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Deng L, Kumar J, Rose R, McIntyre W, Fabris D. Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code. MASS SPECTROMETRY REVIEWS 2024; 43:5-38. [PMID: 36052666 DOI: 10.1002/mas.21798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.
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Affiliation(s)
- L Deng
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - J Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - R Rose
- Department of Advanced Research Technologies, New York University Langone Health Center, New York, USA
| | - W McIntyre
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Daniele Fabris
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
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2
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Krajewski AE, Lee JK. Gas-Phase Experimental and Computational Studies of 5-Halouracils: Intrinsic Properties and Biological Implications. J Org Chem 2021; 86:6361-6370. [PMID: 33891415 DOI: 10.1021/acs.joc.1c00183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The gas-phase acidity and proton affinity (PA) of 5-halouracils (5-fluorouracil, 5-chlorouracil, 5-bromouracil, and 5-iodouracil) have been examined using both theoretical and experimental methods. This work represents a comprehensive study of the thermochemical properties of these nucleobases. Other than 5-fluorouracil acidity, the intrinsic acidity and PA of these halouracils have not been heretofore measured; these new experimental data provide a benchmark for the computational values. Furthermore, we examine these 5-halouracils in the context of the enzyme thymine DNA glycosylase (TDG), which is an enzyme that protects the genome by cleaving these substrates from DNA. Our gas-phase results are compared and contrasted to TDG excision rates to afford insights into the TDG mechanism.
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Affiliation(s)
- Allison E Krajewski
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
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3
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Bay MV, Nam PC, Quang DT, Mechler A, Hien NK, Hoa NT, Vo QV. Theoretical Study on the Antioxidant Activity of Natural Depsidones. ACS OMEGA 2020; 5:7895-7902. [PMID: 32309698 PMCID: PMC7160836 DOI: 10.1021/acsomega.9b04179] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 03/11/2020] [Indexed: 05/16/2023]
Abstract
Depsidones are secondary metabolites in lichens with a range of potential health benefits. Among others, these compounds are believed to exhibit high hydroxyl radical and superoxide scavenging abilities, warranting a detailed investigation of their antioxidant properties. In this study, the radical scavenging activity of natural depsidones from Ramalina lichenized fungi was investigated in silico. Calculations of the thermodynamic parameters suggested that the main radical scavenging pathway follows the formal hydrogen transfer (FHT) mechanism; however, unexpectedly low rate constants were found in the CH3OO• scavenging reaction. Establishing that the depsidones are mostly ionized in an aqueous environment suggested that the single-electron transfer (SET) mechanism should not be ruled out. Consistently, depsidones were revealed to be excellent HO• and O2 •- scavengers in aqueous solutions (k = 4.60 × 105 - 8.60 × 109 M-1 s-1 and k = 2.60 × 108 - 8.30 × 109 M-1 s-1, respectively) following the sequential proton loss electron transfer (SPLET) mechanism. These results suggest that natural fungal depsidones are potent hydroxyl and superoxide radical scavengers in aqueous solutions.
