1
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Muscat S, Martino G, Manigrasso J, Marcia M, De Vivo M. On the Power and Challenges of Atomistic Molecular Dynamics to Investigate RNA Molecules. J Chem Theory Comput 2024. [PMID: 39150960 DOI: 10.1021/acs.jctc.4c00773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2024]
Abstract
RNA molecules play a vital role in biological processes within the cell, with significant implications for science and medicine. Notably, the biological functions exerted by specific RNA molecules are often linked to the RNA conformational ensemble. However, the experimental characterization of such three-dimensional RNA structures is challenged by the structural heterogeneity of RNA and by its multiple dynamic interactions with binding partners such as small molecules, proteins, and metal ions. Consequently, our current understanding of the structure-function relationship of RNA molecules is still limited. In this context, we highlight molecular dynamics (MD) simulations as a powerful tool to complement experimental efforts on RNAs. Despite the recognized limitations of current force fields for RNA MD simulations, examining the dynamics of selected RNAs has provided valuable functional insights into their structures.
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Affiliation(s)
- Stefano Muscat
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Gianfranco Martino
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Jacopo Manigrasso
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Sweden
| | - Marco Marcia
- European Molecular Biology Laboratory Grenoble, 71 Avenue des Martyrs, 38042 Grenoble, France
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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2
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Giese TJ, Ekesan Ş, McCarthy E, Tao Y, York DM. Surface-Accelerated String Method for Locating Minimum Free Energy Paths. J Chem Theory Comput 2024; 20:2058-2073. [PMID: 38367218 PMCID: PMC11059188 DOI: 10.1021/acs.jctc.3c01401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
We present a surface-accelerated string method (SASM) to efficiently optimize low-dimensional reaction pathways from the sampling performed with expensive quantum mechanical/molecular mechanical (QM/MM) Hamiltonians. The SASM accelerates the convergence of the path using the aggregate sampling obtained from the current and previous string iterations, whereas approaches like the string method in collective variables (SMCV) or the modified string method in collective variables (MSMCV) update the path only from the sampling obtained from the current iteration. Furthermore, the SASM decouples the number of images used to perform sampling from the number of synthetic images used to represent the path. The path is optimized on the current best estimate of the free energy surface obtained from all available sampling, and the proposed set of new simulations is not restricted to being located along the optimized path. Instead, the umbrella potential placement is chosen to extend the range of the free energy surface and improve the quality of the free energy estimates near the path. In this manner, the SASM is shown to improve the exploration for a minimum free energy pathway in regions where the free energy surface is relatively flat. Furthermore, it improves the quality of the free energy profile when the string is discretized with too few images. We compare the SASM, SMCV, and MSMCV using 3 QM/MM applications: a ribozyme methyltransferase reaction using 2 reaction coordinates, the 2'-O-transphosphorylation reaction of Hammerhead ribozyme using 3 reaction coordinates, and a tautomeric reaction in B-DNA using 5 reaction coordinates. We show that SASM converges the paths using roughly 3 times less sampling than the SMCV and MSMCV methods. All three algorithms have been implemented in the FE-ToolKit package made freely available.
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Affiliation(s)
- Timothy J. Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Erika McCarthy
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yujun Tao
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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3
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Chang T, Li G, Chang D, Amini R, Zhu X, Zhao T, Gu J, Li Z, Li Y. An RNA-Cleaving DNAzyme That Requires an Organic Solvent to Function. Angew Chem Int Ed Engl 2023; 62:e202310941. [PMID: 37648674 DOI: 10.1002/anie.202310941] [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] [Received: 07/31/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Engineering functional nucleic acids that are active under unusual conditions will not only reveal their hidden abilities but also lay the groundwork for pursuing them for unique applications. Although many DNAzymes have been derived to catalyze diverse chemical reactions in aqueous solutions, no prior study has been set up to purposely derive DNAzymes that require an organic solvent to function. Herein, we utilized in vitro selection to isolate RNA-cleaving DNAzymes from a random-sequence DNA pool that were "compelled" to accept 35 % dimethyl sulfoxide (DMSO) as a cosolvent, via counter selection in a purely aqueous solution followed by positive selection in the same solution containing 35 % DMSO. This experiment led to the discovery of a new DNAzyme that requires 35 % DMSO for its catalytic activity and exhibits drastically reduced activity without DMSO. This DNAzyme also requires divalent metal ions for catalysis, and its activity is enhanced by monovalent ions. A minimized, more efficient DNAzyme was also derived. This work demonstrates that highly functional, organic solvent-dependent DNAzymes can be isolated from random-sequence DNA libraries via forced in vitro selection, thus expanding the capability and potential utility of catalytic DNA.
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Affiliation(s)
- Tianjun Chang
- School of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Guangping Li
- School of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Xiaoni Zhu
- School of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Tongqian Zhao
- School of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Zhongping Li
- Institute of Environmental Science, Shanxi University, Taiyuan, 030006, China
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
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4
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Hu G, Zhou HX. Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch. Commun Biol 2023; 6:791. [PMID: 37524918 PMCID: PMC10390503 DOI: 10.1038/s42003-023-05175-5] [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: 03/24/2023] [Accepted: 07/24/2023] [Indexed: 08/02/2023] Open
Abstract
The SAM/SAH riboswitch binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) with similar affinities. Mg2+ is generally known to stabilize RNA structures by neutralizing phosphates, but how it contributes to ligand binding and conformational transition is understudied. Here, extensive molecular dynamics simulations (totaling 120 μs) predicted over 10 inner-shell Mg2+ ions in the SAM/SAH riboswitch. Six of them line the two sides of a groove to widen it and thereby pre-organize the riboswitch for ligand entry. They also form outer-shell coordination with the ligands and stabilize an RNA-ligand hydrogen bond, which effectively diminishes the selectivity between SAM and SAH. One Mg2+ ion unique to the apo form maintains the Shine-Dalgarno sequence in an autonomous mode and thereby facilitates its release for ribosome binding. Mg2+ thus plays vital roles in SAM/SAH riboswitch function.
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Affiliation(s)
- Guodong Hu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou, 253023, China
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA.
- Department of Physics, University of Illinois Chicago, Chicago, IL, 60607, USA.
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5
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Boychuk BTA, Wetmore SD. Assessment of Density Functional Theory Methods for the Structural Prediction of Transition and Post-Transition Metal-Nucleic Acid Complexes. J Chem Theory Comput 2023. [PMID: 37399186 DOI: 10.1021/acs.jctc.3c00127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Understanding the structure of metal-nucleic acid systems is important for many applications such as the design of new pharmaceuticals, metal detection platforms, and nanomaterials. Herein, we explore the ability of 20 density functional theory (DFT) functionals to reproduce the crystal structure geometry of transition and post-transition metal-nucleic acid complexes identified in the Protein Data Bank and Cambridge Structural Database. The environmental extremes of the gas phase and implicit water were considered, and analysis focused on the global and inner coordination geometry, including the coordination distances. Although gas-phase calculations were unable to describe the structure of 12 out of the 53 complexes in our test set regardless of the DFT functional considered, accounting for the broader environment through implicit solvation or constraining the model truncation points to crystallographic coordinates generally afforded agreement with the experimental structure, suggesting that functional performance for these systems is likely due to the models rather than the methods. For the remaining 41 complexes, our results show that the reliability of functionals depends on the metal identity, with the magnitude of error varying across the periodic table. Furthermore, minimal changes in the geometries of these metal-nucleic acid complexes occur upon use of the Stuttgart-Dresden effective core potential and/or inclusion of an implicit water environment. The overall top three performing functionals are ωB97X-V, ωB97X-D3(BJ), and MN15, which reliably describe the structure of a broad range of metal-nucleic acid systems. Other suitable functionals include MN15-L, which is a cheaper alternative to MN15, and PBEh-3c, which is commonly used in QM/MM calculations of biomolecules. In fact, these five methods were the only functionals tested to reproduce the coordination sphere of Cu2+-containing complexes. For metal-nucleic acid systems that do not contain Cu2+, ωB97X and ωB97X-D are also suitable choices. These top-performing methods can be utilized in future investigations of diverse metal-nucleic acid complexes of relevance to biology and material science.
