1
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Cao G, Yang N, Yang J, Li J, Wang L, Nie F, Huo D, Hou C. Label-Free and DNAzyme-Mediated Biosensor with a High Signal-to-Noise Ratio for a Lumpy Skin Disease Virus Assay. Anal Chem 2024; 96:10927-10934. [PMID: 38934225 DOI: 10.1021/acs.analchem.4c00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Lumpy skin disease virus (LSDV) is a severe and highly contagious form of cowpox. As LSDV continues to mutate and there is no vaccine and treatment in nonendemic countries, early detection of LSDV becomes an important basis for epidemic prevention and control, especially for detection of conserved sequences. A new label-free and sensitive fluorescence method was developed based on a light-up RNA aptamer for detecting LSDV. The method integrated recombinase polymerase amplification (RPA), CRISPR/Cas12a, 10-23 DNAzyme, and Baby Spinach RNA aptamer for triple cascade signal amplification. Based on highly sensitive and specific RPA and CRISPR/Cas12a, DNAzyme achieved a third signal amplification. Additionally, the Baby Spinach RNA aptamer had stronger fluorescence signals and higher quantum yields. The label-free method had ultrahigh sensitivity with the actual detection limit as 1.29 copies·μL-1. The method was 100-fold more sensitive compared to RPA with Cas12a. Moreover, it had no cross-reactivity with viruses belonging to the Capripoxvirus, such as sheep pox virus and goat pox virus with genetic homology as 97%. Furthermore, the method displayed 100% accuracy in 50 actual samples. Therefore, the method based on RPA, Cas12a, and 10-23 DNAzyme had advantages in LSDV detection and provided a new solution for LSD prevention and control.
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Affiliation(s)
- Gaihua Cao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs, Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Nannan Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs, Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Jun Yang
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs, Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Jiali Li
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs, Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Lin Wang
- Science and Technology Research Center of China Customs, Beijing 100026, PR China
| | - Fuping Nie
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs, Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 400044, PR China
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2
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Wieruszewska J, Pawłowicz A, Połomska E, Pasternak K, Gdaniec Z, Andrałojć W. The 8-17 DNAzyme can operate in a single active structure regardless of metal ion cofactor. Nat Commun 2024; 15:4218. [PMID: 38760331 PMCID: PMC11101458 DOI: 10.1038/s41467-024-48638-x] [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: 04/13/2023] [Accepted: 05/09/2024] [Indexed: 05/19/2024] Open
Abstract
DNAzymes - synthetic enzymes made of DNA - have long attracted attention as RNA-targeting therapeutic agents. Yet, as of now, no DNAzyme-based drug has been approved, partially due to our lacking understanding of their molecular mode of action. In this work we report the solution structure of 8-17 DNAzyme bound to a Zn2+ ion solved through NMR spectroscopy. Surprisingly, it turned out to be very similar to the previously solved Pb2+-bound form (catalytic domain RMSD = 1.28 Å), despite a long-standing literature consensus that Pb2+ recruits a different DNAzyme fold than other metal ion cofactors. Our follow-up NMR investigations in the presence of other ions - Mg2+, Na+, and Pb2+ - suggest that at DNAzyme concentrations used in NMR all these ions induce a similar tertiary fold. Based on these findings, we propose a model for 8-17 DNAzyme interactions with metal ions postulating the existence of only a single catalytically-active structure, yet populated to a different extent depending on the metal ion cofactor. Our results provide structural information on the 8-17 DNAzyme in presence of non-Pb2+ cofactors, including the biologically relevant Mg2+ ion.
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Affiliation(s)
- Julia Wieruszewska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland
| | - Aleksandra Pawłowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland
| | - Ewa Połomska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland
| | - Karol Pasternak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland
| | - Witold Andrałojć
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland.