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Affiliation(s)
- Mai Van Bay
- Department
of Chemistry, The University of Da Nang,
University of Science and Education, Da Nang 550000, Vietnam
| | - Pham Cam Nam
- Department
of Chemical Engineering, The University
of Da Nang, University of Science and Technology, Da Nang 550000, Vietnam
| | - Duong Tuan Quang
- University
of Education, Hue University, Hue City 530000, Vietnam
| | - Adam Mechler
- Department
of Chemistry and Physics, La Trobe University, Victoria 3086, Australia
| | - Nguyen Khoa Hien
- Mientrung
Institute for Scientific Research, Academy
of Science and Technology, Hue
City 530000, Vietnam
| | - Nguyen Thi Hoa
- Academic
Affairs, The University of Danang - University
of Technology and Education, Da
Nang 550000, Vietnam
| | - Quan V. Vo
- Institute
of Research and Development, Duy Tan University, Danang 550000, Vietnam
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4
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Vo QV, Van Bay M, Nam PC, Mechler A. Hydroxyl Radical Scavenging of Indole-3-Carbinol: A Mechanistic and Kinetic Study. ACS OMEGA 2019; 4:19375-19381. [PMID: 31763562 PMCID: PMC6868896 DOI: 10.1021/acsomega.9b02782] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/28/2019] [Indexed: 05/19/2023]
Abstract
Indole-3-carbinol (I3C) is the product of the enzymatic hydrolysis of glucobrassicin in the human body. I3C exhibits diverse bioactivities. It is used as a supplement to enhance the efficiency of some cancer therapies and is available as an over-the-counter dietary supplement described as a potential antioxidant, among other health benefits. Thus, it is important to develop an in-depth understanding of its antioxidant activity. In this study, the hydroxyl radical scavenging of I3C has been investigated in silico under physiologically relevant conditions (aqueous and lipid-mimetic pentyl ethanoate environment) using thermochemical and kinetic calculations. For benchmarking purposes, the results were compared to known experimental data. The overall reaction rate constant of the HO• radical scavenging of I3C in water was found to be 2.30 × 1010 M-1 s-1 and over two times lower in lipid-mimetic pentyl ethanoate solvent at 7.74 × 109 M-1 s-1. The results also highlighted that the HO• radical scavenging follows almost exclusively the radical adduct formation mechanism (>94%) in a lipid mimetic medium, whereas this mechanism contributes about 60% in aqueous environments. I3C is considered a dopamine-like antioxidant, its main function being prevention of oxidative degradation of lipids; our study supports this view.
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Affiliation(s)
- Quan V. Vo
- Department
for Management of Science and Technology Development, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang
University, Ho Chi
Minh City 758307, Vietnam
- E-mail:
| | - Mai Van Bay
- Department
of Chemistry, The University of Da Nang−University
of Science and Education, Da Nang 550000, Vietnam
| | - Pham Cam Nam
- Department
of Chemistry, The University of Da Nang−University
of Science and Technology, Da Nang 550000, Vietnam
| | - Adam Mechler
- Department
of Chemistry and Physics, La Trobe University, Melbourne Victoria 3086, Australia
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5
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Das R, Vázquez-Montelongo EA, Cisneros GA, Wu JI. Ground State Destabilization in Uracil DNA Glycosylase: Let's Not Forget "Tautomeric Strain" in Substrates. J Am Chem Soc 2019; 141:13739-13743. [PMID: 31434485 DOI: 10.1021/jacs.9b06447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes like uracil DNA glycosylase (UDG) can achieve ground state destabilization, by polarizing substrates to mimic rare tautomers. On the basis of computed nucleus independent chemical shifts, NICS(1)zz, and harmonic oscillator model of electron delocalization (HOMED) analyses, of quantum mechanics (QM) and quantum mechanics/molecular mechanics (QM/MM) models of the UDG active site, uracil is strongly polarized when bound to UDG and resembles a tautomer >12 kcal/mol higher in energy. Natural resonance theory (NRT) analyses identified a dominant O2 imidate resonance form for residue bound 1-methyl-uracil. This "tautomeric strain" raises the energy of uracil, making uracilate a better than expected leaving group. Computed gas-phase SN2 reactions of free and hydrogen bonded 1-methyl-uracil demonstrate the relationship between the degree of polarization in uracil and the leaving group ability of uracilate.
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Affiliation(s)
- Ranjita Das
- Department of Chemistry , University of Houston , Houston , Texas 77204 , United States
| | | | - G Andrés Cisneros
- Department of Chemistry , University of North Texas , Denton , Texas 76201 , United States
| | - Judy I Wu
- Department of Chemistry , University of Houston , Houston , Texas 77204 , United States
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Abstract
Thermodynamic principles have been applied to enzyme-catalyzed reactions since the beginning of the 1930s in an attempt to understand metabolic pathways. Currently, thermodynamics is also applied to the design and analysis of biotechnological processes. The key thermodynamic quantity is the Gibbs energy of reaction, which must be negative for a reaction to occur spontaneously. However, the application of thermodynamic feasibility studies sometimes yields positive Gibbs energies of reaction even for reactions that are known to occur spontaneously, such as glycolysis. This article reviews the application of thermodynamics in enzyme-catalyzed reactions. It summarizes the basic thermodynamic relationships used for describing the Gibbs energy of reaction and also refers to the nonuniform application of these relationships in the literature. The review summarizes state-of-the-art approaches that describe the influence of temperature, pH, electrolytes, solvents, and concentrations of reacting agents on the Gibbs energy of reaction and, therefore, on the feasibility and yield of biological reactions.
