1
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Zhang K, Ho KP, Chatterjee A, Park G, Li Z, Catalano JG, Parker KM. RNA Hydrolysis at Mineral-Water Interfaces. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37216349 DOI: 10.1021/acs.est.3c01407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
As an essential biomolecule for life, RNA is ubiquitous across environmental systems where it plays a central role in biogeochemical processes and emerging technologies. The persistence of RNA in soils and sediments is thought to be limited by enzymatic or microbial degradation, which occurs on timescales that are orders of magnitude faster than known abiotic pathways. Herein, we unveil a previously unreported abiotic pathway by which RNA rapidly hydrolyzes on the timescale of hours upon adsorption to iron (oxyhydr)oxide minerals such as goethite (α-FeOOH). The hydrolysis products were consistent with iron present in the minerals acting as a Lewis acid to accelerate sequence-independent hydrolysis of phosphodiester bonds comprising the RNA backbone. In contrast to acid- or base-catalyzed RNA hydrolysis in solution, mineral-catalyzed hydrolysis was fastest at circumneutral pH, which allowed for both sufficient RNA adsorption and hydroxide concentration. In addition to goethite, we observed that RNA hydrolysis was also catalyzed by hematite (α-Fe2O3) but not by aluminum-containing minerals (e.g., montmorillonite). Given the extensive adsorption of nucleic acids to environmental surfaces, we anticipate previously overlooked mineral-catalyzed hydrolysis of RNA may be prevalent particularly in iron-rich soils and sediments, which must be considered across biogeochemical applications of nucleic acid analysis in environmental systems.
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Affiliation(s)
- Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kun-Pu Ho
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Grace Park
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Zhiyao Li
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jeffrey G Catalano
- Department of Earth & Planetary Sciences, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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2
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Xu J, Cotruvo JA. Iron-responsive riboswitches. Curr Opin Chem Biol 2022; 68:102135. [PMID: 35427920 PMCID: PMC9133107 DOI: 10.1016/j.cbpa.2022.102135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 11/23/2022]
Abstract
All cells must manage deficiency, sufficiency, and excess of essential metal ions. Although iron has been one of most important metals in biology for billions of years, the mechanisms by which bacteria cope with high intracellular iron concentrations are only recently coming into focus. Recent work has suggested that an RNA riboswitch (czcD or "NiCo"), originally thought to respond specifically to CoII and NiII excess, is more likely a selective regulator of FeII levels in important human gut bacteria and pathogens. We discuss the challenges and controversies encountered in the characterization of iron-responsive riboswitches, and we suggest a physiological role in responding to iron overload, perhaps during anaerobiosis. Finally, we place these riboswitches in the context of the better understood mechanisms of protein-based metal ion regulation, proposing that riboswitch-mediated mechanisms may be particularly important in regulating transport of the weakest-binding biological divalent metal ions, MgII, MnII, and FeII.
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Affiliation(s)
- Jiansong Xu
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Joseph A Cotruvo
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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3
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Chatterjee A, Zhang K, Rao Y, Sharma N, Giammar DE, Parker KM. Metal-Catalyzed Hydrolysis of RNA in Aqueous Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3564-3574. [PMID: 35226478 DOI: 10.1021/acs.est.1c08468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The stability of RNA in aqueous systems is critical for multiple environmental applications including evaluating the environmental fate of RNA interference pesticides and interpreting viral genetic marker abundance for wastewater-based epidemiology. In addition to biological processes, abiotic reactions may also contribute to RNA loss. In particular, some metals are known to dramatically accelerate rates of RNA hydrolysis under certain conditions (i.e., 37 °C or higher temperatures, 0.15-100 mM metal concentrations). In this study, we investigated the extent to which metals catalyze RNA hydrolysis under environmentally relevant conditions. At ambient temperature, neutral pH, and ∼10 μM metal concentrations, we determined that metals that are stronger Lewis acids (i.e., lead, copper) catalyzed single-stranded (ss)RNA, whereas metals that are weaker Lewis acids (i.e., zinc, nickel) did not. In contrast, double-stranded (ds)RNA resisted hydrolysis by all metals. While lead and copper catalyzed ssRNA hydrolysis at ambient temperature and neutral pH values, other factors such as lowering the solution pH and including inorganic and organic ligands reduced the rates of these reactions. Considering these factors along with sub-micromolar metal concentrations typical of environmental systems, we determined that both ssRNA and dsRNA are unlikely to undergo significant metal-catalyzed hydrolysis in most environmental aqueous systems.
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Affiliation(s)
- Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Yue Rao
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Neha Sharma
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Daniel E Giammar
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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4
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Le Vay KK, Mutschler H. Generation of RNA with 2', 3'-Cyclic Phosphates by Deoxyribozyme Cleavage in Frozen Solutions. Methods Mol Biol 2022; 2439:301-309. [PMID: 35226329 DOI: 10.1007/978-1-0716-2047-2_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The generation of terminal 2', 3'-cyclic phosphates on RNA oligomers is an important process in the study of tRNA splicing and repair, ribozyme catalysis, and RNA circularization. Here, we describe a simple method for producing 2', 3'-cyclic phosphate functionalized RNA by the deoxyribozyme-catalyzed cleavage of a short 3'-RNA overhang in frozen solution. This method avoids the nonspecific modification and degradation of RNA and attached functional groups (e.g., fluorophores) inherent in other methods, and the use of frozen conditions enables cleavage at very low divalent metal ion concentrations, limiting RNA hydrolysis.
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Affiliation(s)
- Kristian K Le Vay
- Biomimetic Systems, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Hannes Mutschler
- Biomimetic Systems, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany.
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5
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Zou Z, He L, Deng X, Wang H, Huang Z, Xue Q, Qing Z, Lei Y, Yang R, Liu J. Zn
2+
‐Coordination‐Driven RNA Assembly with Retained Integrity and Biological Functions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Zhen Zou
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
| | - Libei He
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
| | - Xiangxi Deng
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
| | - Huangxiang Wang
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
| | - Ziyun Huang
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
| | - Qian Xue
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
| | - Zhihe Qing
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
| | - Yanli Lei
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
| | - Ronghua Yang
- School of Chemistry and Food Engineering Hunan Provincial Key Laboratory of Cytochemistry Changsha University of Science and Technology Changsha 410114 China
- Laboratory of Chemical Biology & Traditional Chinese Medicine Research Ministry of Education College of Chemistry and Chemical Engineering Hunan Normal University Changsha 410081 China
| | - Juewen Liu
- Department of Chemistry Waterloo Institute for Nanotechnology University of Waterloo Waterloo Ontario N2L 3G1 Canada
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6
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Zou Z, He L, Deng X, Wang H, Huang Z, Xue Q, Qing Z, Lei Y, Yang R, Liu J. Zn 2+ -Coordination-Driven RNA Assembly with Retained Integrity and Biological Functions. Angew Chem Int Ed Engl 2021; 60:22970-22976. [PMID: 34405498 DOI: 10.1002/anie.202110404] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Indexed: 12/29/2022]
Abstract
Metal-coordination-directed biomolecule crosslinking in nature has been used for synthesizing various biopolymers, including DNA, peptides, proteins, and polysaccharides. However, the RNA biopolymer has been avoided so far, as due to the poor stability of the RNA molecules, the formation of a biopolymer may alter the biological function of the molecules. Herein, for the first time, we report Zn2+ -driven RNA self-assembly forming spherical nanoparticles while retaining the integrity and biological function of RNA. Various functional RNAs of different compositions, shapes, and lengths from 20 to nearly 1000 nucleotides were used, highlighting the versatility of this approach. The assembled nanospheres possess a superior RNA-loading efficiency, pharmacokinetics, and bioavailability. In-vitro and in-vivo evaluation demonstrated mRNA delivery for expressing GFP proteins, and microRNA delivery to triple-negative breast cancer. This coordination-directed self-assembly behavior amplifies the horizons of RNA coordination chemistry and the application scope of RNA-based therapeutics.
