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Guzmán Ríos D, Romero MA, González-Delgado JA, Arteaga JF, Pischel U. Metal-Mediated Organocatalysis in Water: Serendipitous Discovery of Aldol Reaction Catalyzed by the [Ru(bpy) 2(nornicotine) 2] 2+ Complex. J Org Chem 2022; 87:5412-5418. [PMID: 35337184 PMCID: PMC10550203 DOI: 10.1021/acs.joc.2c00472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The [Ru(bpy)2(Nor)2]2+ complex (Nor = nornicotine) is an efficient catalyst for the aldol reaction of acetone with activated benzaldehydes in a buffered aqueous solution. The metal plays the role of an activator for the nornicotine organocatalyst ligands. The resulting catalytic activity is potentiated by a factor of about 4.5 as compared to free nornicotine. Similar rate enhancements can be achieved by using Zn(II) cations as the activator. The observations are rationalized with the reduced basicity of the pyrrolidine N in nornicotine due to the enhanced electron withdrawal of the metal-complexed pyridyl moiety.
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Affiliation(s)
- David Guzmán Ríos
- CIQSO—Center for Research in
Sustainable Chemistry and Department of Chemistry, University of Huelva, Campus de El Carmen s/n, Huelva E-21071, Spain
| | - Miguel A. Romero
- CIQSO—Center for Research in
Sustainable Chemistry and Department of Chemistry, University of Huelva, Campus de El Carmen s/n, Huelva E-21071, Spain
| | - José A. González-Delgado
- CIQSO—Center for Research in
Sustainable Chemistry and Department of Chemistry, University of Huelva, Campus de El Carmen s/n, Huelva E-21071, Spain
| | - Jesús F. Arteaga
- CIQSO—Center for Research in
Sustainable Chemistry and Department of Chemistry, University of Huelva, Campus de El Carmen s/n, Huelva E-21071, Spain
| | - Uwe Pischel
- CIQSO—Center for Research in
Sustainable Chemistry and Department of Chemistry, University of Huelva, Campus de El Carmen s/n, Huelva E-21071, Spain
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Okamura H, Crisp A, Hübner S, Becker S, Rovó P, Carell T. Proto-Urea-RNA (Wöhler RNA) Containing Unusually Stable Urea Nucleosides. Angew Chem Int Ed Engl 2019; 58:18691-18696. [PMID: 31573740 PMCID: PMC6916321 DOI: 10.1002/anie.201911746] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Indexed: 12/11/2022]
Abstract
The RNA world hypothesis assumes that life on Earth began with nucleotides that formed information-carrying RNA oligomers able to self-replicate. Prebiotic reactions leading to the contemporary nucleosides are now known, but their execution often requires specific starting materials and lengthy reaction sequences. It was therefore proposed that the RNA world was likely proceeded by a proto-RNA world constructed from molecules that were likely present on the early Earth in greater abundance. Herein, we show that the prebiotic starting molecules bis-urea (biuret) and tris-urea (triuret) are able to directly react with ribose. The urea-ribosides are remarkably stable because they are held together by a network of intramolecular, bifurcated hydrogen bonds. This even allowed the synthesis of phosphoramidite building blocks and incorporation of the units into RNA. Investigations of the nucleotides' base-pairing potential showed that triuret:G RNA base pairs closely resemble U:G wobble base pairs. Based on the probable abundance of urea on the early Earth, we postulate that urea-containing RNA bases are good candidates for a proto-RNA world.
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Affiliation(s)
- Hidenori Okamura
- Center for Integrated Protein Science (CiPS) at the Department of ChemistryLMU MünchenButenandtstr. 5–1381377MünchenGermany
| | - Antony Crisp
- Center for Integrated Protein Science (CiPS) at the Department of ChemistryLMU MünchenButenandtstr. 5–1381377MünchenGermany
| | - Sarah Hübner
- Center for Integrated Protein Science (CiPS) at the Department of ChemistryLMU MünchenButenandtstr. 5–1381377MünchenGermany
| | - Sidney Becker
- Center for Integrated Protein Science (CiPS) at the Department of ChemistryLMU MünchenButenandtstr. 5–1381377MünchenGermany
| | - Petra Rovó
- Center for Integrated Protein Science (CiPS) at the Department of ChemistryLMU MünchenButenandtstr. 5–1381377MünchenGermany
| | - Thomas Carell
- Center for Integrated Protein Science (CiPS) at the Department of ChemistryLMU MünchenButenandtstr. 5–1381377MünchenGermany
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Okamura H, Crisp A, Hübner S, Becker S, Rovó P, Carell T. Proto‐Urea‐RNA (Wöhler RNA) Containing Unusually Stable Urea Nucleosides. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911746] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Hidenori Okamura
- Center for Integrated Protein Science (CiPSM) at the Department of ChemistryLMU München Butenandtstr. 5–13 81377 München Germany
| | - Antony Crisp
- Center for Integrated Protein Science (CiPSM) at the Department of ChemistryLMU München Butenandtstr. 5–13 81377 München Germany
| | - Sarah Hübner
- Center for Integrated Protein Science (CiPSM) at the Department of ChemistryLMU München Butenandtstr. 5–13 81377 München Germany
| | - Sidney Becker