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Affiliation(s)
- Christoph Held
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Technische Universität Dortmund, 44227 Dortmund, Germany;
| | - Gabriele Sadowski
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Technische Universität Dortmund, 44227 Dortmund, Germany;
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Raczyńska ED, Gal JF, Maria PC. Enhanced Basicity of Push-Pull Nitrogen Bases in the Gas Phase. Chem Rev 2016; 116:13454-13511. [PMID: 27739663 DOI: 10.1021/acs.chemrev.6b00224] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrogen bases containing one or more pushing amino-group(s) directly linked to a pulling cyano, imino, or phosphoimino group, as well as those in which the pushing and pulling moieties are separated by a conjugated spacer (C═X)n, where X is CH or N, display an exceptionally strong basicity. The n-π conjugation between the pushing and pulling groups in such systems lowers the basicity of the pushing amino-group(s) and increases the basicity of the pulling cyano, imino, or phosphoimino group. In the gas phase, most of the so-called push-pull nitrogen bases exhibit a very high basicity. This paper presents an analysis of the exceptional gas-phase basicity, mostly in terms of experimental data, in relation with structure and conjugation of various subfamilies of push-pull nitrogen bases: nitriles, azoles, azines, amidines, guanidines, vinamidines, biguanides, and phosphazenes. The strong basicity of biomolecules containing a push-pull nitrogen substructure, such as bioamines, amino acids, and peptides containing push-pull side chains, nucleobases, and their nucleosides and nucleotides, is also analyzed. Progress and perspectives of experimental determinations of GBs and PAs of highly basic compounds, termed as "superbases", are presented and benchmarked on the basis of theoretical calculations on existing or hypothetical molecules.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW) , ul. Nowoursynowska 159c, 02-776 Warszawa, Poland
| | - Jean-François Gal
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
| | - Pierre-Charles Maria
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
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Jin L, Zhao C, Zhang T, Wang Z, Min S, Wang W, Wei Y. Effects of an acid–alkaline environment on the reactivity of 5-carboxycytosine with hydroxyl radicals. RSC Adv 2015. [DOI: 10.1039/c5ra17393k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The addition of ˙OH to C5C6 double bond and abstraction of H5 from 5-caCyt are more favourable in neutral, acidic and alkaline conditions.
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Affiliation(s)
- Lingxia Jin
- Shaanxi Province Key Laboratory of Catalytic Fundamentals & Applications
- School of Chemical & Environment Science
- Shaanxi University of Technology
- Hanzhong
- China
| | - Caibin Zhao
- Shaanxi Province Key Laboratory of Catalytic Fundamentals & Applications
- School of Chemical & Environment Science
- Shaanxi University of Technology
- Hanzhong
- China
| | - Tianlei Zhang
- Shaanxi Province Key Laboratory of Catalytic Fundamentals & Applications
- School of Chemical & Environment Science
- Shaanxi University of Technology
- Hanzhong
- China
| | - Zhiyin Wang
- Shaanxi Province Key Laboratory of Catalytic Fundamentals & Applications
- School of Chemical & Environment Science
- Shaanxi University of Technology
- Hanzhong
- China
| | - Suotian Min
- Shaanxi Province Key Laboratory of Catalytic Fundamentals & Applications
- School of Chemical & Environment Science
- Shaanxi University of Technology
- Hanzhong
- China
| | - Wenliang Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
- China
| | - Yawen Wei
- Institute of Publication Science
- Chang’an University
- Xi’an 710064
- China
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