1
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Šponer JE, Šponer J, Výravský J, Matyášek R, Kovařík A, Dudziak W, Ślepokura K. Crystallization as a selection force at the polymerization of nucleotides in a prebiotic context. iScience 2023; 26:107600. [PMID: 37664611 PMCID: PMC10470394 DOI: 10.1016/j.isci.2023.107600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/14/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
Accumulation and selection of nucleotides is one of the most challenging problems surrounding the origin of the first RNA molecules on our planet. In the current work we propose that guanosine 3',5' cyclic monophosphate could selectively crystallize upon evaporation of an acidic prebiotic pool containing various other nucleotides. The conditions of the evaporative crystallization are fully compatible with the subsequent acid catalyzed polymerization of this cyclic nucleotide reported in earlier studies and may be relevant in a broad range of possible prebiotic environments. Albeit cytidine 3',5' cyclic monophosphate has the ability to selectively accumulate under the same conditions, its crystal structure is not likely to support polymer formation.
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Affiliation(s)
- Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Jakub Výravský
- TESCAN Brno, s.r.o, Libušina třída 1, 62300 Brno, Czech Republic
- Department of Geological Sciences, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Roman Matyášek
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Wojciech Dudziak
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
| | - Katarzyna Ślepokura
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
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2
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Martínez RF, Cuccia LA, Viedma C, Cintas P. On the Origin of Sugar Handedness: Facts, Hypotheses and Missing Links-A Review. ORIGINS LIFE EVOL B 2022; 52:21-56. [PMID: 35796896 DOI: 10.1007/s11084-022-09624-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/24/2022] [Indexed: 11/30/2022]
Abstract
By paraphrasing one of Kipling's most amazing short stories (How the Leopard Got His Spots), this article could be entitled "How Sugars Became Homochiral". Obviously, we have no answer to this still unsolved mystery, and this perspective simply brings recent models, experiments and hypotheses into the homochiral homogeneity of sugars on earth. We shall revisit the past and current understanding of sugar chirality in the context of prebiotic chemistry, with attention to recent developments and insights. Different scenarios and pathways will be discussed, from the widely known formose-type processes to less familiar ones, often viewed as unorthodox chemical routes. In particular, problems associated with the spontaneous generation of enantiomeric imbalances and the transfer of chirality will be tackled. As carbohydrates are essential components of all cellular systems, astrochemical and terrestrial observations suggest that saccharides originated from environmentally available feedstocks. Such substances would have been capable of sustaining autotrophic and heterotrophic mechanisms integrating nutrients, metabolism and the genome after compartmentalization. Recent findings likewise indicate that sugars' enantiomeric bias may have emerged by a transfer of chirality mechanisms, rather than by deracemization of sugar backbones, yet providing an evolutionary advantage that fueled the cellular machinery.
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Affiliation(s)
- R Fernando Martínez
- Departamento de Química Orgánica E Inorgánica, Facultad de Ciencias, and Instituto Universitario de Investigación del Agua, Cambio Climático Y Sostenibilidad, (IACYS), Universidad de Extremadura, Avenida de Elvas s/n, 06006, Badajoz, Spain.
| | - Louis A Cuccia
- Department of Chemistry and Biochemistry, Quebec Centre for Advanced Materials (QCAM/CQMF), FRQNT, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6, Canada
| | - Cristóbal Viedma
- Department of Crystallography and Mineralogy, University Complutense, 28040, Madrid, Spain
| | - Pedro Cintas
- Departamento de Química Orgánica E Inorgánica, Facultad de Ciencias, and Instituto Universitario de Investigación del Agua, Cambio Climático Y Sostenibilidad, (IACYS), Universidad de Extremadura, Avenida de Elvas s/n, 06006, Badajoz, Spain.
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3
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Beyranvand E, Karami B, Farahi M, Akrami S. Silica Tungstic Acid as a Recyclable Catalyst to Synthesis of Benzo[5,6]Chromeno[2,3- b]Quinolins under Green Conditions. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2020.1827274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
| | - Bahador Karami
- Department of Chemistry, Yasouj University, Yasouj, Iran
| | - Mahnaz Farahi
- Department of Chemistry, Yasouj University, Yasouj, Iran
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4
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Lin H, Jiménez EI, Arriola JT, Müller UF, Krishnamurthy R. Concurrent Prebiotic Formation of Nucleoside‐Amidophosphates and Nucleoside‐Triphosphates Potentiates Transition from Abiotic to Biotic Polymerization. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Huacan Lin
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
| | - Eddy I. Jiménez
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Joshua T. Arriola
- Department of Chemistry and Biochemistry UC San Diego 9500 Gilman Drive La Jolla CA 92037 USA
| | - Ulrich F. Müller
- Department of Chemistry and Biochemistry UC San Diego 9500 Gilman Drive La Jolla CA 92037 USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
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5
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Formation of the Codon Degeneracy during Interdependent Development between Metabolism and Replication. Genes (Basel) 2021; 12:genes12122023. [PMID: 34946975 PMCID: PMC8701183 DOI: 10.3390/genes12122023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022] Open
Abstract
Nirenberg's genetic code chart shows a profound correspondence between codons and amino acids. The aim of this article is to try to explain the primordial formation of the codon degeneracy. It remains a puzzle how informative molecules arose from the supposed prebiotic random sequences. If introducing an initial driving force based on the relative stabilities of triplex base pairs, the prebiotic sequence evolution became innately nonrandom. Thus, the primordial assignment of the 64 codons to the 20 amino acids has been explained in detail according to base substitutions during the coevolution of tRNAs with aaRSs; meanwhile, the classification of aaRSs has also been explained.