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Affiliation(s)
- Zhen Zou
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China
| | - Libei He
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China
| | - Xiangxi Deng
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China
| | - Huangxiang Wang
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China
| | - Ziyun Huang
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China
| | - Qian Xue
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China
| | - Zhihe Qing
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China
| | - Yanli Lei
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China
| | - Ronghua Yang
- School of Chemistry and Food Engineering, Hunan Provincial Key Laboratory of Cytochemistry, Changsha University of Science and Technology, Changsha, 410114, China.,Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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7
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Hur J, Chung AJ. Microfluidic and Nanofluidic Intracellular Delivery. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2004595. [PMID: 34096197 PMCID: PMC8336510 DOI: 10.1002/advs.202004595] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/14/2021] [Indexed: 05/05/2023]
Abstract
Innate cell function can be artificially engineered and reprogrammed by introducing biomolecules, such as DNAs, RNAs, plasmid DNAs, proteins, or nanomaterials, into the cytosol or nucleus. This process of delivering exogenous cargos into living cells is referred to as intracellular delivery. For instance, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 gene editing begins with internalizing Cas9 protein and guide RNA into cells, and chimeric antigen receptor-T (CAR-T) cells are prepared by delivering CAR genes into T lymphocytes for cancer immunotherapies. To deliver external biomolecules into cells, tools, including viral vectors, and electroporation have been traditionally used; however, they are suboptimal for achieving high levels of intracellular delivery while preserving cell viability, phenotype, and function. Notably, as emerging solutions, microfluidic and nanofluidic approaches have shown remarkable potential for addressing this open challenge. This review provides an overview of recent advances in microfluidic and nanofluidic intracellular delivery strategies and discusses new opportunities and challenges for clinical applications. Furthermore, key considerations for future efforts to develop microfluidics- and nanofluidics-enabled next-generation intracellular delivery platforms are outlined.
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Affiliation(s)
- Jeongsoo Hur
- School of Biomedical EngineeringKorea UniversitySeoul02841Republic of Korea
| | - Aram J. Chung
- School of Biomedical EngineeringInterdisciplinary Program in Precision Public HealthKorea UniversitySeoul02841Republic of Korea
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8
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Saleh LY, Ora M, Lönnberg T. Cleavage of an RNA Model Compound by an Arylmercury Complex. Chembiochem 2021; 22:1761-1764. [PMID: 33448598 PMCID: PMC8247959 DOI: 10.1002/cbic.202000799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/13/2021] [Indexed: 11/22/2022]
Abstract
A water-soluble arylmercury complex has been synthesized, and its ability to catalyze the cleavage of the phosphodiester linkage of the RNA model compound adenylyl-3',5'-(2',3'-O-methyleneadenosine) has been assessed over a pH range of 3-8.5 and a catalyst concentration range of 0-7 mM. In the presence of 1 mM catalyst, the observed pH-rate profile featured a new pH-independent region between pH 6 and 7, the catalyzed reaction being as much as eight times faster than the background reaction. At pH 7, the acceleration increased linearly from three- to 17-fold upon increasing the catalyst concentration from 1 to 7 mM. The linear dependence indicates a relatively low affinity of the catalyst for the substrate and, hence, the potential for considerable improvement on tethering to an appropriate targeting group, such as an oligonucleotide.
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Affiliation(s)
- Lange Yakubu Saleh
- Department of ChemistryUniversity of TurkuVatselankatu 220014TurkuFinland
| | - Mikko Ora
- Department of ChemistryUniversity of TurkuVatselankatu 220014TurkuFinland
| | - Tuomas Lönnberg
- Department of ChemistryUniversity of TurkuVatselankatu 220014TurkuFinland
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9
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Corsi ID, Dutta S, van Hoof A, Koehler TM. AtxA-Controlled Small RNAs of Bacillus anthracis Virulence Plasmid pXO1 Regulate Gene Expression in trans. Front Microbiol 2021; 11:610036. [PMID: 33519762 PMCID: PMC7843513 DOI: 10.3389/fmicb.2020.610036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/11/2020] [Indexed: 11/13/2022] Open
Abstract
Small regulatory RNAs (sRNAs) are short transcripts that base-pair to mRNA targets or interact with regulatory proteins. sRNA function has been studied extensively in Gram-negative bacteria; comparatively less is known about sRNAs in Firmicutes. Here we investigate two sRNAs encoded by virulence plasmid pXO1 of Bacillus anthracis, the causative agent of anthrax. The sRNAs, named “XrrA and XrrB” (for pXO1-encoded regulatory RNA) are abundant and highly stable primary transcripts, whose expression is dependent upon AtxA, the master virulence regulator of B. anthracis. sRNA levels are highest during culture conditions that promote AtxA expression and activity, and sRNA levels are unaltered in Hfq RNA chaperone null-mutants. Comparison of the transcriptome of a virulent Ames-derived strain to the transcriptome of isogenic sRNA-null mutants revealed multiple 4.0- to >100-fold differences in gene expression. Most regulatory effects were associated with XrrA, although regulation of some transcripts suggests functional overlap between the XrrA and XrrB. Many sRNA-regulated targets were chromosome genes associated with branched-chain amino acid metabolism, proteolysis, and transmembrane transport. Finally, in a mouse model for systemic anthrax, the lungs and livers of animals infected with xrrA-null mutants had a small reduction in bacterial burden, suggesting a role for XrrA in B. anthracis pathogenesis.
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Affiliation(s)
- Ileana D Corsi
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, The University of Texas, Houston, TX, United States
| | - Soumita Dutta
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, The University of Texas, Houston, TX, United States
| | - Theresa M Koehler
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, The University of Texas, Houston, TX, United States
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10
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Guth-Metzler R, Bray MS, Frenkel-Pinter M, Suttapitugsakul S, Montllor-Albalate C, Bowman JC, Wu R, Reddi AR, Okafor CD, Glass JB, Williams LD. Cutting in-line with iron: ribosomal function and non-oxidative RNA cleavage. Nucleic Acids Res 2020; 48:8663-8674. [PMID: 32663277 PMCID: PMC7470983 DOI: 10.1093/nar/gkaa586] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 06/23/2020] [Accepted: 06/30/2020] [Indexed: 02/06/2023] Open
Abstract
Divalent metal cations are essential to the structure and function of the ribosome. Previous characterizations of the ribosome performed under standard laboratory conditions have implicated Mg2+ as a primary mediator of ribosomal structure and function. Possible contributions of Fe2+ as a ribosomal cofactor have been largely overlooked, despite the ribosome's early evolution in a high Fe2+ environment, and the continued use of Fe2+ by obligate anaerobes inhabiting high Fe2+ niches. Here, we show that (i) Fe2+ cleaves RNA by in-line cleavage, a non-oxidative mechanism that has not previously been shown experimentally for this metal, (ii) the first-order in-line rate constant with respect to divalent cations is >200 times greater with Fe2+ than with Mg2+, (iii) functional ribosomes are associated with Fe2+ after purification from cells grown under low O2 and high Fe2+ and (iv) a small fraction of Fe2+ that is associated with the ribosome is not exchangeable with surrounding divalent cations, presumably because those ions are tightly coordinated by rRNA and deeply buried in the ribosome. In total, these results expand the ancient role of iron in biochemistry and highlight a possible new mechanism of iron toxicity.