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3
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Fan H, Lu Y. Improving the Sensitivity of a Mn(II)-Specific DNAzyme for Cellular Imaging Sensor through Sequence Mutations. Anal Chem 2024; 96:3853-3858. [PMID: 38375826 PMCID: PMC11060987 DOI: 10.1021/acs.analchem.3c05280] [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: 02/21/2024]
Abstract
Detection of Mn2+ in living cells is important in understanding the roles of Mn2+ in cellular processes and investigating its potential implications in various diseases and disorders. Toward this goal, we have previously selected a Mn2+-specific 11-5 DNAzyme through an in vitro selection method and converted it into a fluorescence sensor for intracellular Mn2+ sensing. Despite the progress, the nucleotides responsible for the activity are unclear, and the performance of the DNAzyme needs to be improved in order for more effective applications in biological systems. To address these issues, we herein report site-specific mutations within the catalytic domain of the selected 11-5 DNAzyme. As a result, we successfully identified a variant DNAzyme, designated as Mn5V, which exhibited a twofold increase in activity compared to the original 11-5 DNAzyme. Importantly, Mn5V DNAzyme maintained its high selectivity for Mn2+ over other competing metal ions. Upon the addition of Mn2+, Mn5V DNAzyme exhibited a higher fluorescence signal within the tumor cells compared to that of the 11-5 DNAzyme. This study therefore provides a better understanding of how the DNAzyme functions and a more sensitive probe for investigating Mn2+ in biological systems.
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Affiliation(s)
- Huanhuan Fan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
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4
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Xia Y, Lei X, Ma X, Wang S, Yang Z, Wu Y, Ren X. Combination of RCA and DNAzyme for Dual-Signal Isothermal Amplification of Exosome RNA. Molecules 2023; 28:5528. [PMID: 37513400 PMCID: PMC10384651 DOI: 10.3390/molecules28145528] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/29/2023] [Accepted: 07/02/2023] [Indexed: 07/30/2023] Open
Abstract
The RNA contained in exosomes plays a crucial role in information transfer between cells in various life activities. The accurate detection of low-abundance exosome RNA (exRNA) is of great significance for cell function studies and the early diagnosis of diseases. However, their intrinsic properties, such as their short length and high sequence homology, represent great challenges for exRNA detection. In this paper, we developed a dual-signal isothermal amplification method based on rolling circle amplification (RCA) coupled with DNAzyme (RCA-DNAzyme). The sensitive detection of low-abundance exRNA, the specific recognition of their targets and the amplification of the detection signal were studied and explored. By designing padlock probes to specifically bind to the target exRNA, while relying on the ligation reaction to enhance recognition, the precise targeting of exosome RNA was realized. The combination of RCA and DNAzyme could achieve a twice-as-large isothermal amplification of the signal compared to RCA alone. This RCA-DNAzyme assay could sensitively detect a target exRNA at a concentration as low as 527 fM and could effectively distinguish the target from other miRNA sequences. In addition, this technology was successfully proven to be effective for the quantitative detection of miR-21 by spike recovery, providing a new research approach for the accurate detection of low-abundance exRNA and the exploration of unknown exRNA functions.
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Affiliation(s)
- Yuqing Xia
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xin Lei
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xiaochen Ma
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Shizheng Wang
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Zifu Yang
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Yifan Wu
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xiaojun Ren
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
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5
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Ekesan Ş, York DM. Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme. Org Biomol Chem 2022; 20:6219-6230. [PMID: 35452066 PMCID: PMC9378597 DOI: 10.1039/d2ob00234e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The pistol ribozyme (Psr) is one among the most recently discovered classes of small nucleolytic ribozymes that catalyze site-specific RNA self-cleavage through 2'-O-transphosphorylation. The Psr contains a conserved guanine (G40) that in crystal structures is in a position suggesting it plays the role of the general base to abstract a proton from the nucleophile to activate the reaction. Although some functional data is consistent with this mechanistic role, a notable exception is 2-aminopurine (2AP) substitution which has no effect on the rate, unlike similar substitutions across other so-called "G + M" and "G + A" ribozyme classes. Herein we postulate that an alternate conserved guanine, G42, is the primary general base, and provide evidence from molecular simulations that the active site of Psr can undergo local refolding into a structure that is consistent with the common "L-platform/L-scaffold" architecture identified in G + M and G + A ribozyme classes with Psr currently the notable exception. We summarize the key currently available experimental data and present new classical and combined quantum mechanical/molecular mechanical simulation results that collectively suggest a new hypothesis. We hypothesize that there are two available catalytic pathways supported by different conformational states connected by a local refolding of the active site: (1) a primary pathway with an active site architecture aligned with the L-platform/L-scaffold framework where G42 acts as a general base, and (2) a secondary pathway with the crystallographic active site architecture where G40 acts as a general base. We go on to make several experimentally testable predictions, and suggest specific experiments that would ultimately bring closure to the mystery as to "who stole the proton in the pistol ribozyme?".
