1
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He W, Zhang X, Zou Y, Li J, Wang C, He Y, Jin Q, Ye J. Effective Synthesis of High-Integrity mRNA Using In Vitro Transcription. Molecules 2024; 29:2461. [PMID: 38893337 PMCID: PMC11173937 DOI: 10.3390/molecules29112461] [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: 04/10/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024] Open
Abstract
mRNA vaccines are entering a period of rapid development. However, their synthesis is still plagued by challenges related to mRNA impurities and fragments (incomplete mRNA). Most impurities of mRNA products transcribed in vitro are mRNA fragments. Only full-length mRNA transcripts containing both a 5'-cap and a 3'-poly(A) structure are viable for in vivo expression. Therefore, RNA fragments are the primary product-related impurities that significantly hinder mRNA efficacy and must be effectively controlled; these species are believed to originate from either mRNA hydrolysis or premature transcriptional termination. In the manufacturing of commercial mRNA vaccines, T7 RNA polymerase-catalyzed in vitro transcription (IVT) synthesis is a well-established method for synthesizing long RNA transcripts. This study identified a pivotal domain on the T7 RNA polymerase that is associated with erroneous mRNA release. By leveraging the advantageous properties of a T7 RNA polymerase mutant and precisely optimized IVT process parameters, we successfully achieved an mRNA integrity exceeding 91%, thereby further unlocking the immense potential of mRNA therapeutics.
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Affiliation(s)
- Wei He
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China;
- Vazyme Biotech Co., Ltd., Nanjing 210037, China; (X.Z.); (Y.Z.); (J.L.); (C.W.)
| | - Xinya Zhang
- Vazyme Biotech Co., Ltd., Nanjing 210037, China; (X.Z.); (Y.Z.); (J.L.); (C.W.)
| | - Yangxiaoyu Zou
- Vazyme Biotech Co., Ltd., Nanjing 210037, China; (X.Z.); (Y.Z.); (J.L.); (C.W.)
| | - Ji Li
- Vazyme Biotech Co., Ltd., Nanjing 210037, China; (X.Z.); (Y.Z.); (J.L.); (C.W.)
| | - Chong Wang
- Vazyme Biotech Co., Ltd., Nanjing 210037, China; (X.Z.); (Y.Z.); (J.L.); (C.W.)
| | - Yucai He
- School of Pharmacy, Changzhou University, Changzhou 213164, China
| | - Qiuheng Jin
- Vazyme Biotech Co., Ltd., Nanjing 210037, China; (X.Z.); (Y.Z.); (J.L.); (C.W.)
| | - Jianren Ye
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China;
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2
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Zhang M, Li S, Yang H, Song G, Wu C, Li Z. Structure and Ultrafast X-ray Diffraction of the Hydrated Metaphosphate. J Phys Chem A 2024; 128:3086-3094. [PMID: 38605669 DOI: 10.1021/acs.jpca.4c00346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
We study the pathway of metaphosphate hydration when a metaphosphate anion is dissolved in liquid water with an explicit water model. For this purpose, we propose a sequential Monte Carlo algorithm incorporated with the ab initio quantum mechanics/molecular mechanics (QM/MM) method, which can reduce the amount of ab initio QM/MM sampling while retaining the accuracy of the simulation. We demonstrate the numerical calculation of the standard enthalpy change for the successive addition reaction PO3-·2H2O + H2O ⇌ PO3-·3H2O in the liquid phase, which helps to clarify the hydration pathway of the metaphosphate. With the obtained hydrated structure of the metaphosphate anion, we perform ab initio calculations for its relaxation dynamics upon vibrational excitation and characterize the energy transfer process in solution with simulated ultrafast X-ray diffraction signals, which can be experimentally implemented with X-ray free-electron lasers.
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Affiliation(s)
- Ming Zhang
- State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Sizhe Li
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Hanwei Yang
- State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Gaoxing Song
- State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Chengyin Wu
- State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, China
| | - Zheng Li
- State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, China
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3
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Ballay B, Szűcs T, Papp D, Czakó G. Phosphorus-centered ion-molecule reactions: benchmark ab initio characterization of the potential energy surfaces of the X - + PH 2Y [X, Y = F, Cl, Br, I] systems. Phys Chem Chem Phys 2023; 25:28925-28940. [PMID: 37855143 DOI: 10.1039/d3cp03733a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
In the present work we determine the benchmark relative energies and geometries of all the relevant stationary points of the X- + PH2Y [X, Y = F, Cl, Br, I] identity and non-identity reactions using state-of-the-art electronic-structure methods. These phosphorus-centered ion-molecule reactions follow two main reaction routes: bimolecular nucleophilic substitution (SN2), leading to Y- + PH2X, and proton transfer, resulting in HX + PHY- products. The SN2 route can proceed through Walden-inversion, front-side-attack retention, and double-/multiple-inversion pathways. In addition, we also identify the following product channels: H--formation, PH2-- and PH2-formation, 1PH- and 3PH-formation, H2-formation and HY + PHX- formation. The benchmark classical relative energies are obtained by taking into account the core-correlation, scalar relativistic, and post-(T) corrections, which turn out to be necessary to reach subchemical (<1 kcal mol-1) accuracy of the results. Classical relative energies are augmented with zero-point-energy contributions to gain the benchmark adiabatic energies.
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Affiliation(s)
- Boldizsár Ballay
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Tímea Szűcs
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Dóra Papp
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Gábor Czakó
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
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4
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Giricz A, Czakó G, Papp D. Alternating Stereospecificity upon Central-Atom Change: Dynamics of the F - +PH 2 Cl S N 2 Reaction Compared to its C- and N-Centered Analogues. Chemistry 2023; 29:e202302113. [PMID: 37698297 DOI: 10.1002/chem.202302113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Indexed: 09/13/2023]
Abstract
Central-atom effects on bimolecular nucleophilic substitution (SN 2) reactions are well-known in chemistry, however, the atomic-level SN 2 dynamics at phosphorous (P) centers has never been studied. We investigate the dynamics of the F- +PH2 Cl reaction with the quasi-classical trajectory method on a novel full-dimensional analytical potential energy surface fitted on high-level ab initio data. Our computations reveal intermediate dynamics compared to the F- +CH3 Cl and the F- +NH2 Cl SN 2 reactions: phosphorus as central atom leads to a more indirect SN 2 reaction with extensive complex-formation with respect to the carbon-centered one, however, the title reaction is more direct than its N-centered pair. Stereospecificity, characteristic at C-center, does not appear here either, due to the submerged front-side-attack retention path and the repeated entrance-channel inversional motion, whereas the multi-inversion mechanism discovered at nitrogen center is also undermined by the deep Walden-well. At low collision energies, 6 % of the PH2 F products form with retained configuration, mostly through complex-mediated mechanisms, while this ratio reaches 24 % at the highest energy due to the increasing dominance of the direct front-side mechanism and the smaller chance for hitting the deep Walden-inversion minimum. Our results suggest pronounced central-atom effects in SN 2 reactions, which can fundamentally change their (stereo)dynamics.
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Affiliation(s)
- Anett Giricz
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged, H-6720, Hungary
| | - Gábor Czakó
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged, H-6720, Hungary
| | - Dóra Papp
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged, H-6720, Hungary
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5
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Lee EM, Setterholm NA, Hajjar M, Barpuzary B, Chaput JC. Stability and mechanism of threose nucleic acid toward acid-mediated degradation. Nucleic Acids Res 2023; 51:9542-9551. [PMID: 37650628 PMCID: PMC10570051 DOI: 10.1093/nar/gkad716] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/21/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023] Open
Abstract
Xeno-nucleic acids (XNAs) have gained significant interest as synthetic genetic polymers for practical applications in biomedicine, but very little is known about their biophysical properties. Here, we compare the stability and mechanism of acid-mediated degradation of α-l-threose nucleic acid (TNA) to that of natural DNA and RNA. Under acidic conditions and elevated temperature (pH 3.3 at 90°C), TNA was found to be significantly more resistant to acid-mediated degradation than DNA and RNA. Mechanistic insights gained by reverse-phase HPLC and mass spectrometry indicate that the resilience of TNA toward low pH environments is due to a slower rate of depurination caused by induction of the 2'-phosphodiester linkage. Similar results observed for 2',5'-linked DNA and 2'-O-methoxy-RNA implicate the position of the phosphodiester group as a key factor in destabilizing the formation of the oxocarbenium intermediate responsible for depurination and strand cleavage of TNA. Biochemical analysis indicates that strand cleavage occurs by β-elimination of the 2'-phosphodiester linkage to produce an upstream cleavage product with a 2'-threose sugar and a downstream cleavage product with a 3' terminal phosphate. This work highlights the unique physicochemical properties available to evolvable non-natural genetic polymers currently in development for biomedical applications.
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Affiliation(s)
- Erica M Lee
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
| | - Noah A Setterholm
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
| | - Mohammad Hajjar
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
| | - Bhawna Barpuzary
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
- Department of Chemistry, University of California, Irvine, CA 92697-3958, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3958, USA
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697-3958, USA
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6
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Miklavčič R, Megušar P, Kodermac ŠM, Bakalar B, Dolenc D, Sekirnik R, Štrancar A, Černigoj U. High Recovery Chromatographic Purification of mRNA at Room Temperature and Neutral pH. Int J Mol Sci 2023; 24:14267. [PMID: 37762568 PMCID: PMC10532270 DOI: 10.3390/ijms241814267] [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: 08/02/2023] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Messenger RNA (mRNA) is becoming an increasingly important therapeutic modality due to its potential for fast development and platform production. New emerging RNA modalities, such as circular RNA, drive the need for the development of non-affinity purification approaches. Recently, the highly efficient chromatographic purification of mRNA was demonstrated with multimodal monolithic chromatography media (CIM® PrimaS), where efficient mRNA elution was achieved with an ascending pH gradient approach at pH 10.5. Here, we report that a newly developed chromatographic material enables the elution of mRNA at neutral pH and room temperature. This material demonstrates weak anion-exchanging properties and an isoelectric point of 5.3. It enables the baseline separation of mRNA (at least up to 10,000 nucleotides (nt) in size) from parental plasmid DNA (regardless of isoform composition) with both a NaCl gradient and ascending pH gradient approach, while mRNA elution is achieved in a pH range of 5-7. In addition, the basic structure of the novel material is a chromatographic monolith, enabling convection-assisted mass transfer of large RNA molecules to and from the active surface. This facilitates the elution of mRNA in 3-7 column volumes with more than 80% elution recovery and uncompromised integrity. This is demonstrated by the purification of a model mRNA (size 995 nt) from an in vitro transcription reaction mixture. The purified mRNA is stable for at least 34 days, stored in purified H2O at room temperature.