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Affiliation(s)
- Rebecca Guth-Metzler
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Marcus S Bray
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Moran Frenkel-Pinter
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | | | - Jessica C Bowman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Amit R Reddi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - C Denise Okafor
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jennifer B Glass
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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11
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Zhang SJ, Duzdevich D, Szostak JW. Potentially Prebiotic Activation Chemistry Compatible with Nonenzymatic RNA Copying. J Am Chem Soc 2020; 142:14810-14813. [PMID: 32794700 PMCID: PMC9594304 DOI: 10.1021/jacs.0c05300] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
The nonenzymatic replication of ribonucleic
acid (RNA) may have
enabled the propagation of genetic information during the origin of
life. RNA copying can be initiated in the laboratory with chemically
activated nucleotides, but continued copying requires a source of
chemical energy for in situ nucleotide activation.
Recent work has illuminated a potentially prebiotic cyanosulfidic
chemistry that activates nucleotides, but its application to nonenzymatic
RNA copying had not been demonstrated. Here, we report a novel pathway
that activates RNA nucleotides in a manner compatible with template-directed
nonenzymatic copying. We show that this pathway, which we refer to
as bridge-forming activation, selectively yields the reactive imidazolium-bridged
dinucleotide intermediate required for copying. Our results will enable
more realistic simulations of RNA propagation based on continuous in situ nucleotide activation.
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Affiliation(s)
- Stephanie J Zhang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Daniel Duzdevich
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jack W Szostak
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States.,Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
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12
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Mercury(II)-Catalyzed Cleavage, Isomerization and Depurination of RNA and DNA Model Compounds and Desulfurization of Their Phosphoromonothioate Analogs. Catalysts 2020. [DOI: 10.3390/catal10020219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The potential of Hg(II), a metal ion so-far overlooked in the development of artificial nucleases, to cleave RNA and DNA has been assessed. Accordingly, Hg(II)-promoted cleavage and isomerization of the RNA model compound adenylyl-3′,5′-(2′,3′-O-methyleneadenosine) and depurination of 2′-deoxyadenosine were followed by HPLC as a function of pH (5.0–6.0) and the desulfurization of both diastereomers of the phosphoromonothioate analog of adenylyl-3′,5′-(2′,3′-O-methyleneadenosine) at a single pH (6.9). At 5 mM [Hg(II)], cleavage of the RNA model compound was accelerated by two orders of magnitude at the low and by one order of magnitude at the high end of the pH range. Between 0 and 5 mM [Hg(II)], the cleavage rate showed a sigmoidal dependence on [Hg(II)], suggesting the participation of more than one Hg(II) in the reaction. Isomerization and depurination were also facilitated by Hg(II), but much more modestly than cleavage, less than 2-fold over the entire pH range studied. Phosphoromonothioate desulfurization was by far the most susceptible reaction to Hg(II) catalysis, being accelerated by more than four orders of magnitude.
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13
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Babu VMP, Sankari S, Budnick JA, Caswell CC, Walker GC. Sinorhizobium meliloti YbeY is a zinc-dependent single-strand specific endoribonuclease that plays an important role in 16S ribosomal RNA processing. Nucleic Acids Res 2020; 48:332-348. [PMID: 31777930 PMCID: PMC6943124 DOI: 10.1093/nar/gkz1095] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/01/2019] [Accepted: 11/21/2019] [Indexed: 12/19/2022] Open
Abstract
Single-strand specific endoribonuclease YbeY has been shown to play an important role in the processing of the 3' end of the 16S rRNA in Escherichia coli. Lack of YbeY results in the accumulation of the 17S rRNA precursor. In contrast to a previous report, we show that Sinorhizobium meliloti YbeY exhibits endoribonuclease activity on single-stranded RNA substrate but not on the double-stranded substrate. This study also identifies the previously unknown metal ion involved in YbeY function to be Zn2+ and shows that the activity of YbeY is enhanced when the occupancy of zinc is increased. We have identified a pre-16S rRNA precursor that accumulates in the S. meliloti ΔybeY strain. We also show that ΔybeY mutant of Brucella abortus, a mammalian pathogen, also accumulates a similar pre-16S rRNA. The pre-16S species is longer in alpha-proteobacteria than in gamma-proteobacteria. We demonstrate that the YbeY from E. coli and S. meliloti can reciprocally complement the rRNA processing defect in a ΔybeY mutant of the other organism. These results establish YbeY as a zinc-dependent single-strand specific endoribonuclease that functions in 16S rRNA processing in both alpha- and gamma-proteobacteria.
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Affiliation(s)
- Vignesh M P Babu
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Siva Sankari
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - James A Budnick
- Department of Biomedical Sciences and Pathobiology, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, PA, USA
| | - Clayton C Caswell
- Department of Biomedical Sciences and Pathobiology, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Graham C Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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14
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Rapid Hydrolysis of Organophosphates Induced by U(IV) Nanoparticles: A Kinetic and Mechanistic Study using Spectroscopic Analysis. COLLOIDS AND INTERFACES 2019. [DOI: 10.3390/colloids3040063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The heterogeneous interactions of colloidal U particles with organophosphates, leading to the formation of U-phosphate minerals, can retard the migration of U in contaminated sites. Here, we studied the hydrolytic mechanism of p-nitrophenyl phosphate (NPP) on the surfaces of tetravalent uranium nanoparticles (U(IV)NPs), resulting in the formation of U-phosphate precipitates. Our study shows that the reaction rate of NPP hydrolysis is significantly enhanced by U(IV)NPs through a multi-step heterogeneous reaction on the particle surfaces. The end products of the reaction were identified as U(IV)NPs-aggregates with surface-bound phosphates. Colloidal properties, such as high positive values of the zeta-potential (>+30 mV) and large surface areas of U(IV)NPs due to their unique cluster structures consisting of relatively small primary UO2(cr)-particles, are correlated with their reactivity towards hydrolysis reaction. Reaction kinetic modeling studies using spectrophotometric data indicated the presence of two distinct reaction intermediates as the surface complexes of NPP on U(IV)NPs. We suggest the involvement of the NPP inner-sphere complexes in the rate-determining step based on the results obtained by analyzing the ATR-FTIR spectra and the surface-enhanced infrared absorption of NPP bound to substrate surfaces.