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Affiliation(s)
- Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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6
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Parra-Meneses V, Rojas-Hernández F, Cepeda-Plaza M. The role of Na + in catalysis by the 8-17 DNAzyme. Org Biomol Chem 2022; 20:6356-6362. [PMID: 35856910 DOI: 10.1039/d2ob01075e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 8-17 DNAzyme is the most studied deoxyribozyme in terms of its molecular mechanism; hence it has become a model system to understand the basis behind DNA catalysis. New functional studies and the recent attainment of high-resolution X-ray structures, in addition to theoretical calculations have offered a great opportunity to gain a broader comprehension of its mechanism; however many aspects are unclear yet, especially regarding the precise role of metal ions in catalysis. Recently, molecular dynamics simulations have suggested for the first time a specific and dynamical participation of Na+ in the mechanism through the reaction pathway, besides the roles proposed for divalent metal cofactors. Herein, we present experimental evidence of a cooperative role of the monovalent cation Na+ in catalysis that is in line with these theoretical suggestions. Our findings show a clear influence of the concentration of Na+ on the activity of the 8-17 DNAzyme when Pb2+ is used as the cofactor. Interestingly, this effect is not noticed with Mg2+, indicating a particular contribution of the monovalent ion to catalysis that would operate preferentially with Pb2+. We have also found that Na+ affects the pKa of the general base and the general acid, indicating its influence on general acid-base catalysis, already identified as part of the mechanism of the 8-17 DNAzyme. Finally, our results emphasize the need to consider Na+ carefully in the design and analysis of functional studies of catalytic DNAs and its possible specific role in their mechanisms.
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7
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Lönnberg H. Structural modifications as tools in mechanistic studies of the cleavage of RNA phosphodiester linkages. CHEM REC 2022; 22:e202200141. [PMID: 35832010 DOI: 10.1002/tcr.202200141] [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: 05/16/2022] [Revised: 06/28/2022] [Indexed: 11/06/2022]
Abstract
The cleavage of RNA phosphodiester bonds by RNase A and hammerhead ribozyme at neutral pH fundamentally differs from the spontaneous reactions of these bonds under the same conditions. While the predominant spontaneous reaction is isomerization of the 3',5'-phosphodiester linkages to their 2',5'-counterparts, this reaction has never been reported to compete with the enzymatic cleavage reaction, not even as a minor side reaction. Comparative kinetic measurements with structurally modified di-nucleoside monophosphates and oligomeric phosphodiesters have played an important role in clarification of mechanistic details of the buffer-independent and buffer-catalyzed reactions. More recently, heavy atom isotope effects and theoretical calculations have refined the picture. The primary aim of all these studies has been to form a solid basis for mechanistic analyses of the action of more complicated catalytic machineries. In other words, to contribute to conception of a plausible unified picture of RNA cleavage by biocatalysts, such as RNAse A, hammerhead ribozyme and DNAzymes. In addition, structurally modified trinucleoside monophosphates as transition state models for Group I and II introns have clarified some features of the action of large ribozymes.
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Affiliation(s)
- Harri Lönnberg
- Department of Chemistry, University of Turku, FI-20014 University of, Turku
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8
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An RNA-cleaving threose nucleic acid enzyme capable of single point mutation discrimination. Nat Chem 2022; 14:350-359. [PMID: 34916596 DOI: 10.1038/s41557-021-00847-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 10/25/2021] [Indexed: 01/19/2023]
Abstract
Threose nucleic acid has been considered a potential evolutionary progenitor of RNA because of its chemical simplicity, base pairing properties and capacity for higher-order functions such as folding and specific ligand binding. Here we report the in vitro selection of RNA-cleaving threose nucleic acid enzymes. One such enzyme, Tz1, catalyses a site-specific RNA-cleavage reaction with an observed pseudo first-order rate constant (kobs) of 0.016 min-1. The catalytic activity of Tz1 is maximal at 8 mM Mg2+ and remains relatively constant from pH 5.3 to 9.0. Tz1 preferentially cleaves a mutant epidermal growth factor receptor RNA substrate with a single point substitution, while leaving the wild-type intact. We demonstrate that Tz1 mediates selective gene silencing of the mutant epidermal growth factor receptor in eukaryotic cells. The identification of catalytic threose nucleic acids provides further experimental support for threose nucleic acid as an ancestral genetic and functional material. The demonstration of Tz1 mediating selective knockdown of intracellular RNA suggests that functional threose nucleic acids could be developed for future biomedical applications.