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Affiliation(s)
- Briana T A Boychuk
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
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6
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Yoon S, Ollie E, York DM, Piccirilli JA, Harris ME. Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis. Biochemistry 2023. [PMID: 37294744 DOI: 10.1021/acs.biochem.3c00160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Pistol ribozyme (Psr) is a distinct class of small endonucleolytic ribozymes, which are important experimental systems for defining fundamental principles of RNA catalysis and designing valuable tools in biotechnology. High-resolution structures of Psr, extensive structure-function studies, and computation support a mechanism involving one or more catalytic guanosine nucleobases acting as a general base and divalent metal ion-bound water acting as an acid to catalyze RNA 2'-O-transphosphorylation. Yet, for a wide range of pH and metal ion concentrations, the rate of Psr catalysis is too fast to measure manually and the reaction steps that limit catalysis are not well understood. Here, we use stopped-flow fluorescence spectroscopy to evaluate Psr temperature dependence, solvent H/D isotope effects, and divalent metal ion affinity and specificity unconstrained by limitations due to fast kinetics. The results show that Psr catalysis is characterized by small apparent activation enthalpy and entropy changes and minimal transition state H/D fractionation, suggesting that one or more pre-equilibrium steps rather than chemistry is rate limiting. Quantitative analyses of divalent ion dependence confirm that metal aquo ion pKa correlates with higher rates of catalysis independent of differences in ion binding affinity. However, ambiguity regarding the rate-limiting step and similar correlation with related attributes such as ionic radius and hydration free energy complicate a definitive mechanistic interpretation. These new data provide a framework for further interrogation of Psr transition state stabilization and show how thermal instability, metal ion insolubility at optimal pH, and pre-equilibrium steps such as ion binding and folding limit the catalytic power of Psr suggesting potential strategies for further optimization.
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Affiliation(s)
- Suhyun Yoon
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Edward Ollie
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Darrin M York
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Joseph A Piccirilli
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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7
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Xing C, Lin Q, Chen Y, Zeng S, Wang J, Lu C. A Smart Metal-Polyphenol-DNAzyme nanoplatform for Gene-Chemodynamic Synergistic Tumor therapy. Acta Biomater 2023:S1742-7061(23)00305-7. [PMID: 37253417 DOI: 10.1016/j.actbio.2023.05.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/01/2023]
Abstract
DNAzyme-based gene regulation shows great potential for the therapy of many cancers. However, ineffective delivery and insufficient cofactor supply pose challenges for potent gene therapy. In this study, we constructed a smart metal-polyphenol-DNAzyme nanoplatform (TA-Mn@Dz NPs) with intrinsic stability, effective delivery, and cofactor self-supply ability for gene-chemodynamic synergistic tumor therapy. Tannic acid, a plant-derived polyphenol, acts as an intermediate structural unit to mediate the assembly of Mn2+/DNAzyme and tumor acid environment-responsive nanocarriers. Intracellularly, the acidic environment triggers the decomposition of TA-Mn@Dz NPs to release DNAzyme and Mn2+. The Mn2+ ion not only boosts the catalytic cleavage of surviving mRNA for effective gene therapy but also activates chemodynamic therapy (CDT), generating highly toxic ·OH from endogenous H2O2. When tail intravenously injected into MCF-7 tumor-bearing mice, the TA-Mn@Dz NPs display desirable synergistic gene-chemodynamic antitumor effects, paving the way for developing DNAzyme-based multifunctional theranostic platforms for biomedical applications. STATEMENT OF SIGNIFICANCE: 1. A smart metal-polyphenol-DNAzyme nanoplatform was constructed for gene-chemodynamic synergistic tumor therapy. 2. Tannic acid act as intermediate structural units to mediate the assembly of Mn2+/DNAzyme and tumor acid environment-responsive nanocarriers. 3. The Mn2+-ion could not only boost the catalytic cleavage of surviving mRNA for effective gene therapy, but also catalyze endogenous H2O2 to form cytotoxic hydroxyl radicals for chemodynamic therapy. 4. Our work paves an extremely simple way to integrate gene therapy with CDT for the dual-catalytic tumor treatment.
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Affiliation(s)
- Chao Xing
- Fujian Key Laboratory of Functional Marine Sensing Materials, Center for Advanced Marine Materials and Smart Sensors, College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, People's P.R. China; MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350116, P.R. China.
| | - Qitian Lin
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350116, P.R. China
| | - Yiting Chen
- Fujian Key Laboratory of Functional Marine Sensing Materials, Center for Advanced Marine Materials and Smart Sensors, College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, People's P.R. China
| | - Sijie Zeng
- Fujian Key Laboratory of Functional Marine Sensing Materials, Center for Advanced Marine Materials and Smart Sensors, College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, People's P.R. China
| | - Jun Wang
- Fujian Key Laboratory of Functional Marine Sensing Materials, Center for Advanced Marine Materials and Smart Sensors, College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, People's P.R. China.
| | - Chunhua Lu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350116, P.R. China.
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8
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Hu G, Zhou HX. Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.12.532287. [PMID: 36945415 PMCID: PMC10029009 DOI: 10.1101/2023.03.12.532287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
The SAM/SAH riboswitch binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) with similar affinities. Mg 2+ is generally known to stabilize RNA structures by neutralizing phosphates, but how it contributes to ligand binding and conformational transition is understudied. Here, extensive molecular dynamics simulations (totaling 120 μs) identified over 10 inner-shell Mg 2+ ions in the SAM/SAH riboswitch. Six of them line the two sides of a groove to widen it and thereby pre-organize the riboswitch for ligand entry. They also form outer-shell coordination with the ligands and stabilize an RNA-ligand hydrogen bond, which effectively diminish the selectivity between SAM and SAH. One Mg 2+ ion unique to the apo form maintains the Shine-Dalgarno sequence in an autonomous mode and thereby facilitates its release for ribosome binding. Mg 2+ thus plays vital roles in SAM/SAH riboswitch function.
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Affiliation(s)
- Guodong Hu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou 253023, China
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607
- Department of Physics, University of Illinois Chicago, Chicago, IL 60607
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9
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Mahajan PS, Smith SJ, Hughes SH, Zhao X, Burke TR. A Practical Approach to Bicyclic Carbamoyl Pyridones with Application to the Synthesis of HIV-1 Integrase Strand Transfer Inhibitors. Molecules 2023; 28:molecules28031428. [PMID: 36771093 PMCID: PMC9919513 DOI: 10.3390/molecules28031428] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
An efficient one-pot synthetic method has been developed for the preparation of bicyclic carbamoyl pyridones from the known common intermediate methyl 5-((2,4-difluorobenzyl)carbamoyl)-1-(2,2-dimethoxyethyl)-3-methoxy-4-oxo-1,4-dihydropyridine-2-carboxylate (8). The scalable protocol is facile and employs readily available reagents, needing only a single purification as the final step. The utility of the approach was demonstrated by preparing a library of HIV-1 integrase strand transfer inhibitors (INSTIs) that differ by the presence or absence of a double bond in the B-ring of the bicyclic carbamoyl pyridines 6 and 7. Several of the analogs show good antiviral potencies in single-round HIV-1 replication antiviral assays and show no cytotoxicity in cell culture assays. In general, the compounds with a B-ring double bond have higher antiviral potencies than their saturated congeners. Our methodology should be applicable to the synthesis of a range of new metal-chelating analogs.