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15
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Danilevich VN, Kozlov SA, Shevchuk TV, Oleinikov VA, Sizova SV, Khodarovich YM, Mulyukin AL. Ribonucleic acid (RNA) condensation by thermal cycling with metal cations: yield of nanoparticles and their applicability for transfection. J Biomol Struct Dyn 2019; 38:3959-3971. [PMID: 31543001 DOI: 10.1080/07391102.2019.1671228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
To the present, different efficient but expensive, multistage, and time-consuming technologies have been developed to deliver ribonucleic acids (RNA) into eukaryotic cells. Here, we report a simple and feasible solution to design RNA nanocarriers based on nucleic acid condensation by bi- and trivalent metal ions during thermal cycling. Efficient RNA conversion to nanoparticles with small size (10-50 nm) suitable for transfection was achieved using cations Ni2+, Co2+ or Cu2+ alone or in combination with Ca2+ at the specially selected concentrations (2.0 mM-3.5 mM), low ionic strength, and narrow pH range (8.0-8.5). Other ions - Mn2+, Zn2+, Tb3+, or Gd3+ - caused RNA-cleaving effect that was abolished in the presence of Ni2+, Co2+, Zn2+, or Cu2+. Naked RNA-metal ion nanoparticles were extremely unstable in phosphate buffer and sensitive to serum ribonucleases (RNases), and this problem was solved by treatment with polyarginines-16 and 8. Polyarginine-stabilized nanoparticles, containing malachite green (MG) aptamer RNA and metal cations, crossed the cell membrane, dissociated in the cytoplasm, and preserved the functionality of transported RNA, as judged from efficient transfection of human embryonic kidney 293 cells. The technology, involving RNA condensation by metal cations, can be used as a cheap alternative to produce nanoscale carriers to deliver various RNAs into cells in vitro and in vivo.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vasily N Danilevich
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Sergey A Kozlov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Taras V Shevchuk
- Branch of the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow, Russia
| | - Vladimir A Oleinikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Svetlana V Sizova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Yuriy M Khodarovich
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Andrey L Mulyukin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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16
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Chang CA, Lee HY, Lin SL, Meng CN, Wu TT. Dinuclear Lanthanide(III)-m-ODO2A-dimer Macrocyclic Complexes: Solution Speciation, DFT Calculations, Luminescence Properties, and Promoted Nitrophenyl-Phosphate Hydrolysis Rates. Chemistry 2018; 24:6442-6457. [PMID: 29479746 DOI: 10.1002/chem.201800037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Indexed: 12/24/2022]
Abstract
Potentiometric speciation studies, mass spectrometry, and DFT calculations helped to predict the various structural possibilities of the dinuclear trivalent lanthanide ion (LnIII , Ln=La, Eu, Tb, Yb, Y) complexes of a novel macrocyclic ligand, m-ODO2A-dimer (H4 L), to correlate with their luminescence properties and the promoted BNPP and HPNP phosphodiester bond hydrolysis reaction rates. The stability constants of the dinuclear Ln2 (m-ODO2A-dimer) complexes and various hydrolytic species confirmed by mass spectrometry were determined. DFT calculations revealed that the Y2 LH-1 and the Y2 LH-2 species tended to form structures with the respective closed- and open-form conformations. Luminescence lifetime data for the heterodimetallic TbEuL system confirmed the fluorescence resonance energy transfer from the TbIII to EuIII ion. The internuclear distance RTbEu values were estimated to be in the range of 9.4-11.3 Å (pH 6.7-10.6), which were comparable to those of the DFT calculated open-form conformations. Multiple linear regression analysis of the kobs data was performed using the equation: kobs,corr. =kobs -kobs,OH =kLn2LHM->1 [Ln2 LH-1 ]+kLn2LH-2 [Ln2 LH-2 ] for the observed Ln2 L-promoted BNPP/HPNP hydrolysis reactions in solution pH from 7 to 10.5 (Ln=Eu, Yb). The results showed that the second-order rate constants for the Eu2 LH-2 and Yb2 LH-2 species were about 50-400 times more reactive than the structural analogous Zn2 (m-12 N3 O-dimer) system.
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Affiliation(s)
- C Allen Chang
- Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, No. 155, Sec. 2, Li-Nong St., Beitou, Taipei, Taiwan), 112, Republic of China.,Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, No. 155, Sec. 2, Li-Nong Street, Taipei, 112, Taiwan, Republic of China.,Molecular Imaging Research Center (MIRC), National Yang-Ming University, Taipei, 112, Taiwan, Republic of China.,Department of Biological Science and Technology, National Chiao Tung University, No. 75 Po-Ai Street, Hsinchu, Taiwan, 30039, Republic of China
| | - Hwa-Yu Lee
- Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, No. 155, Sec. 2, Li-Nong St., Beitou, Taipei, Taiwan), 112, Republic of China
| | - Syue-Liang Lin
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, No. 155, Sec. 2, Li-Nong Street, Taipei, 112, Taiwan, Republic of China
| | - Ching-Ning Meng
- Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, No. 155, Sec. 2, Li-Nong St., Beitou, Taipei, Taiwan), 112, Republic of China
| | - Tsung-Ta Wu
- Department of Biological Science and Technology, National Chiao Tung University, No. 75 Po-Ai Street, Hsinchu, Taiwan, 30039, Republic of China
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17
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Mikkola S, Lönnberg T, Lönnberg H. Phosphodiester models for cleavage of nucleic acids. Beilstein J Org Chem 2018; 14:803-837. [PMID: 29719577 PMCID: PMC5905247 DOI: 10.3762/bjoc.14.68] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids that store and transfer biological information are polymeric diesters of phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases, is one of the underlying biological processes. The remarkable catalytic efficiency of nucleases, together with the ability of ribonucleic acids to serve sometimes as nucleases, has made the cleavage of phosphodiesters a subject of intensive mechanistic studies. In addition to studies of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on synergistic participation of several catalytic entities. Many nucleases are metalloenzymes and small molecular models offer an excellent tool to construct models for their catalytic centers. The present review tends to be an up to date summary of what has been achieved by mechanistic studies with small molecular phosphodiesters.
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Affiliation(s)
- Satu Mikkola
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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18
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Boone M, De Koker A, Callewaert N. Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction. Nucleic Acids Res 2018; 46:2701-2721. [PMID: 29514322 PMCID: PMC5888575 DOI: 10.1093/nar/gky167] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 02/05/2018] [Accepted: 02/23/2018] [Indexed: 12/14/2022] Open
Abstract
All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences. In the past decade especially, driven by the progress in the field of massively parallel sequencing, numerous studies have comprehensively assessed the impact of particular manipulations on library complexity and quality, and characterized the activities and specificities of several key enzymes used in library construction. Fortunately, careful protocol design and reagent choice can substantially mitigate many of these biases, and enable reliable representation of sequences in libraries. This review aims to guide the reader through the vast expanse of literature on the subject to promote informed library generation, independent of the application.
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Affiliation(s)
- Morgane Boone
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Andries De Koker
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Nico Callewaert
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
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19
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Francis AJ, Resendiz MJE. Protocol for the Solid-phase Synthesis of Oligomers of RNA Containing a 2'-O-thiophenylmethyl Modification and Characterization via Circular Dichroism. J Vis Exp 2017. [PMID: 28784951 DOI: 10.3791/56189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Solid-phase synthesis has been used to obtain canonical and modified polymers of nucleic acids, specifically of DNA or RNA, which has made it a popular methodology for applications in various fields and for different research purposes. The procedure described herein focuses on the synthesis, purification, and characterization of dodecamers of RNA 5'-[CUA CGG AAU CAU]-3' containing zero, one, or two modifications located at the C2'-O-position. The probes are based on 2-thiophenylmethyl groups, incorporated into RNA nucleotides via standard organic synthesis and introduced into the corresponding oligonucleotides via their respective phosphoramidites. This report makes use of phosphoramidite chemistry via the four canonical nucleobases (Uridine (U), Cytosine (C), Guanosine (G), Adenosine (A)), as well as 2-thiophenylmethyl functionalized nucleotides modified at the 2'-O-position; however, the methodology is amenable for a large variety of modifications that have been developed over the years. The oligonucleotides were synthesized on a controlled-pore glass (CPG) support followed by cleavage from the resin and deprotection under standard conditions, i.e., a mixture of ammonia and methylamine (AMA) followed by hydrogen fluoride/triethylamine/N-methylpyrrolidinone. The corresponding oligonucleotides were purified via polyacrylamide electrophoresis (20% denaturing) followed by elution, desalting, and isolation via reversed-phase chromatography (Sep-pak, C18-column). Quantification and structural parameters were assessed via ultraviolet-visible (UV-vis) and circular dichroism (CD) photometric analysis, respectively. This report aims to serve as a resource and guide for beginner and expert researchers interested in embarking in this field. It is expected to serve as a work-in-progress as new technologies and methodologies are developed. The description of the methodologies and techniques within this document correspond to a DNA/RNA synthesizer (refurbished and purchased in 2013) that uses phosphoramidite chemistry.