- Center for Integrated Protein Science (CiPSM) at the Department of ChemistryLMU München Butenandtstr. 5–13 81377 München Germany
| | - Petra Rovó
- Center for Integrated Protein Science (CiPSM) at the Department of ChemistryLMU München Butenandtstr. 5–13 81377 München Germany
| | - Thomas Carell
- Center for Integrated Protein Science (CiPSM) at the Department of ChemistryLMU München Butenandtstr. 5–13 81377 München Germany
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Katsuyama I, Chouthaiwale PV, Akama H, Cui HL, Tanaka F. Fluorogenic probes for aldol reactions: tuning of fluorescence using π-conjugation systems. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2013.10.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Photochemically relevant DNA-based molecular systems enabling chemical and signal transductions and their analytical applications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2012.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Silverman SK. DNA as a versatile chemical component for catalysis, encoding, and stereocontrol. Angew Chem Int Ed Engl 2011; 49:7180-201. [PMID: 20669202 DOI: 10.1002/anie.200906345] [Citation(s) in RCA: 201] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNA (deoxyribonucleic acid) is the genetic material common to all of Earth's organisms. Our biological understanding of DNA is extensive and well-exploited. In recent years, chemists have begun to develop DNA for nonbiological applications in catalysis, encoding, and stereochemical control. This Review summarizes key advances in these three exciting research areas, each of which takes advantage of a different subset of DNA's useful chemical properties.
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Affiliation(s)
- Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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Silverman SK. DNA - eine vielseitige chemische Verbindung für die Katalyse, zur Kodierung und zur Stereokontrolle. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906345] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Guo HM, Tanaka F. A fluorogenic aldehyde bearing a 1,2,3-triazole moiety for monitoring the progress of aldol reactions. J Org Chem 2009; 74:2417-24. [PMID: 19222210 PMCID: PMC2663967 DOI: 10.1021/jo900013w] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed a new type of fluorogenic aldehyde bearing a 1,2,3-triazole moiety that is useful for monitoring the progress of aldol reactions through an increase in fluorescence. Whereas 6-methoxy-2-naphthaldehyde was highly fluorescent, the fluorogenic aldehyde, 4-formylbenzene connected to the 6-methoxy-2-naphthyl group through a 1,2,3-triazole moiety, was essentially nonfluorescent in aqueous solutions. We suggest that the 4-formylphenyl group acts as a quencher to suppress the fluorescence of the 6-methoxy-2-naphthyltriazole moiety. The product of the aldol reaction of this aldehyde does not have a quenching moiety and showed more than 800-fold higher fluorescence than the aldehyde. Assay systems using the fluorogenic aldehyde were validated by screening of aldol catalysts, ranking of the activities of the catalysts, and evaluation of reaction conditions.
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Affiliation(s)
- Hai-Ming Guo
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Fujie Tanaka
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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Burton AS, Lehman N. DNA before proteins? Recent discoveries in nucleic acid catalysis strengthen the case. ASTROBIOLOGY 2009; 9:125-130. [PMID: 19215202 DOI: 10.1089/ast.2008.0240] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
An RNA-DNA World could arise from an all-RNA system with the development of as few as three ribozymes-a DNA-dependent RNA polymerase, an RNA-dependent DNA polymerase, and a catalyst for the production of DNA nucleotides. A significant objection to DNA preceding proteins is that RNA has not been shown to catalyze the production of DNA. However, RNA- and DNAzymes have been recently discovered that catalyze chemical reactions capable of forming deoxyribose, such as mixed aldol condensation of 5'-glyceryl- and 3'-glycoaldehyde-terminated DNA strands. Thus, the only remaining obstacles to RNA-catalyzed in vitro DNA synthesis are alterations of substrate and template specificities of known ribozymes. The RNA-DNA World lessens genomic size constraints through a relaxed error threshold, affording the evolutionary time needed to develop protein synthesis. Separation of information from catalyst enables genotype and phenotype to be readily discriminated by absence or presence, respectively, of the 2'-OH. Novel ribozymes that arise through mutation can be preserved in DNA by reverse transcription, which makes them much more likely to be retained than in an RNA-genome milieu. The extra degree of separation between protein and mRNA, in terms of identifying and then retaining a useful enzyme, may have in fact necessitated storing information in DNA prior to the advent of translation.
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Affiliation(s)
- Aaron S Burton
- Department of Chemistry, Portland State University, Portland, Oregon 97207, USA.
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Duarte FJS, Cabrita EJ, Frenking G, Santos AG. Mechanistic Study of Intramolecular Aldol Reactions of Dialdehydes. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800222] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Fan J, Sun G, Wan C, Wang Z, Li Y. Investigation of DNA as a catalyst for Henry reaction in water. Chem Commun (Camb) 2008:3792-4. [PMID: 18685779 DOI: 10.1039/b805767b] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Double-stranded DNA of natural origin can be used to facilitate nitro-aldol (or Henry) reaction in aqueous solution.
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Affiliation(s)
- Jinmin Fan
- Hefei National Laboratory for Physical Science at Microscale, Joint-Lab of Green Synthetic Chemistry and Department of Chemistry, University of Science and Technology of China, Hefei, 230026, P. R. China
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Fusz S, Srivatsan SG, Ackermann D, Famulok M. Photocleavable initiator nucleotide substrates for an aldolase ribozyme. J Org Chem 2008; 73:5069-77. [PMID: 18517252 DOI: 10.1021/jo800639p] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have previously reported the in vitro selection of a ribozyme that catalyzes an aldol reaction between a levulinic amide aldol donor and a benzaldehyde substrate. The selection scheme involved the priming of the RNA library with a levulinic amide aldol donor group that was introduced via transcription priming in the presence of a modified guanosine mononucleotide derivative. Here we provide a detailed description of the synthesis of the ribozyme substrates and the substrate oligonucleotides used for its isolation and characterization. The aldol donor group was attached to the phosphate moiety of guanosine monophosphate via a photocleavable linker molecule. This initiator nucleotide was efficiently incorporated into RNA molecules of differing sizes and composition by transcription priming with T7 RNA polymerase. With this method modified RNA oligonucleotides as small as a 6-mer sequence can be generated. A temperature profile of the intermolecular reaction indicates that the modified RNA hexamer binds the ribozyme largely by Watson-Crick pairing and only to a minor extent via the non-RNA moiety, whereas the ribozyme appears to have evolved a specific binding site for the aldehyde substrate.
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Affiliation(s)
- Stefan Fusz
- LIMES Institute, Program Unit Chemical Biology and Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie & Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
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Affiliation(s)
- Zhuo Tang
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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Egli M, Pallan PS, Pattanayek R, Wilds CJ, Lubini P, Minasov G, Dobler M, Leumann CJ, Eschenmoser A. Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system. J Am Chem Soc 2007; 128:10847-56. [PMID: 16910680 DOI: 10.1021/ja062548x] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An experimental rationalization of the structure type encountered in DNA and RNA by systematically investigating the chemical and physical properties of alternative nucleic acids has identified systems with a variety of sugar-phosphate backbones that are capable of Watson-Crick base pairing and in some cases cross-pairing with the natural nucleic acids. The earliest among the model systems tested to date, (4' --> 6')-linked oligo(2',3'-dideoxy-beta-d-glucopyranosyl)nucleotides or homo-DNA, shows stable self-pairing, but the pairing rules for the four natural bases are not the same as those in DNA. However, a complete interpretation and understanding of the properties of the hexapyranosyl (4' --> 6') family of nucleic acids has been impeded until now by the lack of detailed 3D-structural data. We have determined the crystal structure of a homo-DNA octamer. It reveals a weakly twisted right-handed duplex with a strong inclination between the hexose-phosphate backbones and base-pair axes, and highly irregular values for helical rise and twist at individual base steps. The structure allows a rationalization of the inability of allo-, altro-, and glucopyranosyl-based oligonucleotides to form stable pairing systems.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA.
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Brogan AP, Dickerson TJ, Janda KD. Enamine-Based Aldol Organocatalysis in Water: Are They Really “All Wet”? Angew Chem Int Ed Engl 2006; 45:8100-2. [PMID: 17001595 DOI: 10.1002/anie.200601392] [Citation(s) in RCA: 268] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Brogan AP, Dickerson TJ, Janda KD. Enamine-Based Aldol Organocatalysis in Water: Are They Really “All Wet”? Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200601392] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Miduturu CV, Silverman SK. Synthesis and Application of a 5‘-Aldehyde Phosphoramidite for Covalent Attachment of DNA to Biomolecules. J Org Chem 2006; 71:5774-7. [PMID: 16839163 DOI: 10.1021/jo060723m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We recently reported the use of covalently attached DNA as a structural constraint for rational control of macromolecular conformation. Reductive amination was employed to attach each strand of the duplex DNA constraint to RNA, utilizing an aldehyde tethered to the 5'-terminus of the DNA. Here we describe the synthesis of a thymidine phosphoramidite that has the 5'-tethered aldehyde masked as a 1,2-diol. We also describe optimized reductive amination conditions for linking 5'-aldehyde-DNA with 2'-amino-2'-deoxy-RNA. These procedures should be generally applicable for attaching DNA to biomolecules.
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Affiliation(s)
- Chandrasekhar V Miduturu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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Affiliation(s)
- Magnus Rueping
- Degussa Endowed Professorship, Institute for Organic Chemistry und Chemical Biology, Johann Wolfgang Goethe University Frankfurt am Main, Germany.
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