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Affiliation(s)
- Pankaj S. Mahajan
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Steven J. Smith
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Xuezhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Terrence R. Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
- Correspondence: ; Tel.: +1-301-846-5906; Fax: +1-301-846-6033
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10
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Azemin WA, Alias N, Ali AM, Shamsir MS. Structural and functional characterisation of HepTH1-5 peptide as a potential hepcidin replacement. J Biomol Struct Dyn 2023; 41:681-704. [PMID: 34870559 DOI: 10.1080/07391102.2021.2011415] [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: 01/04/2023]
Abstract
Hepcidin is a principal regulator of iron homeostasis and its dysregulation has been recognised as a causative factor in cancers and iron disorders. The strategy of manipulating the presence of hepcidin peptide has been used for cancer treatment. However, this has demonstrated poor efficiency and has been short-lived in patients. Many studies reported using minihepcidin therapy as an alternative way to treat hepcidin dysregulation, but this was only applied to non-cancer patients. Highly conserved fish hepcidin protein, HepTH1-5, was investigated to determine its potential use in developing a hepcidin replacement for human hepcidin (Hepc25) and as a therapeutic agent by targeting the tumour suppressor protein, p53, through structure-function analysis. The authors found that HepTH1-5 is stably bound to ferroportin, compared to Hepc25, by triggering the ferroportin internalisation via Lys42 and Lys270 ubiquitination, in a similar manner to the Hepc25 activity. Moreover, the residues Ile24 and Gly24, along with copper and zinc ligands, interacted with similar residues, Lys24 and Asp1 of Hepc25, respectively, showing that those molecules are crucial to the hepcidin replacement strategy. HepTH1-5 interacts with p53 and activates its function through phosphorylation. This finding shows that HepTH1-5 might be involved in the apoptosis signalling pathway upon a DNA damage response. This study will be very helpful for understanding the mechanism of the hepcidin replacement and providing insights into the HepTH1-5 peptide as a new target for hepcidin and cancer therapeutics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wan-Atirah Azemin
- School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut, Terengganu, Malaysia.,Bioinformatics Research Group (BIRG), Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Nadiawati Alias
- School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut, Terengganu, Malaysia
| | - Abdul Manaf Ali
- School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut, Terengganu, Malaysia
| | - Mohd Shahir Shamsir
- Bioinformatics Research Group (BIRG), Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia.,Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor, Malaysia
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11
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Tellurium-Modified Nucleosides, Nucleotides, and Nucleic Acids with Potential Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238379. [PMID: 36500495 PMCID: PMC9737395 DOI: 10.3390/molecules27238379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022]
Abstract
Tellurium was successfully incorporated into proteins and applied to protein structure determination through X-ray crystallography. However, studies on tellurium modification of DNA and RNA are limited. This review highlights the recent development of Te-modified nucleosides, nucleotides, and nucleic acids, and summarizes the main synthetic approaches for the preparation of 5-PhTe, 2'-MeTe, and 2'-PhTe modifications. Those modifications are compatible with solid-phase synthesis and stable during Te-oligonucleotide purification. Moreover, the ideal electronic and atomic properties of tellurium for generating clear isomorphous signals give Te-modified DNA and RNA great potential applications in 3D crystal structure determination through X-ray diffraction. STM study also shows that Te-modified DNA has strong topographic and current peaks, which immediately suggests potential applications in nucleic acid direct imaging, nanomaterials, molecular electronics, and diagnostics. Theoretical studies indicate the potential application of Te-modified nucleosides in cancer therapy.
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12
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Wang Q, Wang Z, He Y, Xiong B, Li Y, Wang F. Chemical and structural modification of RNA-cleaving DNAzymes for efficient biosensing and biomedical applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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13
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Egger M, Bereiter R, Mair S, Micura R. Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202207590. [PMID: 38505292 PMCID: PMC10946891 DOI: 10.1002/ange.202207590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Indexed: 11/08/2022]
Abstract
Nucleolytic ribozymes utilize general acid-base catalysis to perform phosphodiester cleavage. In most ribozyme classes, a conserved active site guanosine is positioned to act as general base, thereby activating the 2'-OH group to attack the scissile phosphate (γ-catalysis). Here, we present an atomic mutagenesis study for the pistol ribozyme class. Strikingly, "general base knockout" by replacement of the guanine N1 atom by carbon results in only 2.7-fold decreased rate. Therefore, the common view that γ-catalysis critically depends on the N1 moiety becomes challenged. For pistol ribozymes we found that γ-catalysis is subordinate in overall catalysis, made up by two other catalytic factors (α and δ). Our approach allows scaling of the different catalytic contributions (α, β, γ, δ) with unprecedented precision and paves the way for a thorough mechanistic understanding of nucleolytic ribozymes with active site guanines.
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Affiliation(s)
- Michaela Egger
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Stefan Mair
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
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14
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Egger M, Bereiter R, Mair S, Micura R. Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes. Angew Chem Int Ed Engl 2022; 61:e202207590. [PMID: 35982640 PMCID: PMC9826390 DOI: 10.1002/anie.202207590] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Indexed: 01/11/2023]
Abstract
Nucleolytic ribozymes utilize general acid-base catalysis to perform phosphodiester cleavage. In most ribozyme classes, a conserved active site guanosine is positioned to act as general base, thereby activating the 2'-OH group to attack the scissile phosphate (γ-catalysis). Here, we present an atomic mutagenesis study for the pistol ribozyme class. Strikingly, "general base knockout" by replacement of the guanine N1 atom by carbon results in only 2.7-fold decreased rate. Therefore, the common view that γ-catalysis critically depends on the N1 moiety becomes challenged. For pistol ribozymes we found that γ-catalysis is subordinate in overall catalysis, made up by two other catalytic factors (α and δ). Our approach allows scaling of the different catalytic contributions (α, β, γ, δ) with unprecedented precision and paves the way for a thorough mechanistic understanding of nucleolytic ribozymes with active site guanines.