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20
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Zhang S, Gu H, Chen H, Strong E, Ollie EW, Kellerman D, Liang D, Miyagi M, Anderson VE, Piccirilli JA, York DM, Harris ME. Isotope effect analyses provide evidence for an altered transition state for RNA 2'-O-transphosphorylation catalyzed by Zn(2+). Chem Commun (Camb) 2016; 52:4462-5. [PMID: 26859380 DOI: 10.1039/c5cc10212j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Solvent D2O and (18)O kinetic isotope effects on RNA 2'-O-transphosphorylation catalyzed by Zn(2+) demonstrate an altered transition state relative to specific base catalysis. A recent model from DFT calculations involving inner sphere coordination to the non-bridging and leaving group oxygens is consistent with the data.
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Affiliation(s)
- Shuming Zhang
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Hong Gu
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Haoyuan Chen
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University Piscataway, NJ 08854, USA
| | - Emily Strong
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Edward W Ollie
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Daniel Kellerman
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Danni Liang
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Masaru Miyagi
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Vernon E Anderson
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Joseph A Piccirilli
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Darrin M York
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University Piscataway, NJ 08854, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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21
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Bím D, Svobodová E, Eigner V, Rulíšek L, Hodačová J. Copper(II) and Zinc(II) Complexes of Conformationally Constrained Polyazamacrocycles as Efficient Catalysts for RNA Model Substrate Cleavage in Aqueous Solution at Physiological pH. Chemistry 2016; 22:10426-37. [DOI: 10.1002/chem.201601175] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Daniel Bím
- Department of Organic Chemistry, Faculty of Chemical Technology; University of Chemistry and Technology; Technická 5 166 28 Prague 6 Czech Republic), Fax: (+420) 220-444-288
- Institute of Organic Chemistry and Biochemistry; v.v.i. and Gilead Sciences Research Center, Academy of Sciences of the Czech Republic; Flemingovo náměstí 2 166 10 Prague 6 Czech Republic
| | - Eva Svobodová
- Department of Organic Chemistry, Faculty of Chemical Technology; University of Chemistry and Technology; Technická 5 166 28 Prague 6 Czech Republic), Fax: (+420) 220-444-288
| | - Václav Eigner
- Department of Solid State Chemistry, Faculty of Chemical Technology; University of Chemistry and Technology; Technická 5 166 28 Prague 6 Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry; v.v.i. and Gilead Sciences Research Center, Academy of Sciences of the Czech Republic; Flemingovo náměstí 2 166 10 Prague 6 Czech Republic
| | - Jana Hodačová
- Department of Organic Chemistry, Faculty of Chemical Technology; University of Chemistry and Technology; Technická 5 166 28 Prague 6 Czech Republic), Fax: (+420) 220-444-288
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22
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Fanning AM, Plush SE, Gunnlaugsson T. Tri- and tetra-substituted cyclen based lanthanide(III) ion complexes as ribonuclease mimics: a study into the effect of log Ka, hydration and hydrophobicity on phosphodiester hydrolysis of the RNA-model 2-hydroxypropyl-4-nitrophenyl phosphate (HPNP). Org Biomol Chem 2016; 13:5804-16. [PMID: 25909178 DOI: 10.1039/c4ob02384f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A series of tetra-substituted 'pseudo' dipeptide ligands of cyclen (1,4,7,10,-tetraazacyclododecane) and a tri-substituted 3'-pyridine ligand of cyclen, and the corresponding lanthanide(III) complexes were synthesised and characterised as metallo-ribonuclease mimics. All complexes were shown to promote hydrolysis of the phosphodiester bond of 2-hydroxypropyl-4-nitrophenyl phosphate (HPNP, τ1/2 = 5.87 × 10(3) h), a well known RNA mimic. The La(III) and Eu(III) tri-substituted 3'-pyridine lanthanide(III) complexes being the most efficient in promoting such hydrolysis at pH 7.4 and at 37 °C; with τ1/2 = 1.67 h for La(III) and 1.74 h for Eu(III). The series was developed to provide the opportunity to investigate the consequences of altering the lanthanide(III) ion, coordination ability and hydrophobicity of a metallo-cavity on the rate of hydrolysis using the model phosphodiester, HPNP, at 37 °C. To further provide information on the role that the log Ka of the metal bound water plays in phosphodiester hydrolysis the protonation constants and the metal ion stability constants of both a tri and tetra-substituted 3'pyridine complex were determined. Our results highlighted several key features for the design of lanthanide(III) ribonucelase mimics; the presence of two metal bound water molecules are vital for pH dependent rate constants for Eu(III) complexes, optimal pH activity approximating physiological pH (∼7.4) may be achieved if the log Ka values for both MLOH and ML(OH)2 species occur in this region, small changes to hydrophobicity within the metallo cavity influence the rate of hydrolysis greatly and an amide adjacent to the metal ion capable of forming hydrogen bonds with the substrate is required for achieving fast hydrolysis.
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Affiliation(s)
- Ann-Marie Fanning
- School of Chemistry and Trinity Biomedical Sciences Institute, University of Dublin, Trinity College Dublin, Dublin 2, Ireland.
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23
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Phosphodiester cleavage by trivalent lanthanides in the presence of native cyclodextrins. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2015.10.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Abstract
We have prepared L- and D-deoxypolypeptides (DOPPs) by selective reduction of appropriately protected polyhistidines with borane, reducing the carbonyl groups to methylenes. The result is a chiral polyamine, not amide, with a mainly protonated backbone and chirally mounted imidazolylmethylene side chains that are mostly unprotonated at neutrality because of the nearby polycationic backbone. We found that, in contrast with the D-octahistidine DOPP, the L-octahistidine DOPP is able to cooperatively bind to a D-polyuridylic acid RNA; this is consistent with results of previous studies showing that, relative to D-histidine, L-histidine is able to more strongly bind to RNA. The L-DOPP was also a better catalyst for cleaving the RNA than the D-DOPP, consistent with evidence that the L-DOPP uses its imidazole groups for catalysis, in addition to the backbone cations, but the D-DOPP does not use the imidazoles. The L-DOPP bifunctional process probably forms a phosphorane intermediate. This is a mechanism we have proposed for models of ribonuclease cleavage and for the ribonuclease A enzyme itself, based on our studies of the cleavage and isomerization of UpU catalyzed by imidazole buffers as well as other relevant studies. This mechanism contrasts with earlier, generally accepted ribonuclease cleavage mechanisms where the proton donor coordinates with the oxygen of the leaving group as the 2-hydroxyl of ribose attacks the unprotonated phosphate.