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Affiliation(s)
- Rok Miklavčič
- Sartorius BIA Separations d.o.o., Mirce 21, 5270 Ajdovščina, Slovenia
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Polona Megušar
- Sartorius BIA Separations d.o.o., Mirce 21, 5270 Ajdovščina, Slovenia
| | | | - Blaž Bakalar
- Sartorius BIA Separations d.o.o., Mirce 21, 5270 Ajdovščina, Slovenia
| | - Darko Dolenc
- Sartorius BIA Separations d.o.o., Mirce 21, 5270 Ajdovščina, Slovenia
| | - Rok Sekirnik
- Sartorius BIA Separations d.o.o., Mirce 21, 5270 Ajdovščina, Slovenia
| | - Aleš Štrancar
- Sartorius BIA Separations d.o.o., Mirce 21, 5270 Ajdovščina, Slovenia
| | - Urh Černigoj
- Sartorius BIA Separations d.o.o., Mirce 21, 5270 Ajdovščina, Slovenia
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7
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Ross D, Deamer D. Template-Directed Replication and Chiral Resolution during Wet-Dry Cycling in Hydrothermal Pools. Life (Basel) 2023; 13:1749. [PMID: 37629605 PMCID: PMC10456050 DOI: 10.3390/life13081749] [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: 07/18/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
The commonly supposed template-based format for RNA self-replication requires both duplex assembly and disassembly. This requisite binary provision presents a challenge to the development of a serviceable self-replication model since chemical reactions are thermochemically unidirectional. We submit that a solution to this problem lies in volcanic landmasses that engage in continuous cycles of wetting and drying and thus uniquely provide the twofold state required for self-replication. Moreover, they offer conditions that initiate chain branching, and thus furnish a path to autocatalytic self-replication. The foundations of this dual thermochemical landscape arise from the broad differences in the properties of the bulk water phase on the one hand, and the air/water interfacial regions that emerge in the evaporative stages on the other. With this reaction system as a basis and employing recognized thermochemical and kinetic parameters, we present simulations displaying the spontaneous and autocatalyzed conversion of racemic and unactivated RNA monomers to necessarily homochiral duplex structures over characteristic periods of years.
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Affiliation(s)
- David Ross
- SRI International, Menlo Park, CA 94025, USA
| | - David Deamer
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
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8
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Schroeder JW, Hurto RL, Randall JR, Wozniak KJ, Timko TA, Nye TM, Wang JD, Freddolino PL, Simmons LA. RNase H genes cause distinct impacts on RNA:DNA hybrid formation and mutagenesis genome wide. SCIENCE ADVANCES 2023; 9:eadi5945. [PMID: 37494439 PMCID: PMC10371020 DOI: 10.1126/sciadv.adi5945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/23/2023] [Indexed: 07/28/2023]
Abstract
RNA:DNA hybrids compromise replication fork progression and genome integrity in all cells. The overall impacts of naturally occurring RNA:DNA hybrids on genome integrity, and the relative contributions of ribonucleases H to mitigating the negative effects of hybrids, remain unknown. Here, we investigate the contributions of RNases HII (RnhB) and HIII (RnhC) to hybrid removal, DNA replication, and mutagenesis genome wide. Deletion of either rnhB or rnhC triggers RNA:DNA hybrid accumulation but with distinct patterns of mutagenesis and hybrid accumulation. Across all cells, hybrids accumulate strongly in noncoding RNAs and 5'-UTRs of coding sequences. For ΔrnhB, hybrids accumulate preferentially in untranslated regions and early in coding sequences. We show that hybrid accumulation is particularly sensitive to gene expression in ΔrnhC cells. DNA replication in ΔrnhC cells is disrupted, leading to transversions and structural variation. Our results resolve the outstanding question of how hybrids in native genomic contexts cause mutagenesis and shape genome organization.
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Affiliation(s)
- Jeremy W. Schroeder
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Rebecca L. Hurto
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Justin R. Randall
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katherine J. Wozniak
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Room 743E, Houston, TX 77030, USA
| | - Taylor A. Timko
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Taylor M. Nye
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jue D. Wang
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Peter L. Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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9
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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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10
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Li NS, Dai Q, Weissman B, Harris ME, Piccirilli JA. A general and efficient approach to synthesize the phosphoramidites of 5'- 18O labeled purine nucleosides. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 42:930-943. [PMID: 37233721 PMCID: PMC10529648 DOI: 10.1080/15257770.2023.2218421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 05/27/2023]
Abstract
5'-18O labeled RNA oligos are important probes to investigate the mechanism of 2'-O-transphosphorylation reactions. Here we describe a general and efficient synthetic approach to the phosphoramidite derivatives of 5'-18O labeled nucleosides starting from the corresponding commercially available 5'-O-DMT protected nucleosides. Using this method, we prepared 5'-18O-guanosine phosphoramidite in 8 steps (13.2% overall yield), 5'-18O-adenosine phosphoramidite in 9 steps (10.1% overall yield) and 5'-18O-2'-deoxyguanosine phosphoramidite in 6 steps (12.8% overall yield). These 5'-18O labeled phosphoramidites can be incorporated into RNA oligos by solid phase synthesis for determination of heavy atom isotope effects in RNA 2'-O-transphosphorylation reactions.
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Affiliation(s)
- Nan-Sheng Li
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Qing Dai
- Department of Chemistry, University of Chicago, Chicago, Illinois, USA
| | - Benjamin Weissman
- Department of Chemistry, University of Chicago, Chicago, Illinois, USA
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Joseph A Piccirilli
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, Illinois, USA
- Department of Chemistry, University of Chicago, Chicago, Illinois, USA
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11
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Zhang K, Ho KP, Chatterjee A, Park G, Li Z, Catalano JG, Parker KM. RNA Hydrolysis at Mineral-Water Interfaces. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37216349 DOI: 10.1021/acs.est.3c01407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
As an essential biomolecule for life, RNA is ubiquitous across environmental systems where it plays a central role in biogeochemical processes and emerging technologies. The persistence of RNA in soils and sediments is thought to be limited by enzymatic or microbial degradation, which occurs on timescales that are orders of magnitude faster than known abiotic pathways. Herein, we unveil a previously unreported abiotic pathway by which RNA rapidly hydrolyzes on the timescale of hours upon adsorption to iron (oxyhydr)oxide minerals such as goethite (α-FeOOH). The hydrolysis products were consistent with iron present in the minerals acting as a Lewis acid to accelerate sequence-independent hydrolysis of phosphodiester bonds comprising the RNA backbone. In contrast to acid- or base-catalyzed RNA hydrolysis in solution, mineral-catalyzed hydrolysis was fastest at circumneutral pH, which allowed for both sufficient RNA adsorption and hydroxide concentration. In addition to goethite, we observed that RNA hydrolysis was also catalyzed by hematite (α-Fe2O3) but not by aluminum-containing minerals (e.g., montmorillonite). Given the extensive adsorption of nucleic acids to environmental surfaces, we anticipate previously overlooked mineral-catalyzed hydrolysis of RNA may be prevalent particularly in iron-rich soils and sediments, which must be considered across biogeochemical applications of nucleic acid analysis in environmental systems.
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Affiliation(s)
- Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kun-Pu Ho
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Grace Park
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Zhiyao Li
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jeffrey G Catalano
- Department of Earth & Planetary Sciences, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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12
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Schroeder JW, Hurto RL, Randall JR, Wozniak KJ, Timko TA, Nye TM, Wang JD, Freddolino PL, Simmons LA. RNase H genes cause distinct impacts on RNA:DNA hybrid formation and mutagenesis genome-wide. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539860. [PMID: 37214986 PMCID: PMC10197577 DOI: 10.1101/2023.05.08.539860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
RNA:DNA hybrids such as R-loops affect genome integrity and DNA replication fork progression. The overall impacts of naturally occurring RNA:DNA hybrids on genome integrity, and the relative contributions of ribonucleases H to mitigating the negative effects of hybrids, remain unknown. Here, we investigate the contributions of RNases HII (RnhB) and HIII (RnhC) to hybrid removal, DNA replication, and mutagenesis genome-wide. Deletion of either rnhB or rnhC triggers RNA:DNA hybrid accumulation, but with distinct patterns of mutagenesis and hybrid accumulation. Across all cells, hybrids accumulate most strongly in non-coding RNAs and 5'-UTRs of coding sequences. For Δ rnhB , hybrids accumulate preferentially in untranslated regions and early in coding sequences. Hybrid accumulation is particularly sensitive to gene expression in Δ rnhC ; in cells lacking RnhC, DNA replication is disrupted leading to transversions and structural variation. Our results resolve the outstanding question of how hybrids in native genomic contexts interact with replication to cause mutagenesis and shape genome organization.
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Affiliation(s)
- Jeremy W. Schroeder
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706
| | - Rebecca L. Hurto
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Justin R. Randall
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Katherine J. Wozniak
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Taylor A. Timko
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Taylor M. Nye
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
- Department of Molecular Microbiology and Center for Women’s Infectious Disease Research, Washington University School of Medicine, Saint Louis, MO 63110-1093, USA
| | - Jue D. Wang
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706
| | - Peter L. Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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13
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Huang T, Snell KC, Kalia N, Gardezi S, Guo L, Harris ME. Kinetic analysis of RNA cleavage by coronavirus Nsp15 endonuclease: Evidence for acid base catalysis and substrate dependent metal ion activation. J Biol Chem 2023:104787. [PMID: 37149147 PMCID: PMC10158045 DOI: 10.1016/j.jbc.2023.104787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/08/2023] Open
Abstract
Understanding the functional properties of SARS-CoV-2 nonstructural proteins is essential for defining their roles in the viral life cycle, developing improved therapeutics and diagnostics, and countering future variants. Coronavirus nonstructural protein Nsp15 is a hexameric U-specific endonuclease whose functions, substrate specificity, mechanism, and dynamics have not been fully defined. Previous studies report SARS-CoV-2 Nsp15 requires Mn2+ ions for optimal activity; however, the effects of divalent ions on Nsp15 reaction kinetics have not been investigated in detail. Here, we analyzed the single and multiple turnover kinetics for model single-stranded RNA substrates. Our data confirm that divalent ions are dispensable for catalysis and show that Mn2+ activates Nsp15 cleavage of two different ssRNA oligonucleotide substrates, but not a dinucleotide. Furthermore, biphasic kinetics of ssRNA substrates demonstrates that Mn2+ stabilizes alternative enzyme states that have faster substrate cleavage on the enzyme. However, we did not detect Mn2+-induced conformational changes using CD and fluorescence spectroscopy. The pH-rate profiles in the presence and absence of Mn2+ are consistent with active site ionizable groups with similar pKas of ca. 4.8-5.2. We found the Rp stereoisomer phosphorothioate modification at the scissile phosphate had minimal effect on catalysis, which supports a mechanism involving an anionic transition state. In contrast, the Sp stereoisomer is inactive due to weak binding, consistent with models that position the non-bridging phosphoryl oxygen deep in the active site. Together, these kinetic data demonstrate that Nsp15 employs a conventional acid-base catalytic mechanism passing through an anionic transition state, and that divalent ion activation is substrate-dependent.