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Affiliation(s)
- Michaela Egger
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Stefan Mair
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
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15
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Li X, Loh TJ, Lim JJ, Er Saw P, Liao Y. Glycan-RNA: a new class of non-coding RNA. BIO INTEGRATION 2022. [DOI: 10.15212/bioi-2021-0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Xiuling Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Tiing Jen Loh
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jia Jia Lim
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Phei Er Saw
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yong Liao
- Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Institute for Viral Hepatitis, and Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
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16
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Ekesan Ş, McCarthy E, Case DA, York DM. RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis. J Phys Chem B 2022; 126:5982-5990. [PMID: 35862934 PMCID: PMC9496635 DOI: 10.1021/acs.jpcb.2c03727] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Electrostatic interactions are fundamental to RNA structure and function, and intimately influenced by solvation and the ion atmosphere. RNA enzymes, or ribozymes, are catalytic RNAs that are able to enhance reaction rates over a million-fold, despite having only a limited repertoire of building blocks and available set of chemical functional groups. Ribozyme active sites usually occur at junctions where negatively charged helices come together, and in many cases leverage this strained electrostatic environment to recruit metal ions in solution that can assist in catalysis. Similar strategies have been implicated in related artificially engineered DNA enzymes. Herein, we apply Poisson-Boltzmann, 3D-RISM, and molecular simulations to study a set of metal-dependent small self-cleaving ribozymes (hammerhead, pistol, and Varkud satellite) as well as an artificially engineered DNAzyme (8-17) to examine electrostatic features and their relation to the recruitment of monovalent and divalent metal ions important for activity. We examine several fundamental roles for these ions that include: (1) structural integrity of the catalytically active state, (2) pKa tuning of residues involved in acid-base catalysis, and (3) direct electrostatic stabilization of the transition state via Lewis acid catalysis. Taken together, these examples demonstrate how RNA electrostatics orchestrates the site-specific and territorial binding of metal ions to play important roles in catalysis.
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Affiliation(s)
- Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Erika McCarthy
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - David A. Case
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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17
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Ekesan Ş, York DM. Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme. Org Biomol Chem 2022; 20:6219-6230. [PMID: 35452066 PMCID: PMC9378597 DOI: 10.1039/d2ob00234e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The pistol ribozyme (Psr) is one among the most recently discovered classes of small nucleolytic ribozymes that catalyze site-specific RNA self-cleavage through 2'-O-transphosphorylation. The Psr contains a conserved guanine (G40) that in crystal structures is in a position suggesting it plays the role of the general base to abstract a proton from the nucleophile to activate the reaction. Although some functional data is consistent with this mechanistic role, a notable exception is 2-aminopurine (2AP) substitution which has no effect on the rate, unlike similar substitutions across other so-called "G + M" and "G + A" ribozyme classes. Herein we postulate that an alternate conserved guanine, G42, is the primary general base, and provide evidence from molecular simulations that the active site of Psr can undergo local refolding into a structure that is consistent with the common "L-platform/L-scaffold" architecture identified in G + M and G + A ribozyme classes with Psr currently the notable exception. We summarize the key currently available experimental data and present new classical and combined quantum mechanical/molecular mechanical simulation results that collectively suggest a new hypothesis. We hypothesize that there are two available catalytic pathways supported by different conformational states connected by a local refolding of the active site: (1) a primary pathway with an active site architecture aligned with the L-platform/L-scaffold framework where G42 acts as a general base, and (2) a secondary pathway with the crystallographic active site architecture where G40 acts as a general base. We go on to make several experimentally testable predictions, and suggest specific experiments that would ultimately bring closure to the mystery as to "who stole the proton in the pistol ribozyme?".
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Affiliation(s)
- Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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18
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Giese TJ, Zeng J, Ekesan Ş, York DM. Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions. J Chem Theory Comput 2022; 18:4304-4317. [PMID: 35709391 DOI: 10.1021/acs.jctc.2c00151] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a fast, accurate, and robust approach for determination of free energy profiles and kinetic isotope effects for RNA 2'-O-transphosphorylation reactions with inclusion of nuclear quantum effects. We apply a deep potential range correction (DPRc) for combined quantum mechanical/molecular mechanical (QM/MM) simulations of reactions in the condensed phase. The method uses the second-order density-functional tight-binding method (DFTB2) as a fast, approximate base QM model. The DPRc model modifies the DFTB2 QM interactions and applies short-range corrections to the QM/MM interactions to reproduce ab initio DFT (PBE0/6-31G*) QM/MM energies and forces. The DPRc thus enables both QM and QM/MM interactions to be tuned to high accuracy, and the QM/MM corrections are designed to smoothly vanish at a specified cutoff boundary (6 Å in the present work). The computational speed-up afforded by the QM/MM+DPRc model enables free energy profiles to be calculated that include rigorous long-range QM/MM interactions under periodic boundary conditions and nuclear quantum effects through a path integral approach using a new interface between the AMBER and i-PI software. The approach is demonstrated through the calculation of free energy profiles of a native RNA cleavage model reaction and reactions involving thio-substitutions, which are important experimental probes of the mechanism. The DFTB2+DPRc QM/MM free energy surfaces agree very closely with the PBE0/6-31G* QM/MM results, and it is vastly superior to the DFTB2 QM/MM surfaces with and without weighted thermodynamic perturbation corrections. 18O and 34S primary kinetic isotope effects are compared, and the influence of nuclear quantum effects on the free energy profiles is examined.
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Affiliation(s)
- Timothy J Giese
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Jinzhe Zeng
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
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19
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20
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Xia X, Yang H, Cao J, Zhang J, He Q, Deng R. Isothermal nucleic acid amplification for food safety analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116641] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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21
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Lorenzo-Aparicio C, Gómez Gallego M, Ramírez de Arellano C, Sierra MA. Phosphorescent Ir(III) complexes derived from purine nucleobases. Dalton Trans 2022; 51:5138-5150. [PMID: 35266928 DOI: 10.1039/d1dt04148g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the preparation and the study of new types of neutral and cationic phosphorescent heteroleptic Ir(III) complexes derived from 6-phenylpurine nucleosides and nucleotides. Neutral complexes of general formula Ir(C^N)2(acac) 7, and 8a-c (HC^N = 9-substituted-6-phenyl purine) are orange-red emissive upon photoexcitation, with short lifetimes and good quantum yields (0.42-0.65) in both PMMA films and 2-MeTHF at room temperature. In turn, cationic complexes [Ir(C^N)2(dtb-bpy)][PF6] 9, 12a and 12c (dtb-bpy = 4,4'-di-tert-butyl-2,2'-dipyridine) are yellow-green emitters with moderate quantum yields (0.24-0.32).
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Affiliation(s)
- Carmen Lorenzo-Aparicio
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain. .,Centro de Innovación en Química Avanzada (ORFEO-CINQA), Spain
| | - Mar Gómez Gallego
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain. .,Centro de Innovación en Química Avanzada (ORFEO-CINQA), Spain
| | - Carmen Ramírez de Arellano
- Centro de Innovación en Química Avanzada (ORFEO-CINQA), Spain.,Departamento de Química Orgánica, Universidad de Valencia, 46100-Valencia, Spain
| | - Miguel A Sierra
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain. .,Centro de Innovación en Química Avanzada (ORFEO-CINQA), Spain
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22
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Jones SP, Goossen C, Lewis SD, Delaney AM, Gleghorn ML. Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes. J Struct Biol X 2022; 6:100066. [PMID: 35340590 PMCID: PMC8943300 DOI: 10.1016/j.yjsbx.2022.100066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 11/16/2022] Open
Abstract
RNases are varied in the RNA structures and sequences they target for cleavage and are an important type of enzyme in cells. Despite the numerous examples of RNases known, and of those with determined three-dimensional structures, relatively few examples exist with the RNase bound to intact cognate RNA substrate prior to cleavage. To better understand RNase structure and sequence specificity for RNA targets, in vitro methods used to assemble these enzyme complexes trapped in a pre-cleaved state have been developed for a number of different RNases. We have surveyed the Protein Data Bank for such structures and in this review detail methodologies that have successfully been used and relate them to the corresponding structures. We also offer ideas and suggestions for future method development. Many strategies within this review can be used in combination with X-ray crystallography, as well as cryo-EM, and other structure-solving techniques. Our hope is that this review will be used as a guide to resolve future yet-to-be-determined RNase-substrate complex structures.