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9
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Wang X, Yi X, Huang Z, He J, Wu Z, Chu X, Jiang J. “Repaired and Activated” DNAzyme Enables the Monitoring of DNA Alkylation Repair in Live Cells. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xiangnan Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Xin Yi
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Zhimei Huang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Jianjun He
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Zhenkun Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Jian‐Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
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10
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Wang X, Yi X, Huang Z, He J, Wu Z, Chu X, Jiang JH. "Repaired and Activated" DNAzyme Enables the Monitoring of DNA Alkylation Repair in Live Cells. Angew Chem Int Ed Engl 2021; 60:19889-19896. [PMID: 34165234 DOI: 10.1002/anie.202106557] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/16/2021] [Indexed: 12/31/2022]
Abstract
Direct measurement of DNA repair is critical for the annotation of their clinical relevance and the discovery of drugs for cancer therapy. Here we reported a "repaired and activated" DNAzyme (RADzyme) by incorporating a single methyl lesion (O6 MeG, 3MeC, or 1MeA) at designated positions through systematic screening. We found that the catalytic activity of the RADzyme was remarkably suppressed and could be restored via enzyme-mediated DNA repair. Benefit from these findings, a fluorogenic RADzyme sensor was developed for the monitoring of MGMT-mediated repair of O6 MeG lesion. Importantly, the sensor allowed the evaluation of MGMT repair activity in different cells and under drugs treatment. Furthermore, another RADzyme sensor was engineered for the monitoring of ALKBH2-mediated repair of 3MeC lesion. This strategy provides a simple and versatile tool for the study of the basic biology of DNA repair, clinical diagnosis and therapeutic assessment.
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Affiliation(s)
- Xiangnan Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Xin Yi
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Zhimei Huang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Jianjun He
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Zhenkun Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
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11
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Cortés-Guajardo C, Rojas-Hernández F, Paillao-Bustos R, Cepeda-Plaza M. Hydrated metal ion as a general acid in the catalytic mechanism of the 8-17 DNAzyme. Org Biomol Chem 2021; 19:5395-5402. [PMID: 34047747 DOI: 10.1039/d1ob00366f] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The RNA-cleaving 8-17 DNAzyme, which is a metalloenzyme that depends on divalent metal ions for its function, is the most studied catalytic DNA in terms of its mechanism. By the end of 2017, a report of the crystal structure of the enzyme-substrate complex in the presence of Pb2+ probed some of the previous findings and opened new questions, especially around the participation of the metal ion in the catalytic mechanism and the promiscuity exhibited by the enzyme in terms of the metal cofactor required for catalysis. In this article we explore the role of the divalent metal ion in the mechanism of the 8-17 DNAzyme as a general acid, by measuring the influence of pH over the activity of a slower variant of the enzyme in the presence of Pb2+. We replaced G14, which has been identified as a general base in the mechanism of the enzyme, by the unnatural analog 2-aminopurine, with a lower pKa value of the N1 group. With this approach, we obtained a bell-shaped pH-rate profile with experimental pKa values of 5.4 and 7.0. Comparing these results with previous pH-rate profiles in the presence of Mg2+, our findings suggest the stabilization of the 5'-O leaving group by the hydrated metal ion acting as a general acid, in addition to the activation of the 2'-OH nucleophile by the general base G14.
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12
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Moon WJ, Huang PJJ, Liu J. Probing Metal-Dependent Phosphate Binding for the Catalysis of the 17E DNAzyme. Biochemistry 2021; 60:1909-1918. [PMID: 34106684 DOI: 10.1021/acs.biochem.1c00091] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The RNA-cleaving 17E DNAzyme exhibits different levels of cleavage activity in the presence of various divalent metal ions, with Pb2+ giving the fastest cleavage. In this study, the metal-phosphate interaction is probed to understand the trend of activity with different metal ions. For the first-row transition metals, the lowest activity shown by Ni2+ correlates with the inhibition by the inorganic phosphate and its water ligand exchange rate, suggesting inner-sphere metal coordination. Cleavage activity with the two stereoisomers of the phosphorothioate-modified substrates, Rp and Sp, indicated that Mg2+, Mn2+, Fe2+, and Co2+ had the highest Sp:Rp activity ratio of >900. Comparatively, the activity was much less affected using the thiophilic metals, including Pb2+, suggesting inner-sphere coordination. The pH-rate profiles showed that Pb2+ was different than the rest of the metal ions in having a smaller slope and a similar fitted apparent pKa and the pKa of metal-bound water. Combining previous reports and our current results, we propose that Pb2+ most likely plays the role of a general acid while the other metal ions are Lewis acid catalysts interacting with the scissile phosphate.