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Affiliation(s)
- Tong Huang
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Kimberly C Snell
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Nidhi Kalia
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Shahbaz Gardezi
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Lily Guo
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, FL 32611.
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14
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Lowder FC, Simmons LA. Bacillus subtilis encodes a discrete flap endonuclease that cleaves RNA-DNA hybrids. PLoS Genet 2023; 19:e1010585. [PMID: 37146086 PMCID: PMC10191290 DOI: 10.1371/journal.pgen.1010585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/17/2023] [Accepted: 04/18/2023] [Indexed: 05/07/2023] Open
Abstract
The current model for Okazaki fragment maturation in bacteria invokes RNA cleavage by RNase H, followed by strand displacement synthesis and 5' RNA flap removal by DNA polymerase I (Pol I). RNA removal by Pol I is thought to occur through the 5'-3' flap endo/exonuclease (FEN) domain, located in the N-terminus of the protein. In addition to Pol I, many bacteria encode a second, Pol I-independent FEN. The contribution of Pol I and Pol I-independent FENs to DNA replication and genome stability remains unclear. In this work we purified Bacillus subtilis Pol I and FEN, then assayed these proteins on a variety of RNA-DNA hybrid and DNA-only substrates. We found that FEN is far more active than Pol I on nicked double-flap, 5' single flap, and nicked RNA-DNA hybrid substrates. We show that the 5' nuclease activity of B. subtilis Pol I is feeble, even during DNA synthesis when a 5' flapped substrate is formed modeling an Okazaki fragment intermediate. Examination of Pol I and FEN on DNA-only substrates shows that FEN is more active than Pol I on most substrates tested. Further experiments show that ΔpolA phenotypes are completely rescued by expressing the C-terminal polymerase domain while expression of the N-terminal 5' nuclease domain fails to complement ΔpolA. Cells lacking FEN (ΔfenA) show a phenotype in conjunction with an RNase HIII defect, providing genetic evidence for the involvement of FEN in Okazaki fragment processing. With these results, we propose a model where cells remove RNA primers using FEN while upstream Okazaki fragments are extended through synthesis by Pol I. Our model resembles Okazaki fragment processing in eukaryotes, where Pol δ catalyzes strand displacement synthesis followed by 5' flap cleavage using FEN-1. Together our work highlights the conservation of ordered steps for Okazaki fragment processing in cells ranging from bacteria to human.
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Affiliation(s)
- Frances Caroline Lowder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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15
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Yamamoto K, Fuchi Y, Ito Y, Hari Y. Expansion of Phosphoramidite Chemistry in Solid-Phase Oligonucleotide Synthesis: Rapid 3'-Dephosphorylation and Strand Cleavage. J Org Chem 2023; 88:2726-2734. [PMID: 36812161 DOI: 10.1021/acs.joc.2c02195] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
In solid-phase oligonucleotide synthesis, a solid support modified with a universal linker is frequently used to prepare oligonucleotides bearing non-natural- or non-nucleosides at the 3'-end. Generally, harsh basic conditions such as hot aqueous ammonia or methylamine are required to release oligonucleotides by 3'-dephosphorylation via the formation of cyclic phosphate with the universal linker. To achieve 3'-dephosphorylation under milder conditions, we used O-alkyl phosphoramidites instead of the commonly used O-cyanoethyl phosphoramidites at the 3'-end of oligonucleotides. Alkylated phosphotriesters are more alkali-tolerant than their cyanoethyl counterparts because the latter generates phosphodiesters via E2 elimination under basic conditions. Among the designed phosphoramidites, alkyl-extended analogs exhibited rapid and efficient 3'-dephosphorylation compared to conventional cyanoethyl and methyl analogs under mild basic conditions such as aqueous ammonia at room temperature for 2 h. Moreover, nucleoside phosphoramidites bearing 1,2-diols were synthesized and incorporated into oligonucleotides. 1,2,3,4-Tetrahydro-1,4-epoxynaphthalene-2,3-diol-bearing phosphoramidite behaved like a universal linker at the 3'-terminus, allowing dephosphorylation and strand cleavage of the oligonucleotide chain to occur efficiently. Our strategy using this new phosphoramidite chemistry is promising for the tandem solid-phase synthesis of diverse oligonucleotides.
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Affiliation(s)
- Kazuki Yamamoto
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Yasufumi Fuchi
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Yuta Ito
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
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16
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Xu Y, Harris ME, York DM, Wong KY. Altered Mechanisms for Acid-Catalyzed RNA Cleavage and Isomerization Reactions Models. J Chem Theory Comput 2023; 19:1322-1332. [PMID: 36753428 PMCID: PMC10069163 DOI: 10.1021/acs.jctc.2c01277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
RNA strand cleavage by 2'-O-transphosphorylation is catalyzed not only by numerous nucleolytic RNA enzymes (ribozymes) but also by hydroxide or hydronium ions. In experiments, both cleavage of the 5'-linked nucleoside and isomerization between 3',5'- and 2',5'-phosphodiesters occur under acidic conditions, while only the cleavage reaction is observed under basic conditions. An ab initio path-integral approach for simulating kinetic isotope effects is used to reveal the reaction mechanisms for RNA cleavage and isomerization reactions under acidic conditions. Moreover, the proposed mechanisms can also be combined through the experimental pH-rate profiles.
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Affiliation(s)
- Yuqing Xu
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Michael E Harris
- 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
| | - Kin-Yiu Wong
- Department of Physics, High Performance Cluster Computing Centre, Institute of Advanced Materials, Institute of Computational and Theoretical Studies, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong
- Institute of Research and Continuing Education, Hong Kong Baptist University (Shenzhen), Shenzhen 518057, China
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17
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Weissman B, Ekesan Ş, Lin HC, Gardezi S, Li NS, Giese TJ, McCarthy E, Harris ME, York DM, Piccirilli JA. Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. J Am Chem Soc 2023; 145:2830-2839. [PMID: 36706353 PMCID: PMC10112047 DOI: 10.1021/jacs.2c10079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ribonucleases and small nucleolytic ribozymes are both able to catalyze RNA strand cleavage through 2'-O-transphosphorylation, provoking the question of whether protein and RNA enzymes facilitate mechanisms that pass through the same or distinct transition states. Here, we report the primary and secondary 18O kinetic isotope effects for hepatitis delta virus ribozyme catalysis that reveal a dissociative, metaphosphate-like transition state in stark contrast to the late, associative transition states observed for reactions catalyzed by specific base, Zn2+ ions, or ribonuclease A. This new information provides evidence for a discrete ribozyme active site design that modulates the RNA cleavage pathway to pass through an altered transition state.
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Affiliation(s)
- Benjamin Weissman
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Hsuan-Chun Lin
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Shahbaz Gardezi
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Nan-Sheng Li
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Timothy J Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Erika McCarthy
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, 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
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18
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Pang J, Guo Q, Lu Z. The catalytic mechanism, metal dependence, substrate specificity, and biodiversity of ribonuclease H. Front Microbiol 2022; 13:1034811. [PMID: 36478866 PMCID: PMC9719913 DOI: 10.3389/fmicb.2022.1034811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/31/2022] [Indexed: 11/29/2023] Open
Abstract
Ribonucleoside monophosphates are inevitably misincorporated into the DNA genome inside cells, and they need to be excised to avoid chromosome instability. Ribonucleases H (RNases H) are enzymes that specifically hydrolyze the RNA strand of RNA/DNA hybrids or the RNA moiety from DNA containing a stretch of RNA, they therefore are required for DNA integrity. Extensive studies have drawn a mostly clear picture of the mechanisms of RNase H catalysis, but some questions are still lacking definitive answers. This review summarizes three alternative models of RNase H catalysis. The two-metal model is prevalent, but a three-metal model suggests the involvement of a third cation in catalysis. Apparently, the mechanisms underlying metal-dependent hydrolyzation are more complicated than initially thought. We also discuss the metal choices of RNases H and analyze how chemically similar cations function differently. Substrate and cleavage-site specificities vary among RNases H, and this is explicated in detail. An intriguing phenomenon is that organisms have diverse RNase H combinations, which may provide important hints to how rnh genes were transferred during evolution. Whether RNase H is essential for cellular growth, a key question in the study of in vivo functions, is also discussed. This article may aid in understanding the mechanisms underlying RNase H and in developing potentially promising applications of it.
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Affiliation(s)
| | | | - Zheng Lu
- Department of Biology, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
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19
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Bespalova M, Öz R, Westerlund F, Krishnan M. Single-Molecule Trapping and Measurement in a Nanostructured Lipid Bilayer System. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:13923-13934. [PMID: 36326814 PMCID: PMC9671048 DOI: 10.1021/acs.langmuir.2c02203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/15/2022] [Indexed: 06/16/2023]
Abstract
The repulsive electrostatic force between a biomolecule and a like-charged surface can be geometrically tailored to create spatial traps for charged molecules in solution. Using a parallel-plate system composed of silicon dioxide surfaces, we recently demonstrated single-molecule trapping and high precision molecular charge measurements in a nanostructured free energy landscape. Here we show that surfaces coated with charged lipid bilayers provide a system with tunable surface properties for molecular electrometry experiments. Working with molecular species whose effective charge and geometry are well-defined, we demonstrate the ability to quantitatively probe the electrical charge density of a supported lipid bilayer. Our findings indicate that the fraction of charged lipids in nanoslit lipid bilayers can be significantly different from that in the precursor lipid mixtures used to generate them. We also explore the temporal stability of bilayer properties in nanofluidic systems. Beyond their relevance in molecular measurement, such experimental systems offer the opportunity to examine lipid bilayer formation and wetting dynamics on nanostructured surfaces.