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25
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Chang CA. Dissociation Kinetics of Nickel (II), Zinc (II) and Cadmium (II) Complexes of 1,7-Diaza-4,10,13-trioxacyclopentadecane-N,N′-diacetic Acid and 1,10-Diaza-4,7,13,16-tetraoxacyclooctadecane-N,N′-diacetic Acid. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.199600060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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26
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Allen Chang C, Chen CY, Chen HY. Determination of Stability Constants of Metal Complexes by Capillary Electrophoresis. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.199900070] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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27
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Kooijmans SAA, Stremersch S, Braeckmans K, de Smedt SC, Hendrix A, Wood MJA, Schiffelers RM, Raemdonck K, Vader P. Electroporation-induced siRNA precipitation obscures the efficiency of siRNA loading into extracellular vesicles. J Control Release 2013; 172:229-238. [PMID: 23994516 DOI: 10.1016/j.jconrel.2013.08.014] [Citation(s) in RCA: 430] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 08/06/2013] [Accepted: 08/14/2013] [Indexed: 12/25/2022]
Abstract
Extracellular vesicles (EVs) are specialised endogenous carriers of proteins and nucleic acids and are involved in intercellular communication. EVs are therefore proposed as candidate drug delivery systems for the delivery of nucleic acids and other macromolecules. However, the preparation of EV-based drug delivery systems is hampered by the lack of techniques to load the vesicles with nucleic acids. In this work we have now characterised in detail the use of an electroporation method for this purpose. When EVs were electroporated with fluorescently labelled siRNA, siRNA retention was comparable with previously published results (20-25% based on fluorescence spectroscopy and fluorescence fluctuation spectroscopy), and electroporation with unlabelled siRNA resulted in significant siRNA retention in the EV pellet as measured by RT-PCR. Remarkably, when siRNA was electroporated in the absence of EVs, a similar or even greater siRNA retention was measured. Nanoparticle tracking analysis and confocal microscopy showed extensive formation of insoluble siRNA aggregates after electroporation, which could be dramatically reduced by addition of EDTA. Other strategies to reduce aggregate formation, including the use of cuvettes with conductive polymer electrodes and the use of an acidic citrate electroporation buffer, resulted in a more efficient reduction of siRNA precipitation than EDTA. However, under these conditions, siRNA retention was below 0.05% and no significant differences in siRNA retention could be measured between samples electroporated in the presence or absence of EVs. Our results show that electroporation of EVs with siRNA is accompanied by extensive siRNA aggregate formation, which may cause overestimation of the amount of siRNA actually loaded into EVs. Moreover, our data clearly illustrate that electroporation is far less efficient than previously described, and highlight the necessity for alternative methods to prepare siRNA-loaded EVs.
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Affiliation(s)
- Sander A A Kooijmans
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stephan Stremersch
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium; Centre for Nano- and Biophotonics, Ghent University, Ghent, Belgium
| | - Stefaan C de Smedt
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium
| | - An Hendrix
- Department of Radiation Oncology and Experimental Cancer Research, Laboratory of Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Matthew J A Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Raymond M Schiffelers
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Koen Raemdonck
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium.
| | - Pieter Vader
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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Binding and biomimetic cleavage of the RNA poly(U) by synthetic polyimidazoles. Proc Natl Acad Sci U S A 2012; 109:12884-7. [PMID: 22826260 DOI: 10.1073/pnas.1210846109] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four polyimidazoles were used in the binding and cleavage studies with poly(U). The two polydisperse polyvinylimidazoles were previously described by others, while the other two new polymers of polyethyleneimines were prepared by cationic polymerization of oxazolines. The latter had imidazole units attached to each nitrogen of the polymers. They were characterized by gel permeation chromatography and had very low polydispersities. When they were partially protonated they bound to the poly(U) and catalyzed its cleavage by a process analogous to that used by the enzyme ribonuclease A. The kinetics of the cleavage were followed by an assay we had previously described using phosphodiesterase I from Crotalus venom after the cleavage processes. Cleavage of poly(U) with Zn(2+) was also examined, with and without the polymers. A scheme is described in which these cleavages could be made sequence selective with various RNAs, particularly with important targets, such as viral RNAs.
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29
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Abstract
Metal ions are inextricably involved with nucleic acids due to their polyanionic nature. In order to understand the structure and function of RNAs and DNAs, one needs to have detailed pictures on the structural, thermodynamic, and kinetic properties of metal ion interactions with these biomacromolecules. In this review we first compile the physicochemical properties of metal ions found and used in combination with nucleic acids in solution. The main part then describes the various methods developed over the past decades to investigate metal ion binding by nucleic acids in solution. This includes for example hydrolytic and radical cleavage experiments, mutational approaches, as well as kinetic isotope effects. In addition, spectroscopic techniques like EPR, lanthanide(III) luminescence, IR and Raman as well as various NMR methods are summarized. Aside from gaining knowledge about the thermodynamic properties on the metal ion-nucleic acid interactions, especially NMR can be used to extract information on the kinetics of ligand exchange rates of the metal ions applied. The final section deals with the influence of anions, buffers, and the solvent permittivity on the binding equilibria between metal ions and nucleic acids. Little is known on some of these aspects, but it is clear that these three factors have a large influence on the interaction between metal ions and nucleic acids.
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Affiliation(s)
- Maria Pechlaner
- Institute of Inorganic Chemistry, University of Zürich, Zürich, Switzerland
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Korhonen H, Mikkola S, Williams NH. The mechanism of cleavage and isomerisation of RNA promoted by an efficient dinuclear Zn2+ complex. Chemistry 2011; 18:659-70. [PMID: 22162262 DOI: 10.1002/chem.201100721] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Indexed: 11/11/2022]
Abstract
The cleavage and isomerisation of uridine 3'-alkylphosphates was studied in the presence of a dinuclear Zn(2+) complex, 3. The rate acceleration of the cleavage by 1 mM 3 is approximately 10(6)-fold under neutral conditions. Most remarkably, the complex also promotes the isomerisation of phosphodiester bonds, although the rate-enhancement is more modest: under neutral conditions complex 3 (1 mM) catalyses isomerisation by about 500-fold. The observation of this reaction shows that the reactions of these substrates catalysed by 3 proceed through a stepwise mechanism involving an intermediate phosphorane. A β(lg) value of -0.92 was determined for the 3-promoted cleavage reaction, and modest kinetic solvent deuterium isotope effects ranging from 1.5 to 2.8 were observed. Isomerisation was less sensitive to the nature of the esterifying group, with a β value of -0.5, and the kinetic solvent deuterium isotope effects were less than 1.5. Most of these characteristics of the 3-promoted cleavage are very similar to those for the cleavage of nucleoside 3'-phosphotriesters. These data are explained by a mechanism in which the complex primarily acts as an electrophilic catalyst neutralising the charge on the phosphate and stabilising an intermediate phosphorane, with general acid catalysis promoting the cleavage reaction. In contrast to the behaviour of triesters, isomerisation is significantly slower than cleavage; this suggests that the changes in geometry that occur during isomerisation lead to a much less stable complex between 3 and the phosphorane intermediate.