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6
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Lin H, Jiménez EI, Arriola JT, Müller UF, Krishnamurthy R. Concurrent Prebiotic Formation of Nucleoside-Amidophosphates and Nucleoside-Triphosphates Potentiates Transition from Abiotic to Biotic Polymerization. Angew Chem Int Ed Engl 2021; 61:e202113625. [PMID: 34738300 DOI: 10.1002/anie.202113625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Indexed: 11/10/2022]
Abstract
Polymerization of nucleic acids in biology utilizes 5'-nucleoside triphosphates (NTPs) as substrates. The prebiotic availability of NTPs has been unresolved and other derivatives of nucleoside-monophosphates (NMPs) have been studied. However, this latter approach necessitates a change in chemistries when transitioning to biology. Herein we show that diamidophosphate (DAP), in a one-pot amidophosphorylation-hydrolysis setting converts NMPs into the corresponding NTPs via 5'-nucleoside amidophosphates (NaPs). The resulting crude mixture of NTPs are accepted by proteinaceous- and ribozyme-polymerases as substrates for nucleic acid polymerization. This phosphorylation also operates at the level of oligonucleotides enabling ribozyme-mediated ligation. This one-pot protocol for simultaneous generation of NaPs and NTPs suggests that the transition from prebiotic-phosphorylation and oligomerization to an enzymatic processive-polymerization can be more continuous than previously anticipated.
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Affiliation(s)
- Huacan Lin
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.,NSF-NASA Center for Chemical Evolution, Atlanta, GA, 30332, USA
| | - Eddy I Jiménez
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Joshua T Arriola
- Department of Chemistry and Biochemistry, UC San Diego, 9500 Gilman Drive, La Jolla, CA, 92037, USA
| | - Ulrich F Müller
- Department of Chemistry and Biochemistry, UC San Diego, 9500 Gilman Drive, La Jolla, CA, 92037, USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.,NSF-NASA Center for Chemical Evolution, Atlanta, GA, 30332, USA
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7
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Jiménez EI, Gibard C, Krishnamurthy R. Prebiotic Phosphorylation and Concomitant Oligomerization of Deoxynucleosides to form DNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Eddy I. Jiménez
- The Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Clémentine Gibard
- The Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Ramanarayanan Krishnamurthy
- The Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
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8
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Jiménez EI, Gibard C, Krishnamurthy R. Prebiotic Phosphorylation and Concomitant Oligomerization of Deoxynucleosides to form DNA. Angew Chem Int Ed Engl 2021; 60:10775-10783. [PMID: 33325148 DOI: 10.1002/anie.202015910] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Indexed: 12/14/2022]
Abstract
Recent demonstrations of RNA-DNA chimeras (RDNA) enabling RNA and DNA replication, coupled with prebiotic co-synthesis of deoxyribo- and ribo-nucleotides, have resurrected the hypothesis of co-emergence of RNA and DNA. As further support, we show that diamidophosphate (DAP) with 2-aminoimidazole (amido)phosphorylates and oligomerizes deoxynucleosides to form DNA-under conditions similar to those of ribonucleosides. The pyrimidine deoxynucleoside 5'-O-amidophosphates are formed in good (≈60 %) yields. Intriguingly, the presence of pyrimidine deoxynucleos(t)ides increased the yields of purine deoxynucleotides (≈20 %). Concomitantly, oligomerization (≈18-31 %) is observed with predominantly 3',5'-phosphodiester DNA linkages, and some (<5 %) pyrophosphates. Combined with previous observations of DAP-mediated chemistries and the constructive role of RDNA chimeras, the results reported here help set the stage for systematic investigation of a systems chemistry approach of RNA-DNA coevolution.
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Affiliation(s)
- Eddy I Jiménez
- The Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Clémentine Gibard
- The Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Ramanarayanan Krishnamurthy
- The Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
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9
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Imtiaz S, Ahmad War J, Banoo S, Khan S. α-Aminoazoles/azines: key reaction partners for multicomponent reactions. RSC Adv 2021; 11:11083-11165. [PMID: 35423648 PMCID: PMC8695948 DOI: 10.1039/d1ra00392e] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 02/23/2021] [Indexed: 12/28/2022] Open
Abstract
Aromatic α-aminoazaheterocycles are the focus of significant investigations and exploration by researchers owing to their key role in diverse biological and physiological processes. The existence of their derivatives in numerous drugs and alkaloids is due to their heterocyclic nitrogenous nature. Therefore, the synthesis of a structurally diverse range of their derivatives through simple and convenient methods represents a vital field of synthetic organic chemistry. Multicomponent reactions (MCRs) provide a platform to introduce desirable structure diversity and complexity into a molecule in a single operation with a significant reduction in the use of harmful organic waste, and hence have attracted particular attention as an excellent tool to access these derivatives. This review covers the advances made from 2010 to the beginning of 2020 in terms of the utilization of α-aminoazaheterocycles as synthetic precursors in MCRs.
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Affiliation(s)
- Shah Imtiaz
- Department of Chemistry, Aligarh Muslim University Aligarh India-202002
| | - Jahangir Ahmad War
- Department of Chemistry, National Institute of Technology Kashmir India-190006
| | - Syqa Banoo
- Department of Chemistry, Mangalayatan University Beswan Aligarh India-202146
| | - Sarfaraz Khan
- Department of Chemistry, Aligarh Muslim University Aligarh India-202002
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10
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Foden CS, Islam S, Fernández-García C, Maugeri L, Sheppard TD, Powner MW. Prebiotic synthesis of cysteine peptides that catalyze peptide ligation in neutral water. Science 2020; 370:865-869. [PMID: 33184216 DOI: 10.1126/science.abd5680] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/01/2020] [Indexed: 01/26/2023]
Abstract
Peptide biosynthesis is performed by ribosomes and several other classes of enzymes, but a simple chemical synthesis may have created the first peptides at the origins of life. α-Aminonitriles-prebiotic α-amino acid precursors-are generally produced by Strecker reactions. However, cysteine's aminothiol is incompatible with nitriles. Consequently, cysteine nitrile is not stable, and cysteine has been proposed to be a product of evolution, not prebiotic chemistry. We now report a high-yielding, prebiotic synthesis of cysteine peptides. Our biomimetic pathway converts serine to cysteine by nitrile-activated dehydroalanine synthesis. We also demonstrate that N-acylcysteines catalyze peptide ligation, directly coupling kinetically stable-but energy-rich-α-amidonitriles to proteinogenic amines. This rare example of selective and efficient organocatalysis in water implicates cysteine as both catalyst and precursor in prebiotic peptide synthesis.