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Affiliation(s)
- Woohyun J Moon
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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13
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Zhang Y, Wu C, Liu H, Khan MR, Zhao Z, He G, Luo A, Zhang J, Deng R, He Q. Label-free DNAzyme assays for dually amplified and one-pot detection of lead pollution. JOURNAL OF HAZARDOUS MATERIALS 2021; 406:124790. [PMID: 33316668 DOI: 10.1016/j.jhazmat.2020.124790] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/16/2020] [Accepted: 12/05/2020] [Indexed: 02/05/2023]
Abstract
Lead pollution in water and soil often transfers to food, advocating tools for on-site detection of lead pollution to ensure both environmental and food safety. We proposed a label-free, dually amplified and homogeneous DNAzyme assay for sensitive and one-pot detection of lead pollution. Instead of using chemically modified DNA substrate, a structure-response digestion process was introduced to monitor Pb2+ presence-induced cleavage process of unlabeled substrate, further amplifying the response signals and eliminating the use of labeled DNA probes. The DNAzyme assay allowed to detect Pb2+ as low as 0.12 nM and endued a dynamic range from 0.1 nM to 30 nM. In addition, it can specifically identify Pb2+ among other metal ions. We demonstrated that the DNAzyme assay can precisely detect Pb2+ in tap water, milk and fish. Thus, the DNAzyme assay is promising for on-site monitoring lead pollution risk and ensuring environmental and food safety.
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Affiliation(s)
- Yong Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
| | - Chengyong Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China
| | - Hongxin Liu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
| | - Mohammad Rizwan Khan
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Zhifeng Zhao
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
| | - Guiping He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
| | - Aimin Luo
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 10048, China
| | - Jiaqi Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China.
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
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14
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Zhang D, Yu X, Wu L, Jin H, Wei M. Ultrasensitive electrochemical detection of Pb2+ based on DNAzyme coupling with exonuclease III –Assisted target recycling. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2020.114960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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15
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Characterization of a DNA-hydrolyzing DNAzyme for generation of PCR strands of unequal length. Biochimie 2020; 179:181-189. [PMID: 33022314 DOI: 10.1016/j.biochi.2020.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/13/2020] [Accepted: 10/01/2020] [Indexed: 11/21/2022]
Abstract
I-R3 DNAzyme is a small, highly active catalytic DNA for DNA hydrolysis. In here, we designed two cis-structure DNAzymes (I-R3N and I-R3S) based on the different locates of the joint linker between I-R3 and its substrate. Data demonstrated that both DNAzymes were highly dependent on Zn2+, and worked at a narrow range around pH 7.0. They exhibited strong anti-interference with Mg2+ and Ca2+, but inhibited by Na+ and K+. Moreover, single and multiple-site mutations were generated within the catalytic core to carry out a comprehensive mutational study of I-R3 motif, in which most nucleotides were highly conserved and the nucleotides A5, T11 and T8 were identified as the mutational hotspots. Furthermore, an efficient variant A5G was obtained and its reaction condition was optimized. Finally, we constructed A5G to the 3' end of a single-stranded DNA (ssDNA) and applied it for asymmetrical PCR amplification to produce a single and double-stranded DNA mixture, in which A5G within ssDNA can self-cleave to generate a shorter desired ssDNA by denaturing gel separation. This would provide a new non-chemical modification approach for preparation of the expected ssDNA for in vitro selection of DNAzymes.