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Affiliation(s)
- Maria Bespalova
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OxfordOX1 3QZ, United Kingdom
| | - Robin Öz
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, 412 96Gothenburg, Sweden
| | - Fredrik Westerlund
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, 412 96Gothenburg, Sweden
| | - Madhavi Krishnan
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OxfordOX1 3QZ, United Kingdom
- The
Kavli Institute for Nanoscience Discovery, Sherrington Road, OxfordOX1 3QU, United Kingdom
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20
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Gupta M, Levine SR, Spitale RC. Probing Nascent RNA with Metabolic Incorporation of Modified Nucleosides. Acc Chem Res 2022; 55:2647-2659. [PMID: 36073807 DOI: 10.1021/acs.accounts.2c00347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The discovery of previously unknown functional roles of RNA in biological systems has led to increased interest in revealing novel RNA molecules as therapeutic targets and the development of tools to better understand the role of RNA in cells. RNA metabolic labeling broadens the scope of studying RNA by incorporating of unnatural nucleobases and nucleosides with bioorthogonal handles that can be utilized for chemical modification of newly synthesized cellular RNA. Such labeling of RNA provides access to applications including measurement of the rates of synthesis and decay of RNA, cellular imaging for RNA localization, and selective enrichment of nascent RNA from the total RNA pool. Several unnatural nucleosides and nucleobases have been shown to be incorporated into RNA by endogenous RNA synthesis machinery of the cells. RNA metabolic labeling can also be performed in a cell-specific manner, where only cells expressing an essential enzyme incorporate the unnatural nucleobase into their RNA. Although several discoveries have been enabled by the current RNA metabolic labeling methods, some key challenges still exist: (i) toxicity of unnatural analogues, (ii) lack of RNA-compatible conjugation chemistries, and (iii) background incorporation of modified analogues in cell-specific RNA metabolic labeling. In this Account, we showcase work done in our laboratory to overcome these challenges faced by RNA metabolic labeling.To begin, we discuss the cellular pathways that have been utilized to perform RNA metabolic labeling and study the interaction between nucleosides and nucleoside kinases. Then we discuss the use of vinyl nucleosides for metabolic labeling and demonstrate the low toxicity of 5-vinyluridine (5-VUrd) compared to other widely used nucleosides. Next, we discuss cell-specific RNA metabolic labeling with unnatural nucleobases, which requires the expression of a specific phosphoribosyl transferase (PRT) enzyme for incorporation of the nucleobase into RNA. In the course of this work, we discovered the enzyme uridine monophosphate synthase (UMPS), which is responsible for nonspecific labeling with modified uracil nucleobases. We were able to overcome this background labeling by discovering a mutant uracil PRT (UPRT) that demonstrates highly specific RNA metabolic labeling with 5-vinyluracil (5-VU). Furthermore, we discuss the optimization of inverse-electron-demand Diels-Alder (IEDDA) reactions for performing chemical modification of vinyl nucleosides to achieve covalent conjugation of RNA without transcript degradation. Finally, we highlight our latest endeavor: the development of mutually orthogonal chemical reactions for selective labeling of 5-VUrd and 2-vinyladenosine (2-VAdo), which allows for potential use of multiple vinyl nucleosides for simultaneous investigation of multiple cellular processes involving RNA. We hope that our methods and discoveries encourage scientists studying biological systems to include RNA metabolic labeling in their toolkit for studying RNA and its role in biological systems.
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21
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Sakurai Y, Abe N, Yoshikawa K, Oyama R, Ogasawara S, Murata T, Nakai Y, Tange K, Tanaka H, Akita H. Targeted delivery of lipid nanoparticle to lymphatic endothelial cells via anti-podoplanin antibody. J Control Release 2022; 349:379-387. [PMID: 35787913 DOI: 10.1016/j.jconrel.2022.06.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/20/2022] [Accepted: 06/26/2022] [Indexed: 12/28/2022]
Abstract
Lymphatic endothelial cells (LECs) that form lymphatic vessels play a pivotal role in immune regulation. It was recently reported that LECs suppress the antigen-dependent anti-tumor immunity in cancer tissues. Thus, regulating the function of LECs is a promising strategy for cancer therapy. The objective of this study was to develop a method for the selective delivery of small interfering RNA (siRNA) to LECs. For this purpose, the siRNA was formulated into nanoparticles (LNPs) to prevent them from being degraded in body fluids and to facilitate their penetration of the cell membrane. A breakthrough technology for achieving this is ONPATTRO®, a world's first siRNA drug. Since LNPs are taken up by hepatocytes relatively well via low-density lipoprotein receptors, most of the LNP systems that have been developed so far target hepatocytes. In this study, we report on the development of a new method for the rapid and convenient method for modifying LNPs with antibodies using the CLick reaction on the Interface of the nanoParticle (CLIP). The CLIP approach was faster and more versatile than the conventional method using amide coupling. As a demonstration, we report on the LEC-targeted siRNA delivery by using antibody-modified LNPs both in vitro and in vivo. The method used for the modification of LNPs is highly promising and has the potential for expanding the LNP-based delivery of nucleic acids in the future.
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Affiliation(s)
- Yu Sakurai
- Laboratory of DDS Design and Drug Disposition, Graduate School of Pharmaceutical Sciences, Chiba University, Japan; Laboratory of DDS Design and Drug Disposition, Graduate School of Pharmaceutical Sciences, Tohoku University, Japan.
| | - Nodoka Abe
- Laboratory of DDS Design and Drug Disposition, Graduate School of Pharmaceutical Sciences, Chiba University, Japan
| | - Keito Yoshikawa
- Laboratory of DDS Design and Drug Disposition, Graduate School of Pharmaceutical Sciences, Chiba University, Japan
| | - Ryotaro Oyama
- Laboratory of DDS Design and Drug Disposition, Graduate School of Pharmaceutical Sciences, Chiba University, Japan
| | - Satoshi Ogasawara
- Laboratory of Biostructural Chemistry, Department of Chemistry, Graduate School of Science, Chiba University, Japan; Membrane Protein Research and Molecular Chirality Research Centers, Chiba University, Japan
| | - Takeshi Murata
- Laboratory of Biostructural Chemistry, Department of Chemistry, Graduate School of Science, Chiba University, Japan; Membrane Protein Research and Molecular Chirality Research Centers, Chiba University, Japan
| | - Yuta Nakai
- DDS Research Laboratory, NOF CORPORATION, 3-3 Chidori-cho, Kawasaki-ku, Kawasaki City, Kanagawa 210-0865, Japan
| | - Kota Tange
- DDS Research Laboratory, NOF CORPORATION, 3-3 Chidori-cho, Kawasaki-ku, Kawasaki City, Kanagawa 210-0865, Japan
| | - Hiroki Tanaka
- Laboratory of DDS Design and Drug Disposition, Graduate School of Pharmaceutical Sciences, Chiba University, Japan
| | - Hidetaka Akita
- Laboratory of DDS Design and Drug Disposition, Graduate School of Pharmaceutical Sciences, Chiba University, Japan; Laboratory of DDS Design and Drug Disposition, Graduate School of Pharmaceutical Sciences, Tohoku University, Japan.
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22
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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: 13] [Impact Index Per Article: 6.5] [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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23
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Kagzi K, Hechler RM, Fussmann GF, Cristescu ME. Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions. Mol Ecol Resour 2022; 22:2640-2650. [DOI: 10.1111/1755-0998.13655] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/16/2022] [Accepted: 05/23/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Kaushar Kagzi
- Department of Biology McGill University Montréal QC Canada
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL)
| | - Robert M. Hechler
- Department of Biology McGill University Montréal QC Canada
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL)
| | - Gregor F. Fussmann
- Department of Biology McGill University Montréal QC Canada
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL)
| | - Melania E. Cristescu
- Department of Biology McGill University Montréal QC Canada
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL)
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24
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Stability Modelling of mRNA Vaccine Quality Based on Temperature Monitoring throughout the Distribution Chain. Pharmaceutics 2022; 14:pharmaceutics14020430. [PMID: 35214162 PMCID: PMC8877932 DOI: 10.3390/pharmaceutics14020430] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/31/2022] [Accepted: 02/08/2022] [Indexed: 11/22/2022] Open
Abstract
The vaccine distribution chains in several low- and middle-income countries are not adequate to facilitate the rapid delivery of high volumes of thermosensitive COVID-19 mRNA vaccines at the required low and ultra-low temperatures. COVID-19 mRNA vaccines are currently distributed along with temperature monitoring devices to track and identify deviations from predefined conditions throughout the distribution chain. These temperature readings can feed into computational models to quantify mRNA vaccine critical quality attributes (CQAs) and the remaining vaccine shelf life more accurately. Here, a kinetic modelling approach is proposed to quantify the stability-related CQAs and the remaining shelf life of mRNA vaccines. The CQA and shelf-life values can be computed based on the conditions under which the vaccines have been distributed from the manufacturing facilities via the distribution network to the vaccination centres. This approach helps to quantify the degree to which temperature excursions impact vaccine quality and can also reduce vaccine wastage. In addition, vaccine stock management can be improved due to the information obtained on the remaining shelf life of mRNA vaccines. This model-based quantification of mRNA vaccine quality and remaining shelf life can improve the deployment of COVID-19 mRNA vaccines to low- and middle-income countries.
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25
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Jeon H, Vazquez-Lima H, Jeong H, Cho KB, Hong S. Mono- and dinuclear zinc complexes bearing identical bis(thiosemicarbazone) ligand that exhibit alkaline phosphatase-like catalytic reactivity. J Biol Inorg Chem 2021; 27:37-47. [PMID: 34714402 DOI: 10.1007/s00775-021-01909-0] [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: 07/21/2021] [Accepted: 10/22/2021] [Indexed: 10/20/2022]
Abstract
Mono- and dinuclear zinc(II) complexes bearing bis(thiosemicarbazone) (bTSC) ligand were employed in the cleavage of phosphoester bonds. Comparative kinetic studies combined with theory suggested that the P-O bond cleavage is much accelerated by dinuclear zinc(II) complex in the presence of base. Based on the DFT-optimized structures of the proposed intermediates, it is plausible that (1) the removal of sulfur atoms of bTSC ligand from the zinc center provides two vacant sites for the binding of water (or hydroxide ion) and phosphoester and (2) the H-bonding between water (or hydroxide ion) and phosphoester, through several water molecules, may also assist the P-O bond cleavage and facilitate the nucleophilic attack. The kinetic and catalytic studies on the hydrolysis of phosphoester by dinuclear zinc complex showed a much-enhanced reactivity under basic reaction conditions, reaching over 95% conversion yield within 4 h. The currently presented compounds are arguably one of the faster synthetic Zn-based model performing phosphatase-like activity presented so far.