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Affiliation(s)
- Heidi Korhonen
- Department of Chemistry, 20014 University of Turku, Turku, Finland
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31
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Strauss B, Nierth A, Singer M, Jäschke A. Direct structural analysis of modified RNA by fluorescent in-line probing. Nucleic Acids Res 2011; 40:861-70. [PMID: 21917852 PMCID: PMC3258135 DOI: 10.1093/nar/gkr733] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Chemical probing is a common method for the structural characterization of RNA. Typically, RNA is radioactively end-labelled, subjected to probing conditions, and the cleavage fragment pattern is analysed by gel electrophoresis. In recent years, many chemical modifications, like fluorophores, were introduced into RNA, but methods are lacking that detect the influence of the modification on the RNA structure with single-nucleotide resolution. Here, we first demonstrate that a 5′-terminal 32P label can be replaced by a dye label for in-line probing of riboswitch RNAs. Next, we show that small, highly structured FRET-labelled Diels–Alderase ribozymes can be directly probed, using the internal or terminal FRET dyes as reporters. The probing patterns indeed reveal whether or not the attachment of the dyes influences the structure. The existence of two dye labels in typical FRET constructs is found to be beneficial, as ‘duplexing’ allows observation of the complete RNA on a single gel. Structural information can be derived from the probing gels by deconvolution of the superimposed band patterns. Finally, we use fluorescent in-line probing to experimentally validate the structural consequences of photocaging, unambiguously demonstrating the intentional destruction of selected elements of secondary or tertiary structure.
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Affiliation(s)
- Benjamin Strauss
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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32
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A rapid and cost effective method in purifying small RNA. World J Microbiol Biotechnol 2011; 28:105-11. [DOI: 10.1007/s11274-011-0797-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 05/18/2011] [Indexed: 10/18/2022]
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Jiang W, Xu B, Li J, Lin Q, Liu F. Zn(II)-Catalyzed Cleavage of 2-Hydroxypropyl p-Nitrophenyl Phosphate in Gemini 16-6-16 Micelles. J DISPER SCI TECHNOL 2009. [DOI: 10.1080/01932690802598978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Weidong Jiang
- a Key Laboratory of Green Chemistry & Technology, Sichuan University of Science & Engineering , Sichuan Zigong, P. R. China
| | - Bin Xu
- a Key Laboratory of Green Chemistry & Technology, Sichuan University of Science & Engineering , Sichuan Zigong, P. R. China
| | - Jianzhang Li
- a Key Laboratory of Green Chemistry & Technology, Sichuan University of Science & Engineering , Sichuan Zigong, P. R. China
| | - Qi Lin
- b Department of Chemistry and Chemical Engineering , Minjiang University , Fujian Fuzhou, P. R. China
| | - Fuan Liu
- a Key Laboratory of Green Chemistry & Technology, Sichuan University of Science & Engineering , Sichuan Zigong, P. R. China
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34
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Self-assembled gold nanocrystal micelles act as an excellent artificial nanozyme with ribonuclease activity. J Biol Inorg Chem 2009; 14:653-62. [DOI: 10.1007/s00775-009-0478-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 02/05/2009] [Indexed: 10/21/2022]
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Stern R, Jedrzejas MJ. Carbohydrate Polymers at the Center of Life’s Origins: The Importance of Molecular Processivity. Chem Rev 2008; 108:5061-85. [DOI: 10.1021/cr078240l] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Robert Stern
- Department of Pathology and Comprehensive Cancer Center, School of Medicine, University of California, San Francisco, California 94143, Microdesign Institute, 29 Kingwood Rd., Oakland, California 94619, and Center for Immunobiology and Vaccine Development, Children’s Hospital Oakland Research Institute, 5700 Martin Luther King, Jr. Way, Oakland, California 94609
| | - Mark J. Jedrzejas
- Department of Pathology and Comprehensive Cancer Center, School of Medicine, University of California, San Francisco, California 94143, Microdesign Institute, 29 Kingwood Rd., Oakland, California 94619, and Center for Immunobiology and Vaccine Development, Children’s Hospital Oakland Research Institute, 5700 Martin Luther King, Jr. Way, Oakland, California 94609
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37
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Jiang W, Xu B, Lin Q, Li J, Fu H, Zeng X, Chen H. Cleavage of phosphate diesters mediated by Zn(II) complex in Gemini surfactant micelles. J Colloid Interface Sci 2007; 311:530-6. [PMID: 17445825 DOI: 10.1016/j.jcis.2007.02.056] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2006] [Revised: 02/15/2007] [Accepted: 02/17/2007] [Indexed: 11/16/2022]
Abstract
The cleavage of 2-hydroxypropyl p-nitrophenyl phosphate (HPNP) catalyzed by the Zn(II)-biap (biap: N,N-bis(2-ethyl-5-methylimidazole-4-ylmethyl)aminopropane) complex has been investigated spectrophotometrically in a micellar solution of cationic Gemini surfactant 16-2-16 [bis(hexadecyldimethylammonium)ethane bromide] and CTAB (hexadecyltrimethylammonium bromide) at 25+/-0.1 degrees C. The experimental results reveal that a higher rate of acceleration (about 2016-fold) of HPNP cleavage promoted by the Zn(II)-biap complex has been observed in the 16-2-16 micellar solution in comparison with the background rate (k(0)) of HPNP spontaneous cleavage at 25 degrees C. Reaction rates of HPNP cleavage in CTAB micellar solutions are only about 40% of that in Gemini 16-2-16 micelles under comparable conditions. In addition, the cleavage rates of HPNP in Gemini micelles and in CTAB micelles are respectively 29.5 times and 12 times faster than that in aqueous buffer. Especially, a "sandwich absorptive mode" has been proposed to explain the acceleration of HPNP cleavage in a cationic micellar solution.
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Affiliation(s)
- Weidong Jiang
- Key Laboratory of Green Chemistry & Technology, Sichuan University, Ministry of Education, Sichuan Chengdu 610064, People's Republic of China
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38
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Liu CT, Neverov AA, Brown RS. A Reductionist Biomimetic Model System That Demonstrates Highly Effective Zn(II)-Catalyzed Cleavage of an RNA Model. Inorg Chem 2007; 46:1778-88. [PMID: 17256929 DOI: 10.1021/ic062065u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cyclization of the RNA model 2-hydroxypropyl p-nitrophenyl phosphate (HPNPP, 1) promoted by Zn2+ alone and the 1,5,9-triazacyclododecane complex of Zn2+ (Zn2+:[12]aneN3) is studied in ethanol in the presence of 0.5 equiv of -OEt/Zn2+ to investigate the effect of a low polarity/dielectric medium on a metal-catalyzed reaction of biological relevance. Ethanol exerts a medium effect that promotes strong binding of HPNPP to Zn2+, followed by a dimerization to form a catalytically active complex (HPNPP:Zn2+)2 in which the phosphate undergoes cyclization with a rate constant of kcat = 2.9 s(-1) at s(s)pH 7.1. In the presence of the triaza ligand:Zn2+ complex, the change from water to methanol and then to ethanol brings about a mechanism where two molecules of the complex, suggested as EtOH:Zn2+:[12]aneN3 and its basic form, EtO-:Zn2+:[12]aneN3, bind to HPNPP and catalyze its decomposition with a rate constant of kcat of 0.13 s(-1) at s(s)pH 7.1. Overall, the acceleration exhibited in these two situations is 4 x 10(14)-fold and 1.7 x 10(12)-fold relative to the background ethoxide-promoted reactions at the respective s(s)pH values. The implications of these findings are discussed within the context of the idea that enzymatic catalysis is enhanced by a reduced effective dielectric constant within the active site.