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Affiliation(s)
- Seth P. Jones
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
| | - Christian Goossen
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Lothrop St, Pittsburgh, PA 15261, United States
| | - Sean D. Lewis
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
- Mayo Clinic, 200 1st St SW, Rochester, MN 5590, United States
| | - Annie M. Delaney
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
| | - Michael L. Gleghorn
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
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23
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Yao C, Qi H, Jia X, Xu Y, Tong Z, Gu Z, Yang D. A DNA Nanocomplex Containing Cascade DNAzymes and Promoter‐Like Zn‐Mn‐Ferrite for Combined Gene/Chemo‐dynamic Therapy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Chi Yao
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Hedong Qi
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Xuemei Jia
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Yuwei Xu
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Zhaobin Tong
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Zi Gu
- School of Chemical Engineering Australian Centre for, NanoMedicine University of New South Wales Sydney NSW 2052 Australia
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
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24
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Hunsicker-Wang LM, Vogt MJ, Hoogstraten CG, Cosper NJ, Davenport AM, Hendon CH, Scott RA, Britt RD, DeRose VJ. Spectroscopic characterization of Mn2+ and Cd2+ coordination to phosphorothioates in the conserved A9 metal site of the hammerhead ribozyme. J Inorg Biochem 2022; 230:111754. [DOI: 10.1016/j.jinorgbio.2022.111754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 11/25/2022]
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25
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Yao C, Qi H, Jia X, Xu Y, Tong Z, Gu Z, Yang D. A DNA Nanocomplex Containing Cascade DNAzymes and Promoter-Like Zn-Mn-Ferrite for Combined Gene/Chemo-dynamic Therapy. Angew Chem Int Ed Engl 2021; 61:e202113619. [PMID: 34866297 DOI: 10.1002/anie.202113619] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Indexed: 12/17/2022]
Abstract
Sequential control of exogenous chemical events inside cells is a promising way to regulate cell functions and fate. Herein we report a DNA nanocomplex containing cascade DNAzymes and promoter-like Zn-Mn-Ferrite (ZMF), achieving combined gene/chemo-dynamic therapy. The promoter-like ZMF decomposed in response to intratumoral glutathione to release a sufficient quantity of metal ions, thus promoting cascade DNA/RNA cleavage and free radical generation. Two kinds of DNAzymes were designed for sequential cascade enzymatic reaction, in which metal ions functioned as cofactors. The primary DNAzyme self-cleaved the DNA chain with Zn2+ as cofactor, and produced the secondary DNAzyme; the secondary DNAzyme afterwards cleaved the EGR-1 mRNA, and thus downregulated the expression of target EGR-1 protein, achieving DNAzyme-based gene therapy. Meanwhile, the released Zn2+ , Mn2+ and Fe2+ induced Fenton/Fenton-like reactions, during which free radicals were catalytically generated and efficient chemo-dynamic therapy was achieved. In a breast cancer mouse model, the administration of DNA nanocomplex led to a significant therapeutic efficacy of tumor growth suppression.
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Affiliation(s)
- Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Hedong Qi
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Xuemei Jia
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Yuwei Xu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Zhaobin Tong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Zi Gu
- School of Chemical Engineering, Australian Centre for, NanoMedicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
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26
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Wang C, O'Hagan MP, Willner B, Willner I. Bioinspired Artificial Photosynthetic Systems. Chemistry 2021; 28:e202103595. [PMID: 34854505 DOI: 10.1002/chem.202103595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Indexed: 12/18/2022]
Abstract
Mimicking photosynthesis using artificial systems, as a means for solar energy conversion and green fuel generation, is one of the holy grails of modern science. This perspective presents recent advances towards developing artificial photosynthetic systems. In one approach, native photosystems are interfaced with electrodes to yield photobioelectrochemical cells that transform light energy into electrical power. This is exemplified by interfacing photosystem I (PSI) and photosystem II (PSII) as an electrically contacted assembly mimicking the native Z-scheme, and by the assembly of an electrically wired PSI/glucose oxidase biocatalytic conjugate on an electrode support. Illumination of the functionalized electrodes led to light-induced generation of electrical power, or to the generation of photocurrents using glucose as the fuel. The second approach introduces supramolecular photosensitizer nucleic acid/electron acceptor complexes as functional modules for effective photoinduced electron transfer stimulating the subsequent biocatalyzed generation of NADPH or the Pt-nanoparticle-catalyzed evolution of molecular hydrogen. Application of the DNA machineries for scaling-up the photosystems is demonstrated. A third approach presents the integration of artificial photosynthetic modules into dynamic nucleic acid networks undergoing reversible reconfiguration or dissipative transient operation in the presence of auxiliary triggers. Control over photoinduced electron transfer reactions and photosynthetic transformations by means of the dynamic networks is demonstrated.
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Affiliation(s)
- Chen Wang
- Institute of Chemistry, The Minerva Centre for Bio-Hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michael P O'Hagan
- Institute of Chemistry, The Minerva Centre for Bio-Hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Bilha Willner
- Institute of Chemistry, The Minerva Centre for Bio-Hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Itamar Willner
- Institute of Chemistry, The Minerva Centre for Bio-Hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, Israel
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27
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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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28
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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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29
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Abstract
This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.
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Affiliation(s)
- Erin M McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
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30
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Marathe IA, Lai SM, Zahurancik WJ, Poirier MG, Wysocki VH, Gopalan V. Protein cofactors and substrate influence Mg2+-dependent structural changes in the catalytic RNA of archaeal RNase P. Nucleic Acids Res 2021; 49:9444-9458. [PMID: 34387688 PMCID: PMC8450104 DOI: 10.1093/nar/gkab655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/02/2021] [Accepted: 07/23/2021] [Indexed: 01/07/2023] Open
Abstract
The ribonucleoprotein (RNP) form of archaeal RNase P comprises one catalytic RNA and five protein cofactors. To catalyze Mg2+-dependent cleavage of the 5′ leader from pre-tRNAs, the catalytic (C) and specificity (S) domains of the RNase P RNA (RPR) cooperate to recognize different parts of the pre-tRNA. While ∼250–500 mM Mg2+ renders the archaeal RPR active without RNase P proteins (RPPs), addition of all RPPs lowers the Mg2+ requirement to ∼10–20 mM and improves the rate and fidelity of cleavage. To understand the Mg2+- and RPP-dependent structural changes that increase activity, we used pre-tRNA cleavage and ensemble FRET assays to characterize inter-domain interactions in Pyrococcus furiosus (Pfu) RPR, either alone or with RPPs ± pre-tRNA. Following splint ligation to doubly label the RPR (Cy3-RPRC domain and Cy5-RPRS domain), we used native mass spectrometry to verify the final product. We found that FRET correlates closely with activity, the Pfu RPR and RNase P holoenzyme (RPR + 5 RPPs) traverse different Mg2+-dependent paths to converge on similar functional states, and binding of the pre-tRNA by the holoenzyme influences Mg2+ cooperativity. Our findings highlight how Mg2+ and proteins in multi-subunit RNPs together favor RNA conformations in a dynamic ensemble for functional gains.