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Affiliation(s)
- Hyeri Jeon
- Department of Chemistry, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Hugo Vazquez-Lima
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, Republic of Korea.,Department of Inorganic Chemistry, Meritorious Autonomous University of Puebla, 72000, Puebla, Mexico
| | - Haewon Jeong
- Department of Chemistry, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Kyung-Bin Cho
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, Republic of Korea.
| | - Seungwoo Hong
- Department of Chemistry, Sookmyung Women's University, Seoul, 04310, Republic of Korea.
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26
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Sharma NK, Sarode S, Sarode G. Natural vaccines accumulated in facemasks during COVID-19: Underappreciated role of facial masking. J Oral Biol Craniofac Res 2021; 12:42-44. [PMID: 34660190 PMCID: PMC8511630 DOI: 10.1016/j.jobcr.2021.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/06/2021] [Accepted: 10/01/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a causal agent behind coronavirus disease 2019 (COVID-19). Despite promising developments in therapeutic and preventive avenues, the importance of facial masking is a key factor for the protective measures among exposed human populations. Preclinical and clinical data on the importance of facial masking concerning asymptomatic over symptomatic COVID-19 cases is limited. The recent introduction of the concept of SARS-CoV-2 associated molecular particle patterns (SAMPPs) as a natural vaccine has opened new avenues for the comprehensive development of immunity. To take this further, the scope of natural vaccines accumulated in facemasks during facial masking needs to be highlighted that may directly or indirectly contribute to building adaptive immunity among human populations. This paper attempts to discuss the underappreciated contributions of facial masking in the management of COVID-19 at the global level.
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Affiliation(s)
- Nilesh Kumar Sharma
- Dr. D.Y. Patil Institute of Biotechnology and Bioinformatics, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, 411018, Maharashtra, India
| | - Sachin Sarode
- Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, 411018, Maharashtra, India
| | - Gargi Sarode
- Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, 411018, Maharashtra, India
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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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Wayment-Steele HK, Kim DS, Choe CA, Nicol JJ, Wellington-Oguri R, Watkins AM, Parra Sperberg RA, Huang PS, Participants E, Das R. Theoretical basis for stabilizing messenger RNA through secondary structure design. Nucleic Acids Res 2021; 49:10604-10617. [PMID: 34520542 PMCID: PMC8499941 DOI: 10.1093/nar/gkab764] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/17/2021] [Accepted: 08/27/2021] [Indexed: 01/08/2023] Open
Abstract
RNA hydrolysis presents problems in manufacturing, long-term storage, world-wide delivery and in vivo stability of messenger RNA (mRNA)-based vaccines and therapeutics. A largely unexplored strategy to reduce mRNA hydrolysis is to redesign RNAs to form double-stranded regions, which are protected from in-line cleavage and enzymatic degradation, while coding for the same proteins. The amount of stabilization that this strategy can deliver and the most effective algorithmic approach to achieve stabilization remain poorly understood. Here, we present simple calculations for estimating RNA stability against hydrolysis, and a model that links the average unpaired probability of an mRNA, or AUP, to its overall hydrolysis rate. To characterize the stabilization achievable through structure design, we compare AUP optimization by conventional mRNA design methods to results from more computationally sophisticated algorithms and crowdsourcing through the OpenVaccine challenge on the Eterna platform. We find that rational design on Eterna and the more sophisticated algorithms lead to constructs with low AUP, which we term 'superfolder' mRNAs. These designs exhibit a wide diversity of sequence and structure features that may be desirable for translation, biophysical size, and immunogenicity. Furthermore, their folding is robust to temperature, computer modeling method, choice of flanking untranslated regions, and changes in target protein sequence, as illustrated by rapid redesign of superfolder mRNAs for B.1.351, P.1 and B.1.1.7 variants of the prefusion-stabilized SARS-CoV-2 spike protein. Increases in in vitro mRNA half-life by at least two-fold appear immediately achievable.
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MESH Headings
- Algorithms
- Base Pairing
- Base Sequence
- COVID-19/prevention & control
- Humans
- Hydrolysis
- RNA Stability
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/immunology
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/immunology
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Thermodynamics
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Affiliation(s)
- Hannah K Wayment-Steele
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Eterna Massive Open Laboratory
| | - Do Soon Kim
- Eterna Massive Open Laboratory
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Christian A Choe
- Eterna Massive Open Laboratory
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | | | - Andrew M Watkins
- Eterna Massive Open Laboratory
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Rhiju Das
- Eterna Massive Open Laboratory
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Department of Physics, Stanford University, Stanford, CA 94305, USA
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29
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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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30
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Yoon S, Harris ME. Beyond the Plateau: pL Dependence of Proton Inventories as a Tool for Studying Ribozyme and Ribonuclease Catalysis. Biochemistry 2021; 60:2810-2823. [PMID: 34495648 DOI: 10.1021/acs.biochem.1c00489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acid/base catalysis is an important catalytic strategy used by ribonucleases and ribozymes; however, understanding the number and identity of functional groups involved in proton transfer remains challenging. The proton inventory (PI) technique analyzes the dependence of the enzyme reaction rate on the ratio of D2O to H2O and can provide information about the number of exchangeable sites that produce isotope effects and their magnitude. The Gross-Butler (GB) equation is used to evaluate H/D fractionation factors from PI data typically collected under conditions (i.e., a "plateau" in the pH-rate profile) assuming minimal change in active site residue ionization. However, restricting PI analysis to these conditions is problematic for many ribonucleases, ribozymes, and their variants due to ambiguity in the roles of active site residues, the lack of a plateau within the accessible pL range, or cooperative interactions between active site functional groups undergoing ionization. Here, we extend the integration of species distributions for alternative enzyme states in noncooperative models of acid/base catalysis into the GB equation, first used by Bevilacqua and colleagues for the HDV ribozyme, to develop a general population-weighted GB equation that allows simulation and global fitting of the three-dimensional relationship of the D2O ratio (n) versus pL versus kn/k0. Simulations using the GPW-GB equation of PI results for RNase A, HDVrz, and VSrz illustrate that data obtained at multiple selected pL values across the pL-rate profile can assist in the planning and interpreting of solvent isotope effect experiments to distinguish alternative mechanistic models.
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Affiliation(s)
- Suhyun Yoon
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
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31
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Yamamoto K, Fuchi Y, Ito Y, Hari Y. Bicyclo[2.2.2]octane-2,3-diol as an universal linker for the solid-phase synthesis of oligonucleotides. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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32
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Liu Z, Wang S, Tapeinos C, Torrieri G, Känkänen V, El-Sayed N, Python A, Hirvonen JT, Santos HA. Non-viral nanoparticles for RNA interference: Principles of design and practical guidelines. Adv Drug Deliv Rev 2021; 174:576-612. [PMID: 34019958 DOI: 10.1016/j.addr.2021.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/04/2021] [Accepted: 05/15/2021] [Indexed: 02/08/2023]
Abstract
Ribonucleic acid interference (RNAi) is an innovative treatment strategy for a myriad of indications. Non-viral synthetic nanoparticles (NPs) have drawn extensive attention as vectors for RNAi due to their potential advantages, including improved safety, high delivery efficiency and economic feasibility. However, the complex natural process of RNAi and the susceptible nature of oligonucleotides render the NPs subject to particular design principles and requirements for practical fabrication. Here, we summarize the requirements and obstacles for fabricating non-viral nano-vectors for efficient RNAi. To address the delivery challenges, we discuss practical guidelines for materials selection and NP synthesis in order to maximize RNA encapsulation efficiency and protection against degradation, and to facilitate the cytosolic release of oligonucleotides. The current status of clinical translation of RNAi-based therapies and further perspectives for reducing the potential side effects are also reviewed.
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33
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Zhang K, Hodge J, Chatterjee A, Moon TS, Parker KM. Duplex Structure of Double-Stranded RNA Provides Stability against Hydrolysis Relative to Single-Stranded RNA. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8045-8053. [PMID: 34033461 DOI: 10.1021/acs.est.1c01255] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phosphodiester bonds in the backbones of double-stranded (ds)RNA and single-stranded (ss)RNA are known to undergo alkaline hydrolysis. Consequently, dsRNA agents used in emerging RNA interference (RNAi) products have been assumed to exhibit low chemical persistence in solutions. However, the impact of the duplex structure of dsRNA on alkaline hydrolysis has not yet been evaluated. In this study, we demonstrated that dsRNA undergoes orders-of-magnitude slower alkaline hydrolysis than ssRNA. Furthermore, we observed that dsRNA remains intact for multiple months at neutral pH, challenging the assumption that dsRNA is chemically unstable. In systems enabling both enzymatic degradation and alkaline hydrolysis of dsRNA, we found that increasing pH effectively attenuated enzymatic degradation without inducing alkaline hydrolysis that was observed for ssRNA. Overall, our findings demonstrated, for the first time, that key degradation pathways of dsRNA significantly differ from those of ssRNA. Consideration of the unique properties of dsRNA will enable greater control of dsRNA stability during the application of emerging RNAi technology and more accurate assessment of its fate in environmental and biological systems, as well as provide insights into broader application areas including dsRNA isolation, detection and inactivation of dsRNA viruses, and prebiotic molecular evolution.