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16
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Huang PJ, Liu J. In vitro Selection of Chemically Modified DNAzymes. ChemistryOpen 2020; 9:1046-1059. [PMID: 33101831 PMCID: PMC7570446 DOI: 10.1002/open.202000134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
DNAzymes are in vitro selected DNA oligonucleotides with catalytic activities. RNA cleavage is one of the most extensively studied DNAzyme reactions. To expand the chemical functionality of DNA, various chemical modifications have been made during and after selection. In this review, we summarize examples of RNA-cleaving DNAzymes and focus on those modifications introduced during in vitro selection. By incorporating various modified nucleotides via polymerase chain reaction (PCR) or primer extension, a few DNAzymes were obtained that can be specifically activated by metal ions such as Zn2+ and Hg2+. In addition, some modifications were introduced to mimic RNase A that can cleave RNA substrates in the absence of divalent metal ions. In addition, single modifications at the fixed regions of DNA libraries, especially at the cleavage junctions, have been tested, and examples of DNAzymes with phosphorothioate and histidine-glycine modified tertiary amine were successfully obtained specific for Cu2+, Cd2+, Zn2+, and Ni2+. Labeling fluorophore/quencher pair right next to the cleavage junction was also used to obtain signaling DNAzymes for detecting various metal ions and cells. Furthermore, we reviewed work on the cleavage of 2'-5' linked RNA and L-RNA substrates. Finally, applications of these modified DNAzymes as biosensors, RNases, and biochemical probes are briefly described with a few future research opportunities outlined at the end.
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Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of WaterlooWaterlooOntario, N2L 3G1Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of WaterlooWaterlooOntario, N2L 3G1Canada
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17
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Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
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18
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Yu W, Wang S, Cao D, Rui H, Liu C, Sheng Y, Sun Y, Zhang J, Xu J, Jiang D. Insight into an Oxidative DNA-Cleaving DNAzyme: Multiple Cofactors, the Catalytic Core Map and a Highly Efficient Variant. iScience 2020; 23:101555. [PMID: 33083724 PMCID: PMC7522124 DOI: 10.1016/j.isci.2020.101555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/24/2020] [Accepted: 09/09/2020] [Indexed: 02/07/2023] Open
Abstract
An oxidative DNA-cleaving DNAzyme (PL) employs a double-cofactor model “X/Cu2+” for catalysis. Herein, we verified that reduced nicotinamide adenine dinucleotide (NADH), flavin mononucleotide, cysteine, dithiothreitol, catechol, resorcinol, hydroquinone, phloroglucinol, o-phenylenediamine, 3,3′,5,5'-tetramethylbenzidine, and hydroxylamine acted as cofactor X. According to their structural similarities or fluorescence property, we further confirmed that reduced nicotinamide adenine dinucleotide phosphate (NADPH), 2-mercaptoethanol, dopamine, chlorogenic acid, resveratrol, and 5-carboxyfluorescein also functioned as cofactor X. Superoxide anions might be the commonality behind these cofactors. We subsequently determined the conservative change of individual nucleotides in the catalytic core under four different cofactor X. The nucleotides A4 and C5 are highly conserved, whereas the conservative levels of other nucleotides are dependent on the types of cofactor X. Moreover, we observed that the minor change in the PL's secondary structure affects electrophoretic mobility. Finally, we characterized a highly efficient variant T3G and converted its double-cofactor NADH/Cu2+ to sole-cofactor NADH. An oxidative cleavage DNAzyme works with various cofactor X Catalytic nucleotide conservation fluctuates with different cofactor X The PL DNAzyme's minor secondary structure change affects electrophoretic mobility Double-cofactor model of the variant T3G can be converted to sole-cofactor model
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Affiliation(s)
- Wenqian Yu
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Shijin Wang
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Dongling Cao
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Hongyue Rui
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Chengcheng Liu
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Yongjie Sheng
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Yanhong Sun
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Jin Zhang
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Jiacui Xu
- College of Animal Sciences, Jilin University, 5333# Xi'an Road, Changchun 130062, China
- Corresponding author
| | - Dazhi Jiang
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
- Corresponding author
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19
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Wang SD, Zhang RB, Cadet J. Enhanced reactivity of the pyrimidine peroxyl radical towards the C–H bond in duplex DNA – a theoretical study. Org Biomol Chem 2020; 18:3536-3543. [DOI: 10.1039/d0ob00302f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The peroxyl radical exhibits a much stronger reactivity towards C1′–H1′ in duplex DNA with respect to single-stranded DNA.
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Affiliation(s)
- Shu-dong Wang
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing
- China
| | - Ru-bo Zhang
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing
- China
| | - Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie
- Faculté de Médecine
- Université de Sherbrooke
- Sherbrooke
- Canada JIH 5N4
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20
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Cepeda-Plaza M, Peracchi A. Insights into DNA catalysis from structural and functional studies of the 8-17 DNAzyme. Org Biomol Chem 2020; 18:1697-1709. [DOI: 10.1039/c9ob02453k] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The review examines functional knowledge gathered over two decades of research on the 8-17 DNAzyme, focusing on three aspects: the structural requirements for catalysis, the role of metal ions and the participation of general acid-base catalysis.