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Affiliation(s)
- Ila A Marathe
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Stella M Lai
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Resource for Native Mass Spectrometry-Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Walter J Zahurancik
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Michael G Poirier
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Resource for Native Mass Spectrometry-Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Venkat Gopalan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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31
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Nakano SI, Yamashita H, Sugimoto N. Enhancement of the Catalytic Activity of Hammerhead Ribozymes by Organic Cations. Chembiochem 2021; 22:2721-2728. [PMID: 34240789 DOI: 10.1002/cbic.202100280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/28/2021] [Indexed: 11/05/2022]
Abstract
Catalytic turnover is important for the application of ribozymes to biotechnology. However, the turnover is often impaired because of the intrinsic high stability of base pairs with cleaved RNA products. Here, organic cations were used as additives to improve the catalytic performance of hammerhead ribozyme constructs that exhibit different kinetic behaviors. Kinetic analysis of substrate cleavage demonstrated that bulky cations, specifically tetra-substituted ammonium ions containing pentyl groups or a benzyl group, have the ability to greatly increase the turnover rate of the ribozymes. Thermal stability analysis of RNA structures revealed that the bulky cations promote the dissociation of cleaved products and refolding of incorrectly folded structures with small disruption of the catalytic structure. The use of bulky cations is a convenient method for enhancing the catalytic activity of hammerhead ribozymes, and the approach may be useful for advancing ribozyme technologies.
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Affiliation(s)
- Shu-Ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Hirofumi Yamashita
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.,Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
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32
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Zhao H, Zhang Z, Zuo D, Li L, Li F, Yang D. A Synergistic DNA-polydopamine-MnO 2 Nanocomplex for Near-Infrared-Light-Powered DNAzyme-Mediated Gene Therapy. NANO LETTERS 2021; 21:5377-5385. [PMID: 34100622 DOI: 10.1021/acs.nanolett.1c01727] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNAzyme is emerging for gene therapy. The administration of the in vivo catalytic activity of DNAzyme has proven important but challenging for clinical applications. Herein, we report a synergistic DNA-polydopamine-MnO2 nanocomplex, which enables near-infrared (NIR)-light-powered catalytic activity of DNAzyme in vivo. The nanocomplex has a hierarchical structure: a DNA nanoframework as the scaffold and polydopamine-MnO2 (PM) as the coating layer. The DNA nanoframework contains repeated DNAzyme sequences. PM assembles on the surface of the DNA nanoframework. When the nanocomplex accumulates at tumor sites, upon NIR-light radiation, polydopamine induces a temperature elevation at tumor sites via photothermal conversion; meanwhile, glutathione triggers decomposition of PM to release Mn2+ to activate DNAzyme in the cytoplasm for gene regulation. In vitro and in vivo experiments show that the PM-induced temperature elevation enhances the Egr-1 mRNA cleavage activity of DNAzyme, promoting downregulation of the Egr-1 protein in tumor cells. In addition, the temperature elevation induces heat stress, achieving a synergistic tumor ablation effect.
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Affiliation(s)
- Huaixin Zhao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Zhili Zhang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Duo Zuo
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, People's Republic of China
| | - Linghui Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Feng Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
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33
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Moon WJ, Huang PJJ, Liu J. Probing Metal-Dependent Phosphate Binding for the Catalysis of the 17E DNAzyme. Biochemistry 2021; 60:1909-1918. [PMID: 34106684 DOI: 10.1021/acs.biochem.1c00091] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The RNA-cleaving 17E DNAzyme exhibits different levels of cleavage activity in the presence of various divalent metal ions, with Pb2+ giving the fastest cleavage. In this study, the metal-phosphate interaction is probed to understand the trend of activity with different metal ions. For the first-row transition metals, the lowest activity shown by Ni2+ correlates with the inhibition by the inorganic phosphate and its water ligand exchange rate, suggesting inner-sphere metal coordination. Cleavage activity with the two stereoisomers of the phosphorothioate-modified substrates, Rp and Sp, indicated that Mg2+, Mn2+, Fe2+, and Co2+ had the highest Sp:Rp activity ratio of >900. Comparatively, the activity was much less affected using the thiophilic metals, including Pb2+, suggesting inner-sphere coordination. The pH-rate profiles showed that Pb2+ was different than the rest of the metal ions in having a smaller slope and a similar fitted apparent pKa and the pKa of metal-bound water. Combining previous reports and our current results, we propose that Pb2+ most likely plays the role of a general acid while the other metal ions are Lewis acid catalysts interacting with the scissile phosphate.
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Affiliation(s)
- Woohyun J Moon
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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34
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Peng J, Zhang Y, Jiang Y, Zhang H. Developing and Assessing Nonbonded Dummy Models of Magnesium Ion with Different Hydration Free Energy References. J Chem Inf Model 2021; 61:2981-2997. [PMID: 34080414 DOI: 10.1021/acs.jcim.1c00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A large diversity in the targeted hydration free energies (HFEs) during model parameterization of metal ions was reported in the literature with a difference by dozens of kcal/mol. Here, we developed a series of nonbonded dummy models of the Mg2+ ion targeting different HFE references in TIP3P water, followed by assessments of the designed models in the simulations of MgCl2 solution and biological systems. Together with the comparison of existing models, we conclude that the difference in the targeted HFEs has a limited influence on the model performance, while the usability of these models differs from case to case. The feasibility of reproducing more properties of Mg2+ such as diffusion constants and water exchange rates using a nonbonded dummy model is demonstrated. Underestimated activity derivative and osmotic coefficient of MgCl2 solutions in high concentration reveal a necessity for further optimization of ion-pair interactions. The developed dummy models are applicable to metal coordination with Asp, Glu, and His residues in metalloenzymes, and the performance in predicting monodentate or bidentate binding modes of Asp/Glu residues depends on the complexity of metal centers and the choice of protein force fields. When both the binding modes coexist, the nonbonded dummy models outperform point charge models, probably in need of considering polarization of metal-binding residues by, for instance, charge calibration in classical force fields. This work is valuable for the use and further development of magnesium ion models for simulations of metal-containing systems with good accuracy.
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Affiliation(s)
- Jiarong Peng
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yongguang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
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35
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36
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Lihanova Y, Weinberg CE. Biochemical analysis of cleavage and ligation activities of the pistol ribozyme from Paenibacillus polymyxa. RNA Biol 2021; 18:1858-1866. [PMID: 33622172 DOI: 10.1080/15476286.2021.1874706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Nine distinct classes of self-cleaving ribozymes are known to date, of which the pistol ribozyme class was discovered only 5 years ago. Self-cleaving ribozymes are able to cleave their own phosphodiester backbone at a specific site with rates much higher than those of spontaneous RNA degradation. Our study focuses on a bioinformatically predicted pistol ribozyme from the bacterium Paenibacillus polymyxa. We provide a biochemical characterization of this ribozyme, which includes an investigation of the effect of various metal ions on ribozyme cleavage and a kinetic analysis of ribozyme activity under increasing Mg2+ concentrations and pH. Based on the obtained results, we discuss a possible catalytic role of divalent metal ions. Moreover, we investigated the ligation activity of the P. polymyxa pistol ribozyme - an aspect that has not been previously analysed for this ribozyme class. We determined that the P. polymyxa pistol ribozyme is almost fully cleaved at equilibrium with the ligation rate constant being nearly 30-fold lower than the cleavage rate constant. In summary, we have characterized an additional representative of this recently discovered ribozyme class isolated from P. polymyxa. We expect that our biochemical characterization of a pistol representative in a cultivatable, genetically tractable organism will support our future investigation of the biological roles of this ribozyme class in bacteria.