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Affiliation(s)
- Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Joseph Hodge
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tae Seok Moon
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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34
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Mojarro A, Jin L, Szostak JW, Head JW, Zuber MT. In search of the RNA world on Mars. GEOBIOLOGY 2021; 19:307-321. [PMID: 33565260 PMCID: PMC8248371 DOI: 10.1111/gbi.12433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 05/17/2023]
Abstract
Advances in origins of life research and prebiotic chemistry suggest that life as we know it may have emerged from an earlier RNA World. However, it has been difficult to reconcile the conditions used in laboratory experiments with real-world geochemical environments that may have existed on the early Earth and hosted the origin(s) of life. This challenge is due to geologic resurfacing and recycling that have erased the overwhelming majority of the Earth's prebiotic history. We therefore propose that Mars, a planet frozen in time, comprised of many surfaces that have remained relatively unchanged since their formation > 4 Gya, is the best alternative to search for environments consistent with geochemical requirements imposed by the RNA world. In this study, we synthesize in situ and orbital observations of Mars and modeling of its early atmosphere into solutions containing a range of pHs and concentrations of prebiotically relevant metals (Fe2+ , Mg2+ , and Mn2+ ) spanning various candidate aqueous environments. We then experimentally determine RNA degradation kinetics due to metal-catalyzed hydrolysis (cleavage) and evaluate whether early Mars could have been permissive toward the accumulation of long-lived RNA polymers. Our results indicate that a Mg2+ -rich basalt sourcing metals to a slightly acidic (pH 5.4) environment mediates the slowest rates of RNA cleavage, though geologic evidence and basalt weathering models suggest aquifers on Mars would be near neutral (pH ~ 7). Moreover, the early onset of oxidizing conditions on Mars has major consequences regarding the availability of oxygen-sensitive metals (i.e., Fe2+ and Mn2+ ) due to increased RNA degradation rates and precipitation. Overall, (a) low pH decreases RNA cleavage at high metal concentrations; (b) acidic to neutral pH environments with Fe2+ or Mn2+ cleave more RNA than Mg2+ ; and (c) alkaline environments with Mg2+ dramatically cleaves more RNA while precipitates were observed for Fe2+ and Mn2+ .
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Affiliation(s)
- Angel Mojarro
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Lin Jin
- Department of Molecular Biology, and Center for Computational and Integrative BiologyMassachusetts General HospitalBostonMAUSA
| | - Jack W. Szostak
- Department of Molecular Biology, and Center for Computational and Integrative BiologyMassachusetts General HospitalBostonMAUSA
| | - James W. Head
- Department of Earth, Environmental and Planetary SciencesBrown UniversityProvidenceRIUSA
| | - Maria T. Zuber
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
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35
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van de Berg D, Kis Z, Behmer CF, Samnuan K, Blakney AK, Kontoravdi C, Shattock R, Shah N. Quality by design modelling to support rapid RNA vaccine production against emerging infectious diseases. NPJ Vaccines 2021; 6:65. [PMID: 33927197 PMCID: PMC8085199 DOI: 10.1038/s41541-021-00322-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/07/2021] [Indexed: 12/21/2022] Open
Abstract
Rapid-response vaccine production platform technologies, including RNA vaccines, are being developed to combat viral epidemics and pandemics. A key enabler of rapid response is having quality-oriented disease-agnostic manufacturing protocols ready ahead of outbreaks. We are the first to apply the Quality by Design (QbD) framework to enhance rapid-response RNA vaccine manufacturing against known and future viral pathogens. This QbD framework aims to support the development and consistent production of safe and efficacious RNA vaccines, integrating a novel qualitative methodology and a quantitative bioprocess model. The qualitative methodology identifies and assesses the direction, magnitude and shape of the impact of critical process parameters (CPPs) on critical quality attributes (CQAs). The mechanistic bioprocess model quantifies and maps the effect of four CPPs on the CQA of effective yield of RNA drug substance. Consequently, the first design space of an RNA vaccine synthesis bioreactor is obtained. The cost-yield optimization together with the probabilistic design space contribute towards automation of rapid-response, high-quality RNA vaccine production.
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Affiliation(s)
- Damien van de Berg
- Centre for Process Systems Engineering, Department of Chemical Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Zoltán Kis
- Centre for Process Systems Engineering, Department of Chemical Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Carl Fredrik Behmer
- Centre for Process Systems Engineering, Department of Chemical Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Karnyart Samnuan
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Anna K Blakney
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- University of British Columbia, Michael Smith Laboratories and School of Biomedical Engineering, Vancouver, BC, Canada
| | - Cleo Kontoravdi
- Centre for Process Systems Engineering, Department of Chemical Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Robin Shattock
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Nilay Shah
- Centre for Process Systems Engineering, Department of Chemical Engineering, Faculty of Engineering, Imperial College London, London, UK.
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36
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Pourshahian S. THERAPEUTIC OLIGONUCLEOTIDES, IMPURITIES, DEGRADANTS, AND THEIR CHARACTERIZATION BY MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:75-109. [PMID: 31840864 DOI: 10.1002/mas.21615] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Oligonucleotides are an emerging class of drugs that are manufactured by solid-phase synthesis. As a chemical class, they have unique product-related impurities and degradants, characterization of which is an essential step in drug development. The synthesis cycle, impurities produced during the synthesis and degradation products are presented and discussed. The use of liquid chromatography combined with mass spectrometry for characterization and quantification of product-related impurities and degradants is reviewed. In addition, sequence determination of oligonucleotides by gas-phase fragmentation and indirect mass spectrometric methods is discussed. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Soheil Pourshahian
- Janssen Pharmaceutical Companies of Johnson & Johnson, South San Francisco, CA, 94080
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37
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Wayment-Steele HK, Kim DS, Choe CA, Nicol JJ, Wellington-Oguri R, Watkins AM, Sperberg RAP, Huang PS, Participants E, Das R. Theoretical basis for stabilizing messenger RNA through secondary structure design. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.08.22.262931. [PMID: 32869022 PMCID: PMC7457604 DOI: 10.1101/2020.08.22.262931] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA hydrolysis presents problems in manufacturing, long-term storage, world-wide delivery, and in vivo stability of messenger RNA (mRNA)-based vaccines and therapeutics. A largely unexplored strategy to reduce mRNA hydrolysis is to redesign RNAs to form double-stranded regions, which are protected from in-line cleavage and enzymatic degradation, while coding for the same proteins. The amount of stabilization that this strategy can deliver and the most effective algorithmic approach to achieve stabilization remain poorly understood. Here, we present simple calculations for estimating RNA stability against hydrolysis, and a model that links the average unpaired probability of an mRNA, or AUP, to its overall hydrolysis rate. To characterize the stabilization achievable through structure design, we compare AUP optimization by conventional mRNA design methods to results from more computationally sophisticated algorithms and crowdsourcing through the OpenVaccine challenge on the Eterna platform. These computational tests were carried out on both model mRNAs and COVID-19 mRNA vaccine candidates. We find that rational design on Eterna and the more sophisticated algorithms lead to constructs with low AUP, which we term 'superfolder' mRNAs. These designs exhibit wide diversity of sequence and structure features that may be desirable for translation, biophysical size, and immunogenicity, and their folding is robust to temperature, choice of flanking untranslated regions, and changes in target protein sequence, as illustrated by rapid redesign of superfolder mRNAs for B.1.351, P.1, and B.1.1.7 variants of the prefusion-stabilized SARS-CoV-2 spike protein. Increases in in vitro mRNA half-life by at least two-fold appear immediately achievable.
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Affiliation(s)
- Hannah K Wayment-Steele
- Department of Chemistry, Stanford University, Stanford, CA, 94305
- Eterna Massive Open Laboratory. Consortium authors listed in Table S1
| | - Do Soon Kim
- Eterna Massive Open Laboratory. Consortium authors listed in Table S1
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208
- Department of Biochemistry, Stanford University, Stanford, CA, 94305
| | - Christian A Choe
- Eterna Massive Open Laboratory. Consortium authors listed in Table S1
- Department of Bioengineering, Stanford University, Stanford, CA, 94305
| | - John J Nicol
- Eterna Massive Open Laboratory. Consortium authors listed in Table S1
| | | | - Andrew M Watkins
- Eterna Massive Open Laboratory. Consortium authors listed in Table S1
- Department of Biochemistry, Stanford University, Stanford, CA, 94305
| | | | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305
| | | | - Rhiju Das
- Eterna Massive Open Laboratory. Consortium authors listed in Table S1
- Department of Biochemistry, Stanford University, Stanford, CA, 94305
- Department of Physics, Stanford University, Stanford, CA, 94305
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38
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Mikutis S, Gu M, Sendinc E, Hazemi ME, Kiely-Collins H, Aspris D, Vassiliou GS, Shi Y, Tzelepis K, Bernardes GJL. meCLICK-Seq, a Substrate-Hijacking and RNA Degradation Strategy for the Study of RNA Methylation. ACS CENTRAL SCIENCE 2020; 6:2196-2208. [PMID: 33376781 PMCID: PMC7760485 DOI: 10.1021/acscentsci.0c01094] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Indexed: 06/01/2023]
Abstract
The fates of RNA species in a cell are controlled by ribonucleases, which degrade them by exploiting the universal structural 2'-OH group. This phenomenon plays a key role in numerous transformative technologies, for example, RNA interference and CRISPR/Cas13-based RNA editing systems. These approaches, however, are genetic or oligomer-based and so have inherent limitations. This has led to interest in the development of small molecules capable of degrading nucleic acids in a targeted manner. Here we describe click-degraders, small molecules that can be covalently attached to RNA species through click-chemistry and can degrade them, that are akin to ribonucleases. By using these molecules, we have developed the meCLICK-Seq (methylation CLICK-degradation Sequencing) a method to identify RNA modification substrates with high resolution at intronic and intergenic regions. The method hijacks RNA methyltransferase activity to introduce an alkyne, instead of a methyl, moiety on RNA. Subsequent copper(I)-catalyzed azide-alkyne cycloaddition reaction with the click-degrader leads to RNA cleavage and degradation exploiting a mechanism used by endogenous ribonucleases. Focusing on N6-methyladenosine (m6A), meCLICK-Seq identifies methylated transcripts, determines RNA methylase specificity, and reliably maps modification sites in intronic and intergenic regions. Importantly, we show that METTL16 deposits m6A to intronic polyadenylation (IPA) sites, which suggests a potential role for METTL16 in IPA and, in turn, splicing. Unlike other methods, the readout of meCLICK-Seq is depletion, not enrichment, of modified RNA species, which allows a comprehensive and dynamic study of RNA modifications throughout the transcriptome, including regions of low abundance. The click-degraders are highly modular and so may be exploited to study any RNA modification and design new technologies that rely on RNA degradation.