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Affiliation(s)
| | - Alessio Peracchi
- Department of Chemistry
- Life Sciences and Environmental Sustainability
- University of Parma
- Parma
- Italy
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21
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Lake RJ, Yang Z, Zhang J, Lu Y. DNAzymes as Activity-Based Sensors for Metal Ions: Recent Applications, Demonstrated Advantages, Current Challenges, and Future Directions. Acc Chem Res 2019; 52:3275-3286. [PMID: 31721559 PMCID: PMC7103667 DOI: 10.1021/acs.accounts.9b00419] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metal ions can be beneficial or toxic depending on their identity, oxidation state, and concentration. Therefore, the ability to detect and quantify different types of metal ions using portable sensors or in situ imaging agents is important for better environmental monitoring, in vitro medical diagnostics, and imaging of biological systems. While numerous metal ions in different oxidation states are present in the environment and biological systems, only a limited number of them can be detected effectively using current methods. In this Account, we summarize research results from our group that overcome this limitation by the development of a novel class of activity-based sensors based on metal-dependent DNAzymes, which are DNA molecules with enzymatic activity. First, we have developed an in vitro selection method to obtain DNAzymes from a large DNA library of up to 1015 sequences that can carry out cleavage of an oligonucleotide substrate only in the presence of a specific metal ion with high selectivity. Negative selection steps can further be used to improve the selectivity against potentially competing targets by removing sequences that recognize the competing metal ions. Second, we have developed a patented catalytic beacon method to transform the metal-dependent DNAzyme cleavage reaction into a turn-on fluorescent signal by attaching a fluorophore and quenchers to the DNAzyme complex. Because of the difference in the melting temperatures of DNA hybridization before and after metal-ion-dependent cleavage of the DNAzyme substrate, the fluorophore on the DNA cleavage product can be released from its quenchers to create a turn-on fluorescent signal. Because DNAzymes are easy to conjugate with other signaling moieties, such as gold nanoparticles, lanthanide-doped upconversion nanoparticles, electrochemical agents, and gadolinium complexes, these DNAzymes can also readily be converted into colorimetric sensors, upconversion luminescence sensors, electrochemical sensors, or magnetic resonance contrast agents. In addition to describing recent progress in developing and applying these metal ion sensors for environmental monitoring, point-of-care diagnostics, cellular imaging, and in vivo imaging in zebrafish, we summarize major advantages of this class of activity-based sensors. In addition to advantages common to most activity-based sensors, such as enzymatic turnovers that allow for signal amplification and the use of initial rates instead of absolute signals for quantification to avoid interferences from sample matrices, the DNAzyme-based sensors allow for in vitro selection to expand the method to almost any metal ion under a variety of conditions, negative selection to improve the selectivity against competing targets, and reselection of DNAzymes and combination of active and inactive variants to fine-tune the dynamic range of detection. The use of melting temperature differences to separate target binding from signaling moieties in the catalytic beacon method allows the use of different fluorophores and nanomaterials to extend the versatility and modularity of this sensing platform. Furthermore, sensing and imaging artifacts can be minimized by using an inactive mutant DNAzyme as a negative control, while spatiotemporal control of sensing/imaging can be achieved using optical, photothermal, and endogenous orthogonal caging methods. Finally, current challenges, opportunities, and future perspectives for DNAzymes as activity-based sensors are also discussed.
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Affiliation(s)
- Ryan J. Lake
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Zhenglin Yang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - JingJing Zhang
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
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22
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Ren W, Huang PJJ, He M, Lyu M, Wang S, Wang C, Liu J. The Two Classic Pb 2+ -Selective DNAzymes Are Related: Rational Evolution for Understanding Metal Selectivity. Chembiochem 2019; 21:1293-1297. [PMID: 31755629 DOI: 10.1002/cbic.201900664] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Indexed: 01/09/2023]
Abstract
In 1994, the first DNAzyme named GR5 was reported, which specifically requires Pb2+ for its RNA cleavage activity. Three years later, the 8-17 DNAzyme was isolated. The 8-17 DNAzyme and the related 17E DNAzyme are also most active with Pb2+ , although other divalent metals can work as well. GR5 and 17E have the same substrate sequence, and their catalytic loops in the enzyme strands also have a few similar and conserved nucleotides. Considering these, we hypothesized that 17E might be a special form of GR5. To test this hypothesis, we performed systematic rational evolution experiments to gradually mutate GR5 toward 17E. By using the activity ratio in the presence of Pb2+ and Mg2+ for defining these two DNAzymes, the critical nucleotide was identified to be T12 in 17E for metal specificity. In addition, G9 in GR5 is a position not found in most 17E or 8-17 DNAzymes, and G9 needs to be added to rescue GR5 activity if T12 becomes a cytosine. This study highlights the links between these two classic and widely used DNAzymes, and offers new insight into the sequence-activity relationship related to metal selectivity.