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Affiliation(s)
- Callum S Foden
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Saidul Islam
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | | | - Leonardo Maugeri
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Tom D Sheppard
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Matthew W Powner
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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11
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Yi R, Tran QP, Ali S, Yoda I, Adam ZR, Cleaves HJ, Fahrenbach AC. A continuous reaction network that produces RNA precursors. Proc Natl Acad Sci U S A 2020; 117:13267-13274. [PMID: 32487725 PMCID: PMC7306801 DOI: 10.1073/pnas.1922139117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Continuous reaction networks, which do not rely on purification or timely additions of reagents, serve as models for chemical evolution and have been demonstrated for compounds thought to have played important roles for the origins of life such as amino acids, hydroxy acids, and sugars. Step-by-step chemical protocols for ribonucleotide synthesis are known, but demonstrating their synthesis in the context of continuous reaction networks remains a major challenge. Herein, compounds proposed to be important for prebiotic RNA synthesis, including glycolaldehyde, cyanamide, 2-aminooxazole, and 2-aminoimidazole, are generated from a continuous reaction network, starting from an aqueous mixture of NaCl, NH4Cl, phosphate, and HCN as the only carbon source. No well-timed addition of any other reagents is required. The reaction network is driven by a combination of γ radiolysis and dry-down. γ Radiolysis results in a complex mixture of organics, including the glycolaldehyde-derived glyceronitrile and cyanamide. This mixture is then dried down, generating free glycolaldehyde that then reacts with cyanamide/NH3 to furnish a combination of 2-aminooxazole and 2-aminoimidazole. This continuous reaction network models how precursors for generating RNA and other classes of compounds may arise spontaneously from a complex mixture that originates from simple reagents.
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Affiliation(s)
- Ruiqin Yi
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Quoc Phuong Tran
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sarfaraz Ali
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Isao Yoda
- Co-60 Radiation Facility, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Zachary R Adam
- Department of Planetary Sciences, University of Arizona, Tucson, AZ 85721
- Blue Marble Space Institute of Science, Seattle, WA 98154
| | - H James Cleaves
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
- Blue Marble Space Institute of Science, Seattle, WA 98154
- Program in Interdisciplinary Studies, Institute for Advanced Study, Princeton, NJ 08540
| | - Albert C Fahrenbach
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia;
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12
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Kerkeni B, Bacchus-Montabonel MC. Proton-Induced Charge Transfer on Imidazole and 2-Aminoimidazole. Role of the Substituent and Influence of Stepwise Hydration. J Phys Chem A 2020; 124:1003-1010. [PMID: 31935089 DOI: 10.1021/acs.jpca.9b10602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The behavior of potential prebiotic species in space is of main concern in the chemistry at the origin of life. Their reactivity or stability in spatial conditions, under strong UV radiations or ion bombardments, remains an open question and needs wide investigations. As protons are by far the most abundant ions in space, we focus presently on proton-induced collisions on imidazole and 2-aminoimidazole evidenced as important prebiotic RNA intermediates. Unconstrained full optimization of the structures was performed with B3LYP/cc-pVTZ model chemistry. The calculations were performed in a wide collision energy range in order to model various astrophysical environments, from eV in the interstellar medium, up to keV for solar winds or supernovae shock-wave protons. Such a study provides for the first time a theoretical insight on the influence of the amino substituent on the proton-induced charge transfer. We evaluated the role of icy grain environments through a cluster approach modeling the effect of a stepwise microhydration on the process. Comparisons with oxygenated and sulfurated analogues address further qualitative trends on the respective stability or reactivity of such heterocycles which may be of tremendous interest in prebiotic chemistry. Charge transfer appears to be quite efficient for imidazole compounds and their sulfurated analogue compared to the oxygenated heterocycle.
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Affiliation(s)
- Boutheïna Kerkeni
- Département de Physique, Laboratoire de Physique de la Matière Condensée, Faculté des Sciences de Tunis , Université de Tunis el Manar , Campus Universitaire , 2092 Tunis , Tunisia.,Institut Supérieur des Arts Multimédia de la Manouba , Université de la Manouba , 2010 La Manouba , Tunisia.,Université Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 Villeurbanne , France
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13
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Abstract
The chemistry of abiotic nucleotide synthesis of RNA and DNA in the context of their prebiotic origins on early earth is a continuing challenge. How did (or how can) the nucleotides form and assemble from the small molecule inventories and under conditions that prevailed on early earth 3.5-4 billion years ago? This review provides a background and up-to-date progress that will allow the reader to judge where the field stands currently and what remains to be achieved. We start with a brief primer on the biological synthesis of nucleotides, followed by an extensive focus on the prebiotic formation of the components of nucleotides-either via the synthesis of ribose and the canonical nucleobases and then joining them together or by building both the conjoined sugar and nucleobase, part-by-part-toward the ultimate goal of forming RNA and DNA by polymerization. The review will emphasize that there are-and will continue to be-many more questions than answers from the synthetic, mechanistic, and analytical perspectives. We wrap up the review with a cautionary note in this context about coming to conclusions as to whether the problem of chemistry of prebiotic nucleotide synthesis has been solved.
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Affiliation(s)
- Mahipal Yadav
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Ravi Kumar
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
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14
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Bhowmik S, Krishnamurthy R. The role of sugar-backbone heterogeneity and chimeras in the simultaneous emergence of RNA and DNA. Nat Chem 2019; 11:1009-1018. [PMID: 31527850 PMCID: PMC6815252 DOI: 10.1038/s41557-019-0322-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/31/2019] [Indexed: 01/01/2023]
Abstract
Hypotheses of the origins of RNA and DNA are generally centred on the prebiotic synthesis of a pristine system (pre-RNA or RNA), which gives rise to its descendent. However, a lack of specificity in the synthesis of genetic polymers would probably result in chimeric sequences; the roles and fate of such sequences are unknown. Here, we show that chimeras, exemplified by mixed threose nucleic acid (TNA)-RNA and RNA-DNA oligonucleotides, preferentially bind to, and act as templates for, homogeneous TNA, RNA and DNA ligands. The chimeric templates can act as a catalyst that mediates the ligation of oligomers to give homogeneous backbone sequences, and the regeneration of the chimeric templates potentiates a scenario for a possible cross-catalytic cycle with amplification. This process provides a proof-of-principle demonstration of a heterogeneity-to-homogeneity scenario and also gives credence to the idea that DNA could appear concurrently with RNA, instead of being its later descendent.
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Affiliation(s)
- Subhendu Bhowmik
- The Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
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15
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Abstract
The central dogma of molecular biology rests on two kinds of asymmetry between genomes and enzymes: informatic asymmetry, where information flows from genomes to enzymes but not from enzymes to genomes; and catalytic asymmetry, where enzymes provide chemical catalysis but genomes do not. How did these asymmetries originate? Here, we show that these asymmetries can spontaneously arise from conflict between selection at the molecular level and selection at the cellular level. We developed a model consisting of a population of protocells, each containing a population of replicating catalytic molecules. The molecules are assumed to face a trade-off between serving as catalysts and serving as templates. This trade-off causes conflicting multilevel selection: serving as catalysts is favoured by selection between protocells, whereas serving as templates is favoured by selection between molecules within protocells. This conflict induces informatic and catalytic symmetry breaking, whereby the molecules differentiate into genomes and enzymes, establishing the central dogma. We show mathematically that the symmetry breaking is caused by a positive feedback between Fisher’s reproductive values and the relative impact of selection at different levels. This feedback induces a division of labour between genomes and enzymes, provided variation at the molecular level is sufficiently large relative to variation at the cellular level, a condition that is expected to hinder the evolution of altruism. Taken together, our results suggest that the central dogma is a logical consequence of conflicting multilevel selection.
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Affiliation(s)
- Nobuto Takeuchi
- Research Center for Complex Systems Biology, Graduate School of Arts and Sciences, University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan.,School of Biological Sciences, Faculty of Science, University of Auckland, Private Bag 92019, 1142 Auckland, New Zealand
| | - Kunihiko Kaneko
- Research Center for Complex Systems Biology, Graduate School of Arts and Sciences, University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan.,Department of Basic Science, Graduate School of Arts and Sciences, University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan
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16
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Lavado N, de la Concepción JG, Babiano R, Cintas P, Light ME. Interactions of Amino Acids and Aminoxazole Derivatives: Cocrystal Formation and Prebiotic Implications Enabled by Computational Analysis. ORIGINS LIFE EVOL B 2019; 49:163-185. [PMID: 31327111 DOI: 10.1007/s11084-019-09582-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/01/2019] [Indexed: 11/26/2022]
Abstract
In line with the postulated intermediacy of aminoxazoles derived from small sugars toward the direct assembly of nucleoside precursors, we show here a potential prebiotic scenario where aminoxazolines might have also played further roles as complexing and/or sequestering agents of other primeval blocks, namely amino acids. To this end, a bis-aminoxazoline derivative, generated from dihydroxyacetone and cyanamide, gives rise to stable co-crystal forms with dicarboxylic amino acids (Asp and Glu), while ionic interactions owing to proton transfer are inferred from spectroscopic data in aqueous solution. The structure of a 1:2 aminoxazoline: aspartic acid complex, discussed in detail, was elucidated by X-ray diffractometry. Optimized geometries of such ionic structures with bulk aqueous solvation were assessed by DFT calculations, which disclose preferential arrangements that validate the experimental data. Peripherally, we were able to detect in a few cases amino acid dimerization (i.e. dipeptide formation) after prolonged incubation with the bis-aminoxazole derivative. A mechanistic simulation aided by computation provides some predictive conclusions for future explorations and catalytic design.
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Affiliation(s)
- Nieves Lavado
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, Avenida de Elvas s/n, E-06006, Badajoz, Spain.
| | - Juan García de la Concepción
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, Avenida de Elvas s/n, E-06006, Badajoz, Spain.
| | - Reyes Babiano
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, Avenida de Elvas s/n, E-06006, Badajoz, Spain
| | - Pedro Cintas
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX, Avenida de Elvas s/n, E-06006, Badajoz, Spain
| | - Mark E Light
- Department of Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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Xu J, Green NJ, Gibard C, Krishnamurthy R, Sutherland JD. Prebiotic phosphorylation of 2-thiouridine provides either nucleotides or DNA building blocks via photoreduction. Nat Chem 2019; 11:457-462. [PMID: 30936523 DOI: 10.1038/s41557-019-0225-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 01/25/2019] [Indexed: 11/09/2022]
Abstract
Breakthroughs in the study of the origin of life have demonstrated how some of the building blocks essential to biology could have been formed under various primordial scenarios, and could therefore have contributed to the chemical evolution of life. Missing building blocks are then sometimes inferred to be products of primitive biosynthesis, which can stretch the limits of plausibility. Here, we demonstrate the synthesis of 2'-deoxy-2-thiouridine, and subsequently 2'-deoxyadenosine and 2-deoxyribose, under prebiotic conditions. 2'-Deoxy-2-thiouridine is produced by photoreduction of 2,2'-anhydro-2-thiouridine, which is in turn formed by phosphorylation of 2-thiouridine-an intermediate of prebiotic RNA synthesis. 2'-Deoxy-2-thiouridine is an effective deoxyribosylating agent and may have functioned as such in either abiotic or proto-enzyme-catalysed pathways to DNA, as demonstrated by its conversion to 2'-deoxyadenosine by reaction with adenine, and 2-deoxyribose by hydrolysis. An alternative prebiotic phosphorylation of 2-thiouridine leads to the formation of its 5'-phosphate, showing that hypotheses in which 2-thiouridine was a key component of early RNA sequences are within the bounds of synthetic credibility.
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Affiliation(s)
- Jianfeng Xu
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Clémentine Gibard
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
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18
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Bacchus-Montabonel MC. Role of sulfur in proton-induced collisions of RNA prebiotic precursors. Phys Chem Chem Phys 2019; 21:1428-1434. [PMID: 30601542 DOI: 10.1039/c8cp07204c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A main objective in the synthesis of prebiotic compounds is to remain consistent with reasonable geochemical scenarios, while avoiding concomitant formation of undesirable by-products. In this context, 2-aminothiazole has shown enhanced selectivity in the addition reaction with sugars promoting interest in this sulfur species compared to its oxygenated analogue, 2-aminooxazole. More generally, the role of sulfur in prebiotic chemistry needs to be widely investigated with regard to the numerous sulfur-containing molecules detected recently in different astrophysical environments. However, in parallel to the problematic formation of building blocks of life, how prebiotic molecules could survive under extreme astrophysical conditions remains an open question. Intense UV radiation or ion bombardment may indeed lead to fragmentation and the specific behaviour of sulfur compounds has to be addressed. Focusing on its potentiality in prebiotic multistep synthesis, a detailed analysis of the proton impact on 2-aminothiazole has been investigated theoretically in a wide collision energy range chosen to model various astrophysical environments. The comparison with its oxygenated analogue may suggest qualitative trends on their respective stability under such processes which could be of crucial interest for prebiotic synthesis.