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Affiliation(s)
- Sigitas Mikutis
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Muxin Gu
- Haematological
Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10
1SA, U.K.
| | - Erdem Sendinc
- Boston
Childrens’ Hospital, Harvard Medical
School, 300 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Madoka E. Hazemi
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Hannah Kiely-Collins
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Demetrios Aspris
- Haematological
Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10
1SA, U.K.
- The
Center for the Study of Haematological Malignancies, Karaiskakio Foundation, Nicandrou Papamina Avenue, 2032 Nicosia, Cyprus
| | - George S. Vassiliou
- Haematological
Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10
1SA, U.K.
- The
Center for the Study of Haematological Malignancies, Karaiskakio Foundation, Nicandrou Papamina Avenue, 2032 Nicosia, Cyprus
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Puddicombe Way, Cambridge CB2 0AW, U.K.
| | - Yang Shi
- Boston
Childrens’ Hospital, Harvard Medical
School, 300 Longwood Avenue, Boston, Massachusetts 02115, United States
- Ludwig
Institute for Cancer Research, Oxford University, Old Road Campus Research Build,
Roosevelt Dr., Oxford OX3
7DQ, U.K.
| | - Konstantinos Tzelepis
- Haematological
Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10
1SA, U.K.
- Boston
Childrens’ Hospital, Harvard Medical
School, 300 Longwood Avenue, Boston, Massachusetts 02115, United States
- Milner Therapeutics
Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, U.K.
| | - Gonçalo J. L. Bernardes
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Instituto
de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
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39
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Nye TM, McLean EK, Burrage AM, Dennison DD, Kearns DB, Simmons LA. RnhP is a plasmid-borne RNase HI that contributes to genome maintenance in the ancestral strain Bacillus subtilis NCIB 3610. Mol Microbiol 2020; 115:99-115. [PMID: 32896031 DOI: 10.1111/mmi.14601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/27/2020] [Accepted: 08/30/2020] [Indexed: 01/27/2023]
Abstract
RNA-DNA hybrids form throughout the chromosome during normal growth and under stress conditions. When left unresolved, RNA-DNA hybrids can slow replication fork progression, cause DNA breaks, and increase mutagenesis. To remove hybrids, all organisms use ribonuclease H (RNase H) to specifically degrade the RNA portion. Here we show that, in addition to chromosomally encoded RNase HII and RNase HIII, Bacillus subtilis NCIB 3610 encodes a previously uncharacterized RNase HI protein, RnhP, on the endogenous plasmid pBS32. Like other RNase HI enzymes, RnhP incises Okazaki fragments, ribopatches, and a complementary RNA-DNA hybrid. We show that while chromosomally encoded RNase HIII is required for pBS32 hyper-replication, RnhP compensates for the loss of RNase HIII activity on the chromosome. Consequently, loss of RnhP and RNase HIII impairs bacterial growth. We show that the decreased growth rate can be explained by laggard replication fork progression near the terminus region of the right replichore, resulting in SOS induction and inhibition of cell division. We conclude that all three functional RNase H enzymes are present in B. subtilis NCIB 3610 and that the plasmid-encoded RNase HI contributes to chromosome stability, while the chromosomally encoded RNase HIII is important for chromosome stability and plasmid hyper-replication.
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Affiliation(s)
- Taylor M Nye
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Emma K McLean
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Devon D Dennison
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel B Kearns
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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40
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Dual miRNases for Triple Incision of miRNA Target: Design Concept and Catalytic Performance. Molecules 2020; 25:molecules25102459. [PMID: 32466298 PMCID: PMC7287882 DOI: 10.3390/molecules25102459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/18/2020] [Accepted: 05/21/2020] [Indexed: 02/06/2023] Open
Abstract
Irreversible destruction of disease-associated regulatory RNA sequences offers exciting opportunities for safe and powerful therapeutic interventions against human pathophysiology. In 2017, for the first time we introduced miRNAses–miRNA-targeted conjugates of a catalytic peptide and oligonucleotide capable of cleaving an miRNA target. Herein, we report the development of Dual miRNases against oncogenic miR-21, miR-155, miR-17 and miR-18a, each containing the catalytic peptide placed in-between two short miRNA-targeted oligodeoxyribonucleotide recognition motifs. Substitution of adenines with 2-aminoadenines in the sequence of oligonucleotide “shoulders” of the Dual miRNase significantly enhanced the efficiency of hybridization with the miRNA target. It was shown that sequence-specific cleavage of the target by miRNase proceeded metal-independently at pH optimum 5.5–7.5 with an efficiency varying from 15% to 85%, depending on the miRNA sequence. A distinct advantage of the engineered nucleases is their ability to additionally recruit RNase H and cut miRNA at three different locations. Such cleavage proceeds at the central part by Dual miRNase, and at the 5′- and 3′-regions by RNase H, which significantly increases the efficiency of miRNA degradation. Due to increased activity at lowered pH Dual miRNases could provide an additional advantage in acidic tumor conditions and may be considered as efficient tumor-selective RNA-targeted therapeutic.
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41
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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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42
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Preiner M, Asche S, Becker S, Betts HC, Boniface A, Camprubi E, Chandru K, Erastova V, Garg SG, Khawaja N, Kostyrka G, Machné R, Moggioli G, Muchowska KB, Neukirchen S, Peter B, Pichlhöfer E, Radványi Á, Rossetto D, Salditt A, Schmelling NM, Sousa FL, Tria FDK, Vörös D, Xavier JC. The Future of Origin of Life Research: Bridging Decades-Old Divisions. Life (Basel) 2020; 10:E20. [PMID: 32110893 PMCID: PMC7151616 DOI: 10.3390/life10030020] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022] Open
Abstract
Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In the 1st Interdisciplinary Origin of Life Meeting, early-career researchers gathered to explore the commonalities between theories and approaches, critical divergence points, and expectations for the future. We find that even though classical approaches and theories-e.g. bottom-up and top-down, RNA world vs. metabolism-first-have been prevalent in origin of life research, they are ceasing to be mutually exclusive and they can and should feed integrating approaches. Here we focus on pressing questions and recent developments that bridge the classical disciplines and approaches, and highlight expectations for future endeavours in origin of life research.
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Affiliation(s)
- Martina Preiner
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany; (S.G.G.); (F.D.K.T.)
| | - Silke Asche
- School of Chemistry, University of Glasgow, Glasgow G128QQ, UK;
| | - Sidney Becker
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK;
| | - Holly C. Betts
- School of Earth Sciences, University of Bristol, Bristol BS8 1RL, UK;
| | - Adrien Boniface
- Environmental Microbial Genomics, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, 69130 Ecully, France;
| | - Eloi Camprubi
- Origins Center, Department of Earth Sciences, Utrecht University, 3584 CB Utrecht, The Netherlands;
| | - Kuhan Chandru
- Space Science Center (ANGKASA), Institute of Climate Change, Level 3, Research Complex, National University of Malaysia, UKM Bangi 43600, Selangor, Malaysia;
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technicka 5, 16628 Prague 6–Dejvice, Czech Republic
| | - Valentina Erastova
- UK Centre for Astrobiology, School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK;
| | - Sriram G. Garg
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany; (S.G.G.); (F.D.K.T.)
| | - Nozair Khawaja
- Institut für Geologische Wissenschaften, Freie Universität Berlin, 12249 Berlin, Germany;
| | | | - Rainer Machné
- Institute of Synthetic Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany; (R.M.); (N.M.S.)
- Quantitative and Theoretical Biology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Giacomo Moggioli
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4DQ, UK;
| | - Kamila B. Muchowska
- Université de Strasbourg, CNRS, ISIS, 8 allée Gaspard Monge, 67000 Strasbourg, France;
| | - Sinje Neukirchen
- Archaea Biology and Ecogenomics Division, University of Vienna, 1090 Vienna, Austria; (S.N.); (E.P.); (F.L.S.)
| | - Benedikt Peter
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Edith Pichlhöfer
- Archaea Biology and Ecogenomics Division, University of Vienna, 1090 Vienna, Austria; (S.N.); (E.P.); (F.L.S.)
| | - Ádám Radványi
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary (D.V.)
- Institute of Evolution, MTA Centre for Ecological Research, Klebelsberg Kuno u. 3., H-8237 Tihany, Hungary
| | - Daniele Rossetto
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy;
| | - Annalena Salditt
- Systems Biophysics, Physics Department, Ludwig-Maximilians-Universität München, 80799 Munich, Germany;
| | - Nicolas M. Schmelling
- Institute of Synthetic Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany; (R.M.); (N.M.S.)
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674 Cologne, Germany
| | - Filipa L. Sousa
- Archaea Biology and Ecogenomics Division, University of Vienna, 1090 Vienna, Austria; (S.N.); (E.P.); (F.L.S.)
| | - Fernando D. K. Tria
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany; (S.G.G.); (F.D.K.T.)
| | - Dániel Vörös
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary (D.V.)
- Institute of Evolution, MTA Centre for Ecological Research, Klebelsberg Kuno u. 3., H-8237 Tihany, Hungary
| | - Joana C. Xavier
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany; (S.G.G.); (F.D.K.T.)
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43
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A Polyaddition Model for the Prebiotic Polymerization of RNA and RNA-Like Polymers. Life (Basel) 2020; 10:life10020012. [PMID: 32024223 PMCID: PMC7175168 DOI: 10.3390/life10020012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/24/2020] [Accepted: 01/26/2020] [Indexed: 11/21/2022] Open
Abstract
Implicit in the RNA world hypothesis is that prebiotic RNA synthesis, despite occurring in an environment without biochemical catalysts, produced the long RNA polymers which are essential to the formation of life. In order to investigate the prebiotic formation of long RNA polymers, we consider a general solution of functionally identical monomer units that are capable of bonding to form linear polymers by a step-growth process. Under the assumptions that (1) the solution is well-mixed and (2) bonding/unbonding rates are independent of polymerization state, the concentration of each length of polymer follows the geometric Flory-Schulz distribution. We consider the rate dynamics that produce this equilibrium; connect the rate dynamics, Gibbs free energy of bond formation, and the bonding probability; solve the dynamics in closed form for the representative special case of a Flory-Schulz initial condition; and demonstrate the effects of imposing a maximum polymer length. Afterwards, we derive a lower bound on the error introduced by truncation and compare this lower bound to the actual error found in our simulation. Finally, we suggest methods to connect these theoretical predictions to experimental results.
