemistry of nucleobases. Chemistry 2009; 15:4411-8. [PMID: 19288488 DOI: 10.1002/chem.200802656] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Herein, we report the efficient synthesis of RNA bases and functionalized s-triazines from 0.1 M urea solutions in water after subjection to freeze-thaw cycles for three weeks. The icy solution was under a reductive, methane-based atmosphere, which was subjected to spark discharges as an energy source for the first 72 h of the experiment. Analysis of the products indicates the synthesis of the s-triazines cyanuric acid, ammeline, ammelide, and melamine, the pyrimidines cytosine, uracil, and 2,4-diaminopyrimidine, and the purine adenine. An experiment performed as a control at room temperature, with the urea solution in the liquid phase and with the same atmosphere and energy source, led to the synthesis of hydantoins and insoluble tholin, but there was no evidence of the synthesis of pyrimidines or triazines. The synthesis of pyrimidines from urea is possible under a methane/nitrogen atmosphere only at low temperature, in the solid phase. The generation of both pyrimidines and triazines in comparable yields from urea, together with a possible role for triazines as alternative nucleobases, opens new perspectives on the prebiotic chemistry of informational polymers.
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Affiliation(s)
- César Menor-Salván
- Centro de Astrobiología, Consejo Superior de Investigaciones Científicas, Instituto Nacional de Técnica Aeroespacial, Carretera Torrejón-Ajalvir, Km. 4,2, 28850 Torrejón de Ardoz, Madrid, Spain.
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Katalyse: R. Schrock geehrt / Organische Chemie Eschenmoser ausgezeichnet / Bioorganische Chemie: Preis für Rohmer. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200804463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Catalysis: R. Schrock Honored / Organic Chemistry: Eschenmoser Awarded / Bioorganic Chemistry: Prize to Rohmer. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/anie.200804463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Sutherland J. Die Suche nach einem genetischen Ursystem: jenseits RNA-verwandter Strukturen. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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