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Affiliation(s)
- Yuliia Lihanova
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
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37
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Saran R, Huang Z, Liu J. Phosphorothioate nucleic acids for probing metal binding, biosensing and nanotechnology. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213624] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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38
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Patel AY, Jonnalagadda KS, Paradis N, Vaden TD, Wu C, Caputo GA. Effects of Ionic Liquids on Metalloproteins. Molecules 2021; 26:514. [PMID: 33478102 PMCID: PMC7835893 DOI: 10.3390/molecules26020514] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/04/2021] [Accepted: 01/08/2021] [Indexed: 01/28/2023] Open
Abstract
In the past decade, innovative protein therapies and bio-similar industries have grown rapidly. Additionally, ionic liquids (ILs) have been an area of great interest and rapid development in industrial processes over a similar timeline. Therefore, there is a pressing need to understand the structure and function of proteins in novel environments with ILs. Understanding the short-term and long-term stability of protein molecules in IL formulations will be key to using ILs for protein technologies. Similarly, ILs have been investigated as part of therapeutic delivery systems and implicated in numerous studies in which ILs impact the activity and/or stability of protein molecules. Notably, many of the proteins used in industrial applications are involved in redox chemistry, and thus often contain metal ions or metal-associated cofactors. In this review article, we focus on the current understanding of protein structure-function relationship in the presence of ILs, specifically focusing on the effect of ILs on metal containing proteins.
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Affiliation(s)
- Aashka Y. Patel
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | | | - Nicholas Paradis
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | - Timothy D. Vaden
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | - Chun Wu
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
- Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA
| | - Gregory A. Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
- Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA
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39
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Yue L, Wang S, Zhou Z, Willner I. Nucleic Acid Based Constitutional Dynamic Networks: From Basic Principles to Applications. J Am Chem Soc 2020; 142:21577-21594. [DOI: 10.1021/jacs.0c09891] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Liang Yue
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Shan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zhixin Zhou
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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40
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Li Y, Du S, Chai Z, He J. A new Pb 2+-specific DNAzyme by revisiting the catalytic core of 10-23 DNAzyme. Bioorg Med Chem 2020; 28:115796. [PMID: 33038786 DOI: 10.1016/j.bmc.2020.115796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 10/23/2022]
Abstract
10-23 DNAzyme is a catalytic DNA molecule from in vitro selection, the 15-mer catalytic core was investigated for more DNAzyme variants by block deletions. DNAzyme DZM01 was selected with metal ion dependence of Pb2+ ≫ Mn2+, with no activity in the presence of Mg2+ (20 mM), Ca2+ (20 mM), Zn2+ (20 mM, pH 6). The unique binding properties of Pb2+ with nucleic acids might be responsible for the formation of the catalytic core, which is different from that of other divalent metal ions. More DNAzyme variants are expected to be derived for specific metal ion dependence by various nucleobase sequences and modifications.
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Affiliation(s)
- Yang Li
- School of Life Science and Engineering, Handan University, Handan 056005, China; State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Shanshan Du
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; Hebei Key Laboratory of Heterocyclic Compounds, College of Chemical Engineering and Materials, Handan University, Handan 056005, China
| | - Zhilong Chai
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
| | - Junlin He
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
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41
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Moon WJ, Yang Y, Liu J. Zn 2+ -Dependent DNAzymes: From Solution Chemistry to Analytical, Materials and Therapeutic Applications. Chembiochem 2020; 22:779-789. [PMID: 33007113 DOI: 10.1002/cbic.202000586] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/01/2020] [Indexed: 12/20/2022]
Abstract
Since 1994, deoxyribozymes or DNAzymes have been in vitro selected to catalyze various types of reactions. Metal ions play a critical role in DNAzyme catalysis, and Zn2+ is a very important one among them. Zn2+ has good biocompatibility and can be used for intracellular applications. Chemically, Zn2+ is a Lewis acid and it can bind to both the phosphate backbone and the nucleobases of DNA. Zn2+ undergoes hydrolysis even at neutral pH, and the partially hydrolyzed polynuclear complexes can affect the interactions with DNA. These features have made Zn2+ a unique cofactor for DNAzyme reactions. This review summarizes Zn2+ -dependent DNAzymes with an emphasis on RNA-/DNA-cleaving reactions. A key feature is the sharp Zn2+ concentration and pH-dependent activity for many of the DNAzymes. The applications of these DNAzymes as biosensors for Zn2+ , as therapeutic agents to cleave intracellular RNA, and as chemical biology tools to manipulate DNA are discussed. Future studies can focus on the selection of new DNAzymes with improved performance and detailed biochemical characterizations to understand the role of Zn2+ , which can facilitate practical applications of Zn2+ -dependent DNAzymes.
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Affiliation(s)
- Woohyun J Moon
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Yongjie Yang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.,Department of Food and Biological Science, College of Agricultural, Yanbian University, Yanbian Chaoxianzuzizhizhou, Yanji, 133002, P. R. China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.,Centre for Eye and Vision Research, 17W Hong Kong Science Park, Hong Kong, China
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42
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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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43
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Huang PJ, Liu J. In vitro Selection of Chemically Modified DNAzymes. ChemistryOpen 2020; 9:1046-1059. [PMID: 33101831 PMCID: PMC7570446 DOI: 10.1002/open.202000134] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
DNAzymes are in vitro selected DNA oligonucleotides with catalytic activities. RNA cleavage is one of the most extensively studied DNAzyme reactions. To expand the chemical functionality of DNA, various chemical modifications have been made during and after selection. In this review, we summarize examples of RNA-cleaving DNAzymes and focus on those modifications introduced during in vitro selection. By incorporating various modified nucleotides via polymerase chain reaction (PCR) or primer extension, a few DNAzymes were obtained that can be specifically activated by metal ions such as Zn2+ and Hg2+. In addition, some modifications were introduced to mimic RNase A that can cleave RNA substrates in the absence of divalent metal ions. In addition, single modifications at the fixed regions of DNA libraries, especially at the cleavage junctions, have been tested, and examples of DNAzymes with phosphorothioate and histidine-glycine modified tertiary amine were successfully obtained specific for Cu2+, Cd2+, Zn2+, and Ni2+. Labeling fluorophore/quencher pair right next to the cleavage junction was also used to obtain signaling DNAzymes for detecting various metal ions and cells. Furthermore, we reviewed work on the cleavage of 2'-5' linked RNA and L-RNA substrates. Finally, applications of these modified DNAzymes as biosensors, RNases, and biochemical probes are briefly described with a few future research opportunities outlined at the end.
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Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of WaterlooWaterlooOntario, N2L 3G1Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of WaterlooWaterlooOntario, N2L 3G1Canada
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Kalra K, Gorle S, Cavallo L, Oliva R, Chawla M. Occurrence and stability of lone pair-π and OH-π interactions between water and nucleobases in functional RNAs. Nucleic Acids Res 2020; 48:5825-5838. [PMID: 32392301 PMCID: PMC7293021 DOI: 10.1093/nar/gkaa345] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 04/21/2020] [Accepted: 05/07/2020] [Indexed: 01/15/2023] Open
Abstract
We identified over 1000 instances of water-nucleobase stacking contacts in a variety of RNA molecules from a non-redundant set of crystal structures with resolution ≤3.0 Å. Such contacts may be of either the lone pair-π (lp-π) or the OH-π type, in nature. The distribution of the distances of the water oxygen from the nucleobase plane peaks at 3.5 Å for A, G and C, and approximately at 3.1-3.2 Å for U. Quantum mechanics (QM) calculations confirm, as expected, that the optimal energy is reached at a shorter distance for the lp-π interaction as compared to the OH-π one (3.0 versus 3.5 Å). The preference of each nucleobase for either type of interaction closely correlates with its electrostatic potential map. Furthermore, QM calculations show that for all the nucleobases a favorable interaction, of either the lp-π or the OH-π type, can be established at virtually any position of the water molecule above the nucleobase skeleton, which is consistent with the uniform projection of the OW atoms over the nucleobases ring we observed in the experimental occurrences. Finally, molecular dynamics simulations of a model system for the characterization of water-nucleobase stacking contacts confirm the stability of these interactions also under dynamic conditions.