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44
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Le Vay K, Salibi E, Song EY, Mutschler H. Nucleic Acid Catalysis under Potential Prebiotic Conditions. Chem Asian J 2020; 15:214-230. [PMID: 31714665 PMCID: PMC7003795 DOI: 10.1002/asia.201901205] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/05/2019] [Indexed: 01/25/2023]
Abstract
Catalysis by nucleic acids is indispensable for extant cellular life, and it is widely accepted that nucleic acid enzymes were crucial for the emergence of primitive life 3.5-4 billion years ago. However, geochemical conditions on early Earth must have differed greatly from the constant internal milieus of today's cells. In order to explore plausible scenarios for early molecular evolution, it is therefore essential to understand how different physicochemical parameters, such as temperature, pH, and ionic composition, influence nucleic acid catalysis and to explore to what extent nucleic acid enzymes can adapt to non-physiological conditions. In this article, we give an overview of the research on catalysis of nucleic acids, in particular catalytic RNAs (ribozymes) and DNAs (deoxyribozymes), under extreme and/or unusual conditions that may relate to prebiotic environments.
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Affiliation(s)
- Kristian Le Vay
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Elia Salibi
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Emilie Y. Song
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Hannes Mutschler
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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45
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Zhou X, Zhang XP, Li W, Jiang J, Xu H, Ke Z, Phillips DL, Zhao C. Unraveling mechanisms of the uncoordinated nucleophiles: theoretical elucidations of the cleavage of bis( p-nitrophenyl) phosphate mediated by zinc-complexes with apical nucleophiles. RSC Adv 2019; 9:37696-37704. [PMID: 35541823 PMCID: PMC9075727 DOI: 10.1039/c9ra06737j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/01/2019] [Indexed: 02/01/2023] Open
Abstract
A theoretical approach was used to investigate the hydrolytic cleavage mechanisms of the bis(p-nitrophenyl) phosphate (BNPP−) catalyzed by Zn(ii)-complexes featuring uncoordinated nucleophiles. Ligand-based and alternative solvent-based nucleophilic attack reaction models are proposed. The pKa values of the Zn(ii)-bound water molecules or ligands in the [Zn(LnH)(η-H2O)(H2O)]2+ (n = 1, 2 and 3) complexes, as well as the dimerization tendency of the mononuclear Zn(ii)-complexes, were found to significantly influence the reaction mechanisms. The Zn(ii)-L3 complexes were found to be more favorable for the hydrolytic cleavage of the BNPP−via a ligand-based nucleophilic attack pathway. This was due to the lower pKa value for the deprotonation of the oxime ligand, the hard dimerization of the mononuclear Zn(ii)-L3 species, and the presence of an uncoordinated nucleophile. The origins of the uncoordinated reactions were systematically elucidated. The theoretical results reported here are in good agreement with experimental observations and more importantly, help to elucidate the factors that influence intermolecular nucleophilic attack reactions with coordinated/uncoordinated nucleophiles. A theoretical approach was used to investigate the hydrolytic cleavage mechanisms of the bis(p-nitrophenyl) phosphate (BNPP−) catalyzed by Zn(ii)-complexes featuring uncoordinated nucleophiles.![]()
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Affiliation(s)
- Xiaoyu Zhou
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Xue-Peng Zhang
- School of Chemisty and Chemical Engineering, Shaanxi Normal University Xi'an 710119 P. R. China
| | - Weikang Li
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Jingxing Jiang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, School of Materials Science and Engineering, Sun Yat-sen University Guangzhou 510275 P. R. China
| | - Huiying Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Zhuofeng Ke
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, School of Materials Science and Engineering, Sun Yat-sen University Guangzhou 510275 P. R. China
| | - David Lee Phillips
- Department of Chemistry, University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Cunyuan Zhao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 P. R. China
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46
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Wright TH, Giurgiu C, Zhang W, Radakovic A, O'Flaherty DK, Zhou L, Szostak JW. Prebiotically Plausible "Patching" of RNA Backbone Cleavage through a 3'-5' Pyrophosphate Linkage. J Am Chem Soc 2019; 141:18104-18112. [PMID: 31651170 PMCID: PMC7577263 DOI: 10.1021/jacs.9b08237] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Achieving multiple cycles of RNA
replication within a model protocell
would be a critical step toward demonstrating a path from prebiotic
chemistry to cellular biology. Any model for early life based on an
“RNA world” must account for RNA strand cleavage and
hydrolysis, which would degrade primitive genetic information and
lead to an accumulation of truncated, phosphate-terminated strands.
We show here that cleavage of the phosphodiester backbone is not an
end point for RNA replication. Instead, 3′-phosphate-terminated
RNA strands can participate in template-directed copying reactions
with activated ribonucleotide monomers. These reactions form a pyrophosphate
linkage, the stability of which we have characterized in the context
of RNA copying chemistry. The presence of free magnesium cations results
in cleavage of the pyrophosphate bond within minutes. However, we
found that the pyrophosphate bond is relatively stable within an RNA
duplex and in the presence of chelated magnesium. We show that, under
these conditions, pyrophosphate-linked RNA can act as a template for
the polymerization of ribonucleotides into canonical 3′–5′
phosphodiester-linked RNA. We suggest that primer extension of 3′-phosphate-terminated
RNA followed by template-directed copying represents a plausible nonenzymatic
pathway for the salvage and recovery of genetic information following
strand cleavage.
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Affiliation(s)
- Tom H Wright
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States
| | - Constantin Giurgiu
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States
| | - Wen Zhang
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States
| | - Aleksandar Radakovic
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States
| | - Derek K O'Flaherty
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States
| | - Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States
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47
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Perez‐Ramirez M, Agyekum I, Otoo B. Characterization of Phosphoranes Obtained by the Spontaneous Carbonyl‐Catalyzed Phosphorylation of Monosaccharides and Polyols in Aqueous Media. Chembiochem 2019; 21:473-476. [DOI: 10.1002/cbic.201900328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/14/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Maria Perez‐Ramirez
- School of Arts and SciencesOakland City University 138 N. Lucretia Street Oakland City IN 47660 USA
| | - Isaac Agyekum
- Chemistry and BiochemistryUniversity of North Georgia–Gainesville Campus 3820 Mundy Mill Road Oakwood GA 30566 USA
| | - Barnabas Otoo
- School of Arts and SciencesOakland City University 138 N. Lucretia Street Oakland City IN 47660 USA
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48
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Lietard J, Damha MJ, Somoza MM. Large-Scale Photolithographic Synthesis of Chimeric DNA/RNA Hairpin Microarrays To Explore Sequence Specificity Landscapes of RNase HII Cleavage. Biochemistry 2019; 58:4389-4397. [PMID: 31631649 PMCID: PMC6838787 DOI: 10.1021/acs.biochem.9b00806] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Ribonuclease HII (RNase HII) is an essential endoribonuclease that binds to double-stranded DNA with RNA nucleotide incorporations and cleaves 5' of the ribonucleotide at RNA-DNA junctions. Thought to be present in all domains of life, RNase HII protects genomic integrity by initiating excision repair pathways that protect the encoded information from rapid degradation. There is sparse evidence that the enzyme cleaves some substrates better than others, but a large-scale study is missing. Such large-scale studies can be carried out on microarrays, and we employ chemical photolithography to synthesize very large combinatorial libraries of fluorescently labeled DNA/RNA chimeric sequences that self-anneal to form hairpin structures that are substrates for Escherichia coli RNase HII. The relative activity is determined by the loss of fluorescence upon cleavage. Each substrate includes a double-stranded 5 bp variable region with one to five consecutive ribonucleotide substitutions. We also examined the effect of all possible single and double mismatches, for a total of >9500 unique structures. Differences in cleavage efficiency indicate some level of substrate preference, and we identified the 5'-dC/rC-rA-dX-3' motif in well-cleaved substrates. The results significantly extend known patterns of RNase HII sequence specificity and serve as a template using large-scale photolithographic synthesis to comprehensively map landscapes of substrate specificity of nucleic acid-processing enzymes.
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Affiliation(s)
- Jory Lietard
- Institute of Inorganic Chemistry, Faculty of Chemistry , University of Vienna , Althanstraße 14 (UZA II) , 1090 Vienna , Austria
| | - Masad J Damha
- Department of Chemistry , McGill University , 801 Rue Sherbrooke Ouest , Montreal , QC H3A 0B8 , Canada
| | - Mark M Somoza
- Institute of Inorganic Chemistry, Faculty of Chemistry , University of Vienna , Althanstraße 14 (UZA II) , 1090 Vienna , Austria
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Pourshahian S, Gryaznov SM. Sequencing of Phosphoramidate Oligonucleotides by Acid Hydrolysis and Mass Spectrometry. Anal Chem 2019; 91:11154-11161. [PMID: 31386344 DOI: 10.1021/acs.analchem.9b01858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrolysis of N3'-P5' phosphoramidate and thiophosphoramidate oligonucleotides with 0.1% formic acid leads to the cleavage of the 3' N-P bond and generates two products, one of which contains a 5'-phosphate. Analysis of the hydrolytic products by liquid chromatography, coupled with mass spectrometry, reveals the mass ladder from both termini, which is used to determine the sequence. While acid hydrolysis does not result in depurination, internal fragments especially in the low mass range are detected. The method is applied to DNA and RNA analogues with and without modifications at the 2'-position. This approach enables rapid sequence confirmation of synthetic phosphoramidate oligonucleotides for quality control as well as denovo sequencing.
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Affiliation(s)
- Soheil Pourshahian
- Janssen Pharmaceutical Companies of Johnson & Johnson , South San Francisco , California 94080 , United States
| | - Sergei M Gryaznov
- Janssen Pharmaceutical Companies of Johnson & Johnson , South San Francisco , California 94080 , United States
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Abstract
The nucleolytic ribozymes carry out site-specific RNA cleavage reactions by nucleophilic attack of the 2'-oxygen atom on the adjacent phosphorus with an acceleration of a million-fold or greater. A major part of this arises from concerted general acid-base catalysis. Recent identification of new ribozymes has expanded the group to a total of nine and this provides a new opportunity to identify sub-groupings according to the nature of the general base and acid. These include nucleobases, hydrated metal ions, and 2'-hydroxyl groups. Evolution has selected a number of different combinations of these elements that lead to efficient catalysis. These differences provide a new mechanistic basis for classifying these ribozymes.
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Affiliation(s)
- David M.J. Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
- School of Life Sciences, Xiamen University, Xiamen, China
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