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Affiliation(s)
- C Tony Liu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, Canada
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Nwe K, Richard JP, Morrow JR. Direct excitation luminescence spectroscopy of Eu(iii) complexes of 1,4,7-tris(carbamoylmethyl)-1,4,7,10- tetraazacyclododecane derivatives and kinetic studies of their catalytic cleavage of an RNA analog. Dalton Trans 2007:5171-8. [DOI: 10.1039/b710072h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Chen QY, Luo QH, Mei YH, Liu YJ, Zhou ZY. Synthesis, Characterization and Crystal Structure of an Unsymmetric Samarium(III) Cryptate. J COORD CHEM 2006. [DOI: 10.1080/00958970008055124] [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)
- Qiu-Yun Chen
- a State Key Laboratory of Coordination Chemistry , Nanjing University , Nanjing, 210093, P.R. China
| | - Qin-Hui Luo
- a State Key Laboratory of Coordination Chemistry , Nanjing University , Nanjing, 210093, P.R. China
| | - Yu-Hua Mei
- a State Key Laboratory of Coordination Chemistry , Nanjing University , Nanjing, 210093, P.R. China
| | - Yong-Jiang Liu
- a State Key Laboratory of Coordination Chemistry , Nanjing University , Nanjing, 210093, P.R. China
| | - Zhong-Yuan Zhou
- b Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences , Chengdu, 610015, P.R. China
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41
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de Figueiredo P, Terra B, Anand JK, Hikita T, Sadilek M, Monks DE, Lenskiy A, Hakomori S, Nester EW. A catalytic carbohydrate contributes to bacterial antibiotic resistance. Extremophiles 2006; 11:133-43. [PMID: 17048043 DOI: 10.1007/s00792-006-0024-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Accepted: 07/10/2006] [Indexed: 10/24/2022]
Abstract
Penicillins are widespread in nature and lethal to growing bacteria. Because of the severe threat posed by these antibiotics, bacteria have evolved a wide variety of strategies for combating them. Here, we describe one unusual strategy that involves the activity of a catalytic carbohydrate. We show that the cyclic oligosaccharide, beta-cyclodextrin (betaCD), can hydrolyze, and thereby inactivate, penicillin in vivo. Moreover, we demonstrate that this catalytic activity contributes to the antibiotic resistance of a bacterium that synthesizes this oligosaccharide in the laboratory. Taken together, these data not only expand our understanding of the biochemistry of penicillin resistance, but also provide the first demonstration of natural carbohydrate-mediated catalysis in a living system.
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Affiliation(s)
- Paul de Figueiredo
- Department of Microbiology, University of Washington, Box 357242, Seattle, WA 98195, USA.
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42
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Gupta Y, Mathur GN, Parvez M, Verma S. Phosphodiester modification by zinc metalated adenine polymer with carboxyl pendants. Bioorg Med Chem Lett 2006; 16:5364-7. [PMID: 16908147 DOI: 10.1016/j.bmcl.2006.07.077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Revised: 07/19/2006] [Accepted: 07/22/2006] [Indexed: 11/20/2022]
Abstract
This report describes a novel carboxyl pendant containing adenylated polymeric template, its metalation with Zn (II), and manifestation of catalytic activity for the hydrolysis of model phosphodiester, bis(p-nitrophenyl) phosphate (bNPP), and plasmid cleavage. Observation of a bell-shaped pH-K(obs) profile suggested influence of pH variation over hydrolysis rate. This metalated polymer also afforded facile relaxation of pBR322 supercoiled DNA, with an interesting reusability feature intricately associated with heterogeneous catalysis.
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Affiliation(s)
- Yogita Gupta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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43
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Transesterification of Phosphodiester by a Zinc-Containing Cyclen Derivative: Identification of the Active Species. European J Org Chem 2006. [DOI: 10.1002/jlac.199619960611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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44
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Fanning AM, Plush SE, Gunnlaugsson T. Tuning the properties of cyclen based lanthanide complexes for phosphodiester hydrolysis; the role of basic cofactors. Chem Commun (Camb) 2006:3791-3. [PMID: 16969459 DOI: 10.1039/b609923h] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of several cyclen based lanthanide [Eu(III) and La(III)] complexes is described; these metallo ribonuclease mimics are based on the use of alkyl amines as pendent arms, which give rise to fast hydrolysis within the physiological pH range of HPNP (an RNA model compound) that is highly dependent on the length of the alkyl spacer.
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Affiliation(s)
- Ann-Marie Fanning
- School of Chemistry, Centre for Synthesis and Chemical Biology, Trinity College Dublin, Dublin 2, Ireland
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45
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Cyclen based lanthanide ion ribonuclease mimics: the effect of pyridine cofactors upon phosphodiester HPNP hydrolysis. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.03.150] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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46
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Moss RA, Morales-Rojas H, Vijayaraghavan S, Tian J. Metal-cation-mediated hydrolysis of phosphonoformate diesters: chemoselectivity and catalysis(1). J Am Chem Soc 2004; 126:10923-36. [PMID: 15339177 DOI: 10.1021/ja030437h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrolyses in D(2)O (pD 1.7-3.1) of dimethyl (7), methyl phenyl (8), phenyl methyl (9), and diphenyl (10) phosphonoformate diesters are substantially accelerated by Ce(IV), Th(IV), Zr(IV), and Hf(IV) cations. Chemoselectivity is observed, whereby Zr(IV) and Hf(IV) principally direct P-OR hydrolysis, whereas Th(IV) and Ce(IV) mainly direct C-OR hydrolysis. Leaving group efficiency (OMe vs OPh) modulates the chemoselectivity. The metal cations also mediate further hydrolytic reactions of the initially produced phosphonoformate monoesters 14, 15, 18, and 20. The origins of the P-OR/C-OR selectivity are discussed in terms of the metal cation hydroxo species likely to be present in solution and the kinetics of the reactions.
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Affiliation(s)
- Robert A Moss
- Contribution from the Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA.
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47
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Madhavaiah C, Parvez M, Verma S. Catalytic transformations with copper-metalated diglycine conjugates. Bioorg Med Chem 2004; 12:5973-82. [PMID: 15498673 DOI: 10.1016/j.bmc.2004.08.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Accepted: 08/12/2004] [Indexed: 11/25/2022]
Abstract
A series of copper-metalated, water-soluble bis-diglycine conjugates were synthesized and characterized through spectroscopic methods. These conjugates were evaluated for the cleavage of phosphodiester substrates, supercoiled plasmid relaxation in the presence of co-oxidants, and for the oxidation of a diphenolic substrate, 2,6-dimethoxyphenol. Appreciable rate enhancements were observed for these reactions and the oxidative nucleolytic cleavage activity and phenol oxidative coupling was presumably manifested via formation of reactive oxygen species.
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Affiliation(s)
- C Madhavaiah
- Department of Chemistry, Indian Institute of Technology-Kanpur, Kanpur 208016, India
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48
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Kuusela S, Lönnberg H. Metal ions that promote the hydrolysis of nucleoside phosphoesters do not enhance intramolecular phosphate migration. J PHYS ORG CHEM 2004. [DOI: 10.1002/poc.610060606] [Citation(s) in RCA: 44] [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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49
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Kuusela S, Lönnberg H. Metal ion-promoted hydrolysis of uridine 2′, 3′ - cyclic monophosphate: Effect of metal chelates and uncomplexed aquo ions. J PHYS ORG CHEM 2004. [DOI: 10.1002/poc.610051205] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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50
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