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Affiliation(s)
- Wei Ren
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, P. R. China.,Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, Jiangsu, 222005, P. R. China.,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Meilin He
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, P. R. China
| | - Mingsheng Lyu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, Jiangsu, 222005, P. R. China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, Jiangsu, 222005, P. R. China
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, Jiangsu, 222005, P. R. China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, Jiangsu, 222005, P. R. China
| | - Changhai Wang
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, P. R. China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
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23
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Constructing Controllable Logic Circuits Based on DNAzyme Activity. Molecules 2019; 24:molecules24224134. [PMID: 31731630 PMCID: PMC6891523 DOI: 10.3390/molecules24224134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/30/2022] Open
Abstract
Recently, DNA molecules have been widely used to construct advanced logic devices due to their unique properties, such as a simple structure and predictable behavior. In fact, there are still many challenges in the process of building logic circuits. Among them, the scalability of the logic circuit and the elimination of the crosstalk of the cascade circuit have become the focus of research. Inspired by biological allosteric regulation, we developed a controllable molecular logic circuit strategy based on the activity of DNAzyme. The E6 DNAzyme sequence was temporarily blocked by hairpin DNA and activated under appropriate input trigger conditions. Using a substrate with ribonucleobase (rA) modification as the detection strand, a series of binary basic logic gates (YES, AND, and INHIBIT) were implemented on the computational component platform. At the same time, we demonstrate a parallel demultiplexer and two multi-level cascade circuits (YES-YES and YES-Three input AND (YES-TAND)). In addition, the leakage of the cascade process was reduced by exploring factors such as concentration and DNA structure. The proposed DNAzyme activity regulation strategy provides great potential for the expansion of logic circuits in the future.
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24
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Ekesan Ş, York DM. Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution. Nucleic Acids Res 2019; 47:10282-10295. [PMID: 31511899 PMCID: PMC6821293 DOI: 10.1093/nar/gkz773] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/20/2019] [Accepted: 09/03/2019] [Indexed: 02/01/2023] Open
Abstract
We perform molecular dynamics simulations, based on recent crystallographic data, on the 8-17 DNAzyme at four states along the reaction pathway to determine the dynamical ensemble for the active state and transition state mimic in solution. A striking finding is the diverse roles played by Na+ and Pb2+ ions in the electrostatically strained active site that impact all four fundamental catalytic strategies, and share commonality with some features recently inferred for naturally occurring hammerhead and pistol ribozymes. The active site Pb2+ ion helps to stabilize in-line nucleophilic attack, provides direct electrostatic transition state stabilization, and facilitates leaving group departure. A conserved guanine residue is positioned to act as the general base, and is assisted by a bridging Na+ ion that tunes the pKa and facilitates in-line fitness. The present work provides insight into how DNA molecules are able to solve the RNA-cleavage problem, and establishes functional relationships between the mechanism of these engineered DNA enzymes with their naturally evolved RNA counterparts. This adds valuable information to our growing body of knowledge on general mechanisms of phosphoryl transfer reactions catalyzed by RNA, proteins and DNA.
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Affiliation(s)
- Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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25
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Moon WJ, Liu J. Replacing Mg2+by Fe2+for RNA‐Cleaving DNAzymes. Chembiochem 2019; 21:401-407. [DOI: 10.1002/cbic.201900344] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Woohyun J. Moon
- Department of ChemistryWaterloo Institute for NanotechnologyUniversity of Waterloo Waterloo Ontario N2L 3G1 Canada
| | - Juewen Liu
- Department of ChemistryWaterloo Institute for NanotechnologyUniversity of Waterloo Waterloo Ontario N2L 3G1 Canada
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26
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Gao L, Tong X, Ye T, Gao H, Zhang Q, Yan C, Yu Y, Fei Y, Zhou X, Shao Y. G‐Quadruplex‐Based Photