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Węgrzyn E, Mejdrová I, Carell T. Gradual evolution of a homo-l-peptide world on homo-d-configured RNA and DNA. Chem Sci 2024; 15:d4sc03384a. [PMID: 39129775 PMCID: PMC11306956 DOI: 10.1039/d4sc03384a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 07/26/2024] [Indexed: 08/13/2024] Open
Abstract
Modern life requires the translation of genetic information - encoded by nucleic acids - into proteins, which establishes the essential link between genotype and phenotype. During translation, exclusively l-amino acids are loaded onto transfer RNA molecules (tRNA), which are then connected at the ribosome to give homo-l-proteins. In contrast to the homo-l-configuration of amino acids and proteins, the oligonucleotides involved are all d-configured (deoxy)ribosides. Previously, others and us have shown that if peptide synthesis occurs at homo d-configured oligonucleotides, a pronounced l-amino acid selectivity is observed, which reflects the d-sugar/l-amino acid world that evolved in nature. Here we further explore this astonishing selectivity. We show a peptide-synthesis/recapture-cycle that can lead to a gradual enrichment and hence selection of a homo-l-peptide world. We show that even if peptides with a mixed l/d-stereochemistry are formed, they are not competitive against the homo-l-counterparts. We also demonstrate that this selectivity is not limited to RNA but that peptide synthesis on DNA features the same l-amino acid preference. In total, the data bring us a step closer to an understanding of how homochirality on Earth once evolved.
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Affiliation(s)
- Ewa Węgrzyn
- Department of Chemistry, Center for Nucleic Acids Therapies at the Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München Butenandtstrasse 5-13 81377 Munich Germany
| | - Ivana Mejdrová
- Department of Chemistry, Center for Nucleic Acids Therapies at the Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München Butenandtstrasse 5-13 81377 Munich Germany
| | - Thomas Carell
- Department of Chemistry, Center for Nucleic Acids Therapies at the Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München Butenandtstrasse 5-13 81377 Munich Germany
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Kataoka S, Harada M, Okada T. Microscale pH inhomogeneity in frozen NaCl solutions. Phys Chem Chem Phys 2021; 23:18595-18601. [PMID: 34612396 DOI: 10.1039/d1cp01655e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
When an aqueous solution freezes at temperatures above the eutectic point, a freeze concentrated solution (FCS) is separated from the ice phase. Reactions of environmental importance often occur in the FCS and, in some cases, are accelerated compared to those in solution conditions. The pH of the FCS is an essential factor governing the thermodynamics and kinetics of the reactions occurring therein. It is known that freezing of aqueous NaCl causes an increase in the FCS pH, which arises from the difference in the partition to the ice phase between Na+ and Cl-. It has also been shown that H+ and other ions show surface-specific behaviors on ice. Although the details are not known, the ice/FCS interface can also affect the behaviors of ions. In this study, the pH distribution in the FCS is evaluated using ratiometric fluorescence microscopy, and the pH inhomogeneity is confirmed for frozen aqueous NaCl. However, interestingly, buffered solutions and frozen aqueous glycerol result in a uniform pH value. The pH in frozen NaCl is always higher near the ice/FCS interface than in the middle of the FCS vein.
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Affiliation(s)
- Shun Kataoka
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8551, Japan.
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Influencing Factors in N-nitrosodimethylamine (NDMA) Impurity Detection in Ranitidine and Possible Reactivity of other Histamine H2 Receptor Antagonists. J Pharm Innov 2021. [DOI: 10.1007/s12247-021-09578-x] [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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An LY, Dai Z, Di B, Xu LL. Advances in Cryochemistry: Mechanisms, Reactions and Applications. Molecules 2021; 26:750. [PMID: 33535547 PMCID: PMC7867104 DOI: 10.3390/molecules26030750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 01/23/2023] Open
Abstract
It is counterintuitive that chemical reactions can be accelerated by freezing, but this amazing phenomenon was discovered as early as the 1960s. In frozen systems, the increase in reaction rate is caused by various mechanisms and the freeze concentration effect is the main reason for the observed acceleration. Some accelerated reactions have great application value in the chemistry synthesis and environmental fields; at the same time, certain reactions accelerated at low temperature during the storage of food, medicine, and biological products should cause concern. The study of reactions accelerated by freezing will overturn common sense and provide a new strategy for researchers in the chemistry field. In this review, we mainly introduce various mechanisms for accelerating reactions induced by freezing and summarize a variety of accelerated cryochemical reactions and their applications.
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Affiliation(s)
- Lu-Yan An
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (L.-Y.A.); (Z.D.)
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Zhen Dai
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (L.-Y.A.); (Z.D.)
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Bin Di
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (L.-Y.A.); (Z.D.)
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Li-Li Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (L.-Y.A.); (Z.D.)
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
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Kitada K, Suda Y, Takenaka N. Cyanide Formation in Freezer Stored Foods: Freezing of a Glycine and Nitrite Mixture. Chem Res Toxicol 2020; 33:1809-1814. [PMID: 32283925 DOI: 10.1021/acs.chemrestox.0c00054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Freezing is not always the best way to keep foods safely. Some reactions are known to be accelerated in ice. Furthermore, some other reactions that are not observed in solution are also promoted in ice. We found that the formation of nitrosamines through the reaction of an amine with a nitrite is accelerated in ice. Surprisingly, cyanide is formed through the reaction of glycine with nitrite in ice but not in solution. Amines are present in many kinds of foods. Nitrite is present in vegetables and is used as a food coloring agent and to inhibit the reproduction of Clostridium botulinum. The maximum amount of cyanide formed reaches a dangerous level, and the intake of this formed cyanide in a few tens of cubic centimeters causes some people to get headaches. These facts suggest that hazardous compounds could be generated in frozen processed foods. We report here the formation of cyanide and its possible formation pathway in ice. Finally, we propose a way to prevent cyanide formation in food under frozen conditions.
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Affiliation(s)
- Kodai Kitada
- Laboratory of Environmental Materials Chemistry, Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka 599-8531, Japan
| | - Yusuke Suda
- Laboratory of Environmental Materials Chemistry, Department of Sustainable System Sciences, Graduate School of Humanities and Sustainable System Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka 599-8531, Japan
| | - Norimichi Takenaka
- Laboratory of Environmental Materials Chemistry, Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka 599-8531, Japan.,Laboratory of Environmental Materials Chemistry, Department of Sustainable System Sciences, Graduate School of Humanities and Sustainable System Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka 599-8531, Japan
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Interactions of preservatives in meat processing: Formation of carcinogenic compounds, analytical methods, and inhibitory agents. Food Res Int 2019; 125:108608. [DOI: 10.1016/j.foodres.2019.108608] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 08/02/2019] [Accepted: 08/04/2019] [Indexed: 12/11/2022]
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Choi Y, Yoon HI, Lee C, Vetráková L, Heger D, Kim K, Kim J. Activation of Periodate by Freezing for the Degradation of Aqueous Organic Pollutants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5378-5385. [PMID: 29648451 DOI: 10.1021/acs.est.8b00281] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A new strategy (i.e., freezing) for the activation of IO4- for the degradation of aqueous organic pollutants was developed and investigated. Although the degradation of furfuryl alcohol (FFA) by IO4- was negligible in water at 25 °C, it proceeded rapidly during freezing at -20 °C. The rapid degradation of FFA during freezing should be ascribed to the freeze concentration effect that provides a favorable site (i.e., liquid brine) for the proton-coupled degradation process by concentrating IO4-, FFA, and protons. The maximum absorption wavelength of cresol red (CR) was changed from 434 nm (monoprotonated CR) to 518 nm (diprotonated CR) after freezing, which confirms that the pH of the aqueous IO4- solution decreases by freezing. The degradation experiments with varying experimental parameters demonstrate that the degradation rate increases with increasing IO4- concentration and decreasing pH and freezing temperature. The application of the IO4-/freezing system is not restricted to FFA. The degradation of four other organic pollutants (i.e., tryptophan, phenol, 4-chlorophenol, and bisphenol A) by IO4-, which was negligible in water, proceeded during freezing. In addition, freezing significantly enhanced the IO4--mediated degradation of cimetidine. The outdoor experiments performed on a cold winter night show that the IO4-/freezing system for water treatment can be operated without external electrical energy.
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Affiliation(s)
- Yejin Choi
- Department of Environmental Sciences and Biotechnology , Hallym University , Chuncheon , Gangwon-do 24252 , Republic of Korea
| | - Ho-Il Yoon
- Korea Polar Research Institute (KOPRI) , Incheon 21990 , Republic of Korea
| | - Changha Lee
- School of Urban and Environmental Engineering , Ulsan National Institute of Science and Technology (UNIST) , Ulsan 44919 , Republic of Korea
| | - L'ubica Vetráková
- Department of Chemistry and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science , Masaryk University , Kamenice 5 , 625 00 Brno , Czech Republic
| | - Dominik Heger
- Department of Chemistry and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science , Masaryk University , Kamenice 5 , 625 00 Brno , Czech Republic
| | - Kitae Kim
- Korea Polar Research Institute (KOPRI) , Incheon 21990 , Republic of Korea
- Department of Polar Sciences , University of Science and Technology (UST) , Incheon 21990 , Republic of Korea
| | - Jungwon Kim
- Department of Environmental Sciences and Biotechnology , Hallym University , Chuncheon , Gangwon-do 24252 , Republic of Korea
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Affiliation(s)
- Tianmeng Yu
- Department of Chemistry and Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
| | - Wenhu Zhou
- Department of Chemistry and Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
- Xiangya School of Pharmaceutical Sciences; Central South University; 172 Tongzipo Road Changsha Hunan 410013 China
| | - Juewen Liu
- Department of Chemistry and Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
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