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Anderson BA, Krishnamurthy R. Heterogeneous Pyrophosphate-Linked DNA-Oligonucleotides: Aversion to DNA but Affinity for RNA. Chemistry 2018. [PMID: 29532524 DOI: 10.1002/chem.201800538] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pyrophosphate linkages are important in extant biology and are hypothesized to have played a role in prebiotic chemistry and in the origination of oligonucleotides. Inspired by pyrophosphate as backbones of primordial oligomers, DNA oligomers with varying amounts of pyrophosphate inserts (ppDNA) were synthesized and investigated for their base-pairing properties. As expected, pyrophosphate inserts into the backbone compromised the thermal stability of ppDNA-DNA duplexes. In contrast, the ppDNA-RNA duplex exhibited, remarkably, duplex stability, even with accumulation of pyrophosphate linkages. This seems to be a consequence of an increase in the diameter of the double-helix with eight-bond-repeat units, and higher inclination of the base-pair axis with respect to the backbone in RNA (A-form), compared with that in DNA (B-form). These results suggest that pyrophosphate-linked oligonucleotides could harbor functional capabilities with implications for their roles in the origins of life and chemical biology.
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Affiliation(s)
- Brooke A Anderson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
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20
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Kumar VA. Evolution of specific 3'-5'-linkages in RNA in pre-biotic soup: a new hypothesis. Org Biomol Chem 2018; 14:10123-10133. [PMID: 27714238 DOI: 10.1039/c6ob01796g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This article reviews the different possibilities towards progression of the formation of DNA/RNA in the chemical world, before life, in enzyme-free conditions. The advent of deoxyribo- and ribopentose-sugars, nucleosides, nucleotides and oligonucleotides in the prebiotic soup is briefly discussed. Further, the formation of early single stranded oligomers, base-pairing possibilities and information transfer based on the stability parameters of the derived duplexes is reviewed. Each theory has its own merits and demerits which we have elaborated upon. Lastly, using clues from this literature, a possible explanation for the specific 3'-5'-linkages in RNA is proposed.
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Affiliation(s)
- Vaijayanti A Kumar
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune, 411008, India.
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21
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Farahi M, Karami B, Tanuraghaj HM, Bazrafshan Z. A Novel One-pot Protocol for Silica Sodium Carbonate-Catalyzed Synthesis of Pyrano[2,3- h
]coumarins. J Heterocycl Chem 2018. [DOI: 10.1002/jhet.3014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mahnaz Farahi
- Department of Chemistry; Yasouj University; Yasouj 75918-74831 Iran
| | - Bahador Karami
- Department of Chemistry; Yasouj University; Yasouj 75918-74831 Iran
| | | | - Zahra Bazrafshan
- Department of Chemistry; Yasouj University; Yasouj 75918-74831 Iran
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Fernández-García C, Coggins AJ, Powner MW. A Chemist's Perspective on the Role of Phosphorus at the Origins of Life. Life (Basel) 2017; 7:E31. [PMID: 28703763 PMCID: PMC5617956 DOI: 10.3390/life7030031] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/06/2017] [Accepted: 07/11/2017] [Indexed: 11/17/2022] Open
Abstract
The central role that phosphates play in biological systems, suggests they also played an important role in the emergence of life on Earth. In recent years, numerous important advances have been made towards understanding the influence that phosphates may have had on prebiotic chemistry, and here, we highlight two important aspects of prebiotic phosphate chemistry. Firstly, we discuss prebiotic phosphorylation reactions; we specifically contrast aqueous electrophilic phosphorylation, and aqueous nucleophilic phosphorylation strategies, with dry-state phosphorylations that are mediated by dissociative phosphoryl-transfer. Secondly, we discuss the non-structural roles that phosphates can play in prebiotic chemistry. Here, we focus on the mechanisms by which phosphate has guided prebiotic reactivity through catalysis or buffering effects, to facilitating selective transformations in neutral water. Several prebiotic routes towards the synthesis of nucleotides, amino acids, and core metabolites, that have been facilitated or controlled by phosphate acting as a general acid-base catalyst, pH buffer, or a chemical buffer, are outlined. These facile and subtle mechanisms for incorporation and exploitation of phosphates to orchestrate selective, robust prebiotic chemistry, coupled with the central and universally conserved roles of phosphates in biochemistry, provide an increasingly clear message that understanding phosphate chemistry will be a key element in elucidating the origins of life on Earth.
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Stairs S, Nikmal A, Bučar DK, Zheng SL, Szostak JW, Powner MW. Divergent prebiotic synthesis of pyrimidine and 8-oxo-purine ribonucleotides. Nat Commun 2017; 8:15270. [PMID: 28524845 PMCID: PMC5454461 DOI: 10.1038/ncomms15270] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/15/2017] [Indexed: 01/17/2023] Open
Abstract
Understanding prebiotic nucleotide synthesis is a long standing challenge thought to be essential to elucidating the origins of life on Earth. Recently, remarkable progress has been made, but to date all proposed syntheses account separately for the pyrimidine and purine ribonucleotides; no divergent synthesis from common precursors has been proposed. Moreover, the prebiotic syntheses of pyrimidine and purine nucleotides that have been demonstrated operate under mutually incompatible conditions. Here, we tackle this mutual incompatibility by recognizing that the 8-oxo-purines share an underlying generational parity with the pyrimidine nucleotides. We present a divergent synthesis of pyrimidine and 8-oxo-purine nucleotides starting from a common prebiotic precursor that yields the β-ribo-stereochemistry found in the sugar phosphate backbone of biological nucleic acids. The generational relationship between pyrimidine and 8-oxo-purine nucleotides suggests that 8-oxo-purine ribonucleotides may have played a key role in primordial nucleic acids prior to the emergence of the canonical nucleotides of biology.
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Affiliation(s)
- Shaun Stairs
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Arif Nikmal
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Dejan-Krešimir Bučar
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Shao-Liang Zheng
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Jack W Szostak
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.,Department of Molecular Biology and Center for Computational and Integrative Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
| | - Matthew W Powner
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
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Wang W, Huang F, Sun C, Liu J, Sheng X, Chen D. A theoretical insight into the formation mechanisms of C/N-ribonucleosides with pyrimidine and ribose. Phys Chem Chem Phys 2017; 19:10413-10426. [PMID: 28379245 DOI: 10.1039/c6cp08068e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The detailed formation mechanisms of C-ribonucleoside and N-ribonucleoside via the reaction of 2,4,6-triaminopyrimidine (TAP) with (d)-ribose in aqueous solution were explored using density functional theory (DFT). The calculations indicate that five isomers (α,β-furanose, α,β-pyranose and open-chain aldehyde) of (d)-ribose can exist in equilibrium in aqueous solution. In contrast to cyclic isomers, an open-chain aldehyde is most feasible to react with TAP. In general, the formation pathways of C-nucleoside and N-nucleoside proceed in three steps including nucleophilic addition, dehydration and cyclization. The calculated apparent activation energies are 28.8 kcal mol-1 and 29.2 kcal mol-1, respectively. It suggests that both C- and N-nucleoside can be formed in aqueous solution, which is in good agreement with the experimental results. The water molecule plays an important "H-bridge" role by the hydrogen atom relay. Finally, a model structure of nucleobase, which will be beneficial for the C-C glycosidic bond formation, is proposed.
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Affiliation(s)
- Wenjuan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
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25
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Xu H, Yan L, Qin Y, Xu Z, Ling Z, Rong L. An Efficient and Facile Multicomponent Reaction for the Synthesis of 5′,6′-dihydro-6′-hydroxy-6′-(trifluoromethyl)-1′H
-spiro[indoline-3,4′-pyrimidine]-2,2′(3′H
)-dione Derivatives under Solvent-Free Conditions. J Heterocycl Chem 2017. [DOI: 10.1002/jhet.2851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hui Xu
- School of Chemistry and Materials Science, Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials; Jiangsu Normal University; Xuzhou 221116 China
| | - Lirong Yan
- School of Chemistry and Materials Science, Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials; Jiangsu Normal University; Xuzhou 221116 China
| | - Yaqi Qin
- School of Chemistry and Materials Science, Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials; Jiangsu Normal University; Xuzhou 221116 China
| | - Zhongyun Xu
- School of Chemistry and Materials Science, Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials; Jiangsu Normal University; Xuzhou 221116 China
| | - Zhi Ling
- School of Chemistry and Materials Science, Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials; Jiangsu Normal University; Xuzhou 221116 China
| | - Liangce Rong
- School of Chemistry and Materials Science, Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials; Jiangsu Normal University; Xuzhou 221116 China
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27
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Prebiotic selection and assembly of proteinogenic amino acids and natural nucleotides from complex mixtures. Nat Chem 2017. [DOI: 10.1038/nchem.2703] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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28
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Xu YL, Teng QH, Tong W, Wang HS, Pan YM, Ma XL. Atom-Economic Synthesis of 4-Pyrones from Diynones and Water. Molecules 2017; 22:E109. [PMID: 28075414 PMCID: PMC6155647 DOI: 10.3390/molecules22010109] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/05/2017] [Accepted: 01/05/2017] [Indexed: 12/31/2022] Open
Abstract
Transition-metal-free synthesis of 4-pyrones via TfOH-promoted nucleophilic addition/cyclization of diynones and water has been developed. This transformation is simple, atom economical and environmentally benign, providing rapid and efficient access to substituted 4-pyrones.
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Affiliation(s)
- Yan-Li Xu
- College of Pharmacy, Guilin Medical University, Guilin 541004, China.
| | - Qing-Hu Teng
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, China.
| | - Wei Tong
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, China.
| | - Heng-Shan Wang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, China.
| | - Ying-Ming Pan
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, China.
| | - Xian-Li Ma
- College of Pharmacy, Guilin Medical University, Guilin 541004, China.
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29
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Steer AM, Bia N, Smith DK, Clarke PA. Prebiotic synthesis of 2-deoxy-d-ribose from interstellar building blocks promoted by amino esters or amino nitriles. Chem Commun (Camb) 2017; 53:10362-10365. [DOI: 10.1039/c7cc06083a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Amino esters and amino nitriles can promote the selective formation of 2-deoxy-d-ribose from materials present in interstellar ices. The use of amino nitriles suggests the possibility that carbohydrates may have existed before amino acids on the prebiotic Earth.
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Affiliation(s)
| | - Nicolas Bia
- Department of Chemistry
- University of York
- Heslington
- York
- UK
| | - David K. Smith
- Department of Chemistry
- University of York
- Heslington
- York
- UK
| | - Paul A. Clarke
- Department of Chemistry
- University of York
- Heslington
- York
- UK
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30
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Miyazaki J, Takiyama H, Nakata M. Isocyano compounds newly recognized in photochemical reaction of thiazole: matrix-isolation FT-IR and theoretical studies. RSC Adv 2017. [DOI: 10.1039/c6ra27496j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
UV-induced photoreactions of thiazole isolated in low-temperature argon matrices have been investigated, leading to the conclusion that photoproducts identified newly, including three kind isocyano compounds, are produced by ring-opening reaction.
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Affiliation(s)
- Jun Miyazaki
- Faculty of Pharmaceutical Sciences
- Hokuriku University
- Kanazawa
- Japan
- Department of Chemical Engineering
| | - Hiroshi Takiyama
- Department of Chemical Engineering
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
| | - Munetaka Nakata
- Graduate School of BASE (Bio-Applications and Systems Engineering)
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
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31
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Wu DZ, Zhi YG. An efficient method for the construction of 2-Aminothiazolo[5,4-c]pyridines via K3[Fe(CN)6] oxidized SP2 CH Functionalization. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.11.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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32
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Gavette JV, Stoop M, Hud NV, Krishnamurthy R. RNA-DNA Chimeras in the Context of an RNA World Transition to an RNA/DNA World. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607919] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jesse V. Gavette
- Department of Chemistry; The Scripps Research Institute; 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution; Atlanta GA 30332 USA
| | - Matthias Stoop
- Department of Chemistry; The Scripps Research Institute; 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution; Atlanta GA 30332 USA
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry; Georgia Institute of Technology; Atlanta GA 30332 USA
- NSF-NASA Center for Chemical Evolution; Atlanta GA 30332 USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry; The Scripps Research Institute; 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution; Atlanta GA 30332 USA
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Gavette JV, Stoop M, Hud NV, Krishnamurthy R. RNA-DNA Chimeras in the Context of an RNA World Transition to an RNA/DNA World. Angew Chem Int Ed Engl 2016; 55:13204-13209. [DOI: 10.1002/anie.201607919] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Jesse V. Gavette
- Department of Chemistry; The Scripps Research Institute; 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution; Atlanta GA 30332 USA
| | - Matthias Stoop
- Department of Chemistry; The Scripps Research Institute; 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution; Atlanta GA 30332 USA
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry; Georgia Institute of Technology; Atlanta GA 30332 USA
- NSF-NASA Center for Chemical Evolution; Atlanta GA 30332 USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry; The Scripps Research Institute; 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution; Atlanta GA 30332 USA
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Xie L, Huang F, Sun C, Liu J, Chen D. Mechanistic insight into the prebiotic syntheses of pyrimidine ribonucleotide and pyrimidine deoxynucleotide precursors. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Coggins AJ, Tocher DA, Powner MW. One-step protecting-group-free synthesis of azepinomycin in water. Org Biomol Chem 2015; 13:3378-81. [PMID: 25658692 DOI: 10.1039/c5ob00210a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report an efficient, atom economical general acid-base catalyzed one-step multi-gram synthesis of azepinomycin from commercially available compounds in water. We propose that the described pH-dependent Amadori rearrangement, which couples an amino-imidazole and simple sugar, is of importance as a potential step toward predisposed purine nucleotide synthesis at the origins of life.
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Affiliation(s)
- Adam J Coggins
- University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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36
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Strazewski P. Omne Vivum Ex Vivo … Omne? How to Feed an Inanimate Evolvable Chemical System so as to Let it Self-evolve into Increased Complexity and Life-like Behaviour. Isr J Chem 2015. [DOI: 10.1002/ijch.201400175] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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37
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Zhang J, Yao J, Liu J, Xue S, Li Y, Wang C. Four-component reaction between naphthols, substituted β-nitrostyrenes, substituted benzaldehydes and ammonium acetate in water–PEG-400: an approach to construct polysubstituted naphthofuranamines. RSC Adv 2015. [DOI: 10.1039/c5ra07642k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The diversity-oriented synthesis of naphtho[b]furans via a four-component reaction between naphthanols, substituted β-nitrostyrenes, substituted benzaldehydes and ammonium acetate has been developed.
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Affiliation(s)
- Jungui Zhang
- School of Chemistry and Chemical Engineering
- Yangzhou University
- Yangzhou 225002
- P. R. China
- New Division: School of Hydraulic
| | - Juan Yao
- School of Chemistry and Chemical Engineering
- Yangzhou University
- Yangzhou 225002
- P. R. China
| | - Jiaming Liu
- School of Chemistry and Chemical Engineering
- Yangzhou University
- Yangzhou 225002
- P. R. China
| | - Shuwen Xue
- School of Chemistry and Chemical Engineering
- Yangzhou University
- Yangzhou 225002
- P. R. China
| | - Yang Li
- School of Chemistry and Chemical Engineering
- Yangzhou University
- Yangzhou 225002
- P. R. China
| | - Cunde Wang
- School of Chemistry and Chemical Engineering
- Yangzhou University
- Yangzhou 225002
- P. R. China
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Rahmati A, Pashmforoush N. Synthesis of various heterocyclic compounds via multi-component reactions in water. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2014. [DOI: 10.1007/s13738-014-0562-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Cafferty BJ, Hud NV. Abiotic synthesis of RNA in water: a common goal of prebiotic chemistry and bottom-up synthetic biology. Curr Opin Chem Biol 2014; 22:146-57. [PMID: 25438801 DOI: 10.1016/j.cbpa.2014.09.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/13/2014] [Indexed: 01/01/2023]
Abstract
For more than half a century chemists have searched for a plausible prebiotic synthesis of RNA. The initial advances of the 1960s and 1970s were followed by decades of measured progress and a growing pessimism about overcoming remaining challenges. Fortunately, the past few years have provided a number of important advances, including new abiotic routes for the synthesis of nucleobases, nucleosides, and nucleotides. Recent discoveries also provide additional support for the hypothesis that RNA is the product of evolution, being preceded by ancestral genetic polymers, or pre-RNAs, that are synthesized more easily than RNA. In some cases, parallel searches for plausible prebiotic routes to RNA and pre-RNAs have provided more than one experimentally verified synthesis of RNA substructures and possible predecessors. Just as the synthesis of a contemporary biological molecule cannot be understood without knowledge of cellular metabolism, it is likely that an integrated approach that takes into account both plausible prebiotic reactions and plausible prebiotic environments will ultimately provide the most satisfactory and unifying chemical scenarios for the origin of nucleic acids. In this context, recent advances towards the abiotic synthesis of RNA and candidates for pre-RNAs are beginning to suggest that some molecules (e.g., urea) were multi-faceted contributors to the origin of nucleic acids, and the origin of life.
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Affiliation(s)
- Brian J Cafferty
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nicholas V Hud
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Parker ET, Zhou M, Burton AS, Glavin DP, Dworkin JP, Krishnamurthy R, Fernández FM, Bada JL. A Plausible Simultaneous Synthesis of Amino Acids and Simple Peptides on the Primordial Earth. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403683] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Parker ET, Zhou M, Burton AS, Glavin DP, Dworkin JP, Krishnamurthy R, Fernández FM, Bada JL. A Plausible Simultaneous Synthesis of Amino Acids and Simple Peptides on the Primordial Earth. Angew Chem Int Ed Engl 2014; 53:8132-6. [DOI: 10.1002/anie.201403683] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Indexed: 11/10/2022]
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Banerjee A, Ganguly G, Tripathi R, Nair NN, Paul A. Unearthing the Mechanism of Prebiotic Nitrile Bond Reduction in Hydrogen Cyanide through a Curious Association of Two Molecular Radical Anions. Chemistry 2014; 20:6348-57. [DOI: 10.1002/chem.201304627] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/24/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Ambar Banerjee
- Raman Centre for Atomic Molecular and Optical Sciences, Indian Association for the Cultivation of Science, 2A/2B Raja S.C. Mullick Road, Kolkata, 700032 (India)
| | - Gaurab Ganguly
- Raman Centre for Atomic Molecular and Optical Sciences, Indian Association for the Cultivation of Science, 2A/2B Raja S.C. Mullick Road, Kolkata, 700032 (India)
| | - Ravi Tripathi
- Department of Chemistry, Indian Institute of Technology Kanpur, IIT Kanpur, Kalyanpur, Kanpur, UP 208016 (India)
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, IIT Kanpur, Kalyanpur, Kanpur, UP 208016 (India)
| | - Ankan Paul
- Raman Centre for Atomic Molecular and Optical Sciences, Indian Association for the Cultivation of Science, 2A/2B Raja S.C. Mullick Road, Kolkata, 700032 (India)
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Gong W, Huang F, Sun C, Zhao X, Chen D. Mechanism and diastereoselectivity of the prebiotic synthesis of deoxyribonucleotide precursors C5-thiazoline: A DFT study. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.01.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Affiliation(s)
- Jimmy Gollihar
- Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
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Ruiz-Mirazo K, Briones C, de la Escosura A. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chem Rev 2013; 114:285-366. [DOI: 10.1021/cr2004844] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kepa Ruiz-Mirazo
- Biophysics
Unit (CSIC-UPV/EHU), Leioa, and Department of Logic and Philosophy
of Science, University of the Basque Country, Avenida de Tolosa 70, 20080 Donostia−San Sebastián, Spain
| | - Carlos Briones
- Department
of Molecular Evolution, Centro de Astrobiología (CSIC−INTA, associated to the NASA Astrobiology Institute), Carretera de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Andrés de la Escosura
- Organic
Chemistry Department, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Noe CR, Freissmuth J, Richter P, Miculka C, Lachmann B, Eppacher S. Formaldehyde-a key monad of the biomolecular system. Life (Basel) 2013; 3:486-501. [PMID: 25369818 PMCID: PMC4187169 DOI: 10.3390/life3030486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/17/2013] [Accepted: 07/30/2013] [Indexed: 11/16/2022] Open
Abstract
Experiments will be presented and reviewed to support the hypothesis that the intrinsic reactivity of formaldehyde may lead to the formation of a rather comprehensive set of defined biomolecules, including D-glucose, thus fostering concepts of evolution considering the existence of a premetabolic system as a primordial step in the generation of life.
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Affiliation(s)
- Christian R. Noe
- Department of Medicinal Chemistry, Faculty of Life Science University of Vienna, Althanstr. 14, Vienna 1090, Austria; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +43-676-7315051; Fax: +43-4277-9551
| | - Jerome Freissmuth
- Department of Pharmaceutical Chemistry, University of Frankfurt, Max-von-Laue-Str. 9, Frankfurt D-60438, Germany; E-Mails: (J.F.); (P.R.); (C.M.)
| | - Peter Richter
- Department of Pharmaceutical Chemistry, University of Frankfurt, Max-von-Laue-Str. 9, Frankfurt D-60438, Germany; E-Mails: (J.F.); (P.R.); (C.M.)
| | - Christian Miculka
- Department of Pharmaceutical Chemistry, University of Frankfurt, Max-von-Laue-Str. 9, Frankfurt D-60438, Germany; E-Mails: (J.F.); (P.R.); (C.M.)
| | - Bodo Lachmann
- Department of Medicinal Chemistry, Faculty of Life Science University of Vienna, Althanstr. 14, Vienna 1090, Austria; E-Mail:
| | - Simon Eppacher
- Department of Medicinal Chemistry, Faculty of Life Science University of Vienna, Althanstr. 14, Vienna 1090, Austria; E-Mail:
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Attwater J, Tagami S, Kimoto M, Butler K, Kool ET, Wengel J, Herdewijn P, Hirao I, Holliger P. Chemical fidelity of an RNA polymerase ribozyme. Chem Sci 2013. [DOI: 10.1039/c3sc50574j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Pinheiro VB, Loakes D, Holliger P. Synthetic polymers and their potential as genetic materials. Bioessays 2012; 35:113-22. [PMID: 23281109 DOI: 10.1002/bies.201200135] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DNA and RNA are the only known natural genetic materials. Systematic modification of each of their chemical building blocks (nucleobase, sugar, and phosphate) has enabled the study of the key properties that make those nucleic acids genetic materials. All three moieties contribute to replication and, significantly, all three moieties can be replaced by synthetic analogs without loss of function. Synthetic nucleic acid polymers capable of storing and propagating information not only expand the central dogma, but also highlight that DNA and RNA are not unique chemical solutions for genetic information storage. By considering replication as a question of information transfer, we propose that any polymer that can be replicated could serve as a genetic material.
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Affiliation(s)
- Vitor B Pinheiro
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK.
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Nigst TA, Ammer J, Mayr H. Photogeneration of benzhydryl cations by near-UV laser flash photolysis of pyridinium salts. J Phys Chem A 2012; 116:8494-9. [PMID: 22849534 DOI: 10.1021/jp3049247] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Laser flash irradiation of substituted N-benzhydryl pyridinium salts yields benzhydryl cations (diarylcarbenium ions) and/or benzhydryl radicals (diarylmethyl radicals). The use of 3,4,5-triamino-substituted pyridines as photoleaving groups allowed us to employ the third harmonic of a Nd/YAG laser (355 nm) for the photogeneration of benzhydryl cations. In this way, benzhydryl cations can also be photogenerated in the presence of aromatic compounds and in solvents which are opaque at the wavelength of the quadrupled Nd/YAG laser (266 nm). To demonstrate the scope and limitations of this method, the rate constants for the bimolecular reactions of benzhydryl cations with several substituted pyridines were determined in acetonitrile and with water in acetone. The obtained data agree with results obtained by stopped-flow UV-vis spectroscopic measurements. The rate constants for the reaction of the 4,4'-bis[methyl(2,2,2-trifluoroethyl)amino]benzhydrylium ion with 4-(dimethylamino)pyridine were also determined in dimethyl sulfoxide, N,N-dimethylformamide, and acetone. From the second-order rate constants, we derived the nucleophilicity parameters N and s(N) for the substituted pyridines, as defined by the linear free energy relationship, log k(2) = s(N)(N + E).
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Affiliation(s)
- Tobias A Nigst
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 (Haus F), 81377 München, Germany
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