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Affiliation(s)
- Kanav Kalra
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Suresh Gorle
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
| | - Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
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Cabaj MK, Dominiak PM. Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals. Nucleic Acids Res 2020; 48:8302-8319. [PMID: 32725210 PMCID: PMC7470937 DOI: 10.1093/nar/gkaa629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/10/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022] Open
Abstract
We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar structures. The investigated compounds were either free forms or derivatives of adenine, guanine, hypoxanthine, thymine, uracil and cytosine. We divided our findings into categories including types of pairs, protonation patterns and whether they are formed by free bases or substituted ones. We found base pair types that are exclusive to small molecule crystal structures, some that can be found only in RNA containing crystal structures and many that are native to both environments. With a few exceptions, nucleobase protonation generally followed a standard pattern governed by pKa values. The lengths of hydrogen bonds did not depend on whether the nucleobases forming a base pair were charged or not. The reasons why particular nucleobases formed base pairs in a certain way varied significantly.
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Affiliation(s)
- Małgorzata Katarzyna Cabaj
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
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46
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Photoactivatable fluorescent probes for spatiotemporal-controlled biosensing and imaging. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115811] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Chen H, Snurr RQ. Insights into Catalytic Gas-Phase Hydrolysis of Organophosphate Chemical Warfare Agents by MOF-Supported Bimetallic Metal-Oxo Clusters. ACS APPLIED MATERIALS & INTERFACES 2020; 12:14631-14640. [PMID: 31909586 DOI: 10.1021/acsami.9b19484] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Zirconium-based metal-organic frameworks (Zr-MOFs) have been reported to be efficient catalysts for the hydrolysis of organophosphate chemical warfare agents (CWAs) in buffered solutions. However, for the gas-phase reaction, which is more relevant to the situation in a battlefield gas mask application, the kinetics of Zr-MOF catalysts may be severely hindered by strong product inhibition. To improve the catalytic performance, we computationally screened a series of synthetically accessible Zr-MOF-supported bimetallic metal-oxo clusters in which the metal-oxygen-metal active motif is preserved, aiming to find catalysts that have lower binding affinities to the hydrolysis product. For the promising catalyst Al2O2(OH)2@NU-1000 identified from the screening using density functional theory, we mapped out the full reaction pathway of gas-phase dimethyl p-nitrophenolphosphate (DMNP) hydrolysis and analyzed the free energy profile as well as the turnover frequency (TOF). We found that the catalytic mechanism on the new catalyst is slightly different from the one on NU-1000, which also led to a different TOF-limiting step. Additional factors that can affect the overall catalytic performance in practical application, such as the amount of ambient moisture and the existence of acid gases that may poison the catalyst, have also been evaluated.
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Affiliation(s)
- Haoyuan Chen
- Department of Chemical & Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Randall Q Snurr
- Department of Chemical & Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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48
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Fuku X, Baker P, Iwuoha E. Influence of Quantum Dot Surface on Electrochemical DNA Sensing Mechanism. ChemElectroChem 2020. [DOI: 10.1002/celc.201902079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xolile Fuku
- SensorLab, Department of ChemistryUniversity of the Western Cape Private Bag X17 Bellville 7535, Cape Town South Africa
- Energy CentreCouncil for Scientific and Industrial Research (CSIR) P.O. Box 395 Pretoria 0001 South Africa
| | - Priscilla Baker
- SensorLab, Department of ChemistryUniversity of the Western Cape Private Bag X17 Bellville 7535, Cape Town South Africa
| | - Emmanuel Iwuoha
- SensorLab, Department of ChemistryUniversity of the Western Cape Private Bag X17 Bellville 7535, Cape Town South Africa
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Gaines CS, Piccirilli JA, York DM. The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design. RNA (NEW YORK, N.Y.) 2020; 26:111-125. [PMID: 31776179 PMCID: PMC6961537 DOI: 10.1261/rna.071894.119] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 11/14/2019] [Indexed: 05/13/2023]
Abstract
We develop an L-platform/L-scaffold framework we hypothesize may serve as a blueprint to facilitate site-specific RNA-cleaving nucleic acid enzyme design. Building on the L-platform motif originally described by Suslov and coworkers, we identify new critical scaffolding elements required to anchor a conserved general base guanine ("L-anchor") and bind functionally important metal ions at the active site ("L-pocket"). Molecular simulations, together with a broad range of experimental structural and functional data, connect the L-platform/L-scaffold elements to necessary and sufficient conditions for catalytic activity. We demonstrate that the L-platform/L-scaffold framework is common to five of the nine currently known naturally occurring ribozyme classes (Twr, HPr, VSr, HHr, Psr), and intriguingly from a design perspective, the framework also appears in an artificially engineered DNAzyme (8-17dz). The flexibility of the L-platform/L-scaffold framework is illustrated on these systems, highlighting modularity and trends in the variety of known general acid moieties that are supported. These trends give rise to two distinct catalytic paradigms, building on the classifications proposed by Wilson and coworkers and named for the implicated general base and acid. The "G + A" paradigm (Twr, HPr, VSr) exclusively utilizes nucleobase residues for chemistry, and the "G + M + " paradigm (HHr, 8-17dz, Psr) involves structuring of the "L-pocket" metal ion binding site for recruitment of a divalent metal ion that plays an active role in the chemical steps of the reaction. Finally, the modularity of the L-platform/L-scaffold framework is illustrated in the VS ribozyme where the "L-pocket" assumes the functional role of the "L-anchor" element, highlighting a distinct mechanism, but one that is functionally linked with the hammerhead ribozyme.
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Affiliation(s)
- Colin S Gaines
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology and Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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Ma L, Liu J. Catalytic Nucleic Acids: Biochemistry, Chemical Biology, Biosensors, and Nanotechnology. iScience 2020; 23:100815. [PMID: 31954323 PMCID: PMC6962706 DOI: 10.1016/j.isci.2019.100815] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/11/2019] [Accepted: 12/26/2019] [Indexed: 01/06/2023] Open
Abstract
Since the initial discovery of ribozymes in the early 1980s, catalytic nucleic acids have been used in different areas. Compared with protein enzymes, catalytic nucleic acids are programmable in structure, easy to modify, and more stable especially for DNA. We take a historic view to summarize a few main interdisciplinary areas of research on nucleic acid enzymes that may have broader impacts. Early efforts on ribozymes in the 1980s have broken the notion that all enzymes are proteins, supplying new evidence for the RNA world hypothesis. In 1994, the first catalytic DNA (DNAzyme) was reported. Since 2000, the biosensor applications of DNAzymes have emerged and DNAzymes are particularly useful for detecting metal ions, a challenging task for enzymes and antibodies. Combined with nanotechnology, DNAzymes are key building elements for switches allowing dynamic control of materials assembly. The search for new DNAzymes and ribozymes is facilitated by developments in DNA sequencing and computational algorithms, further broadening our fundamental understanding of their biochemistry.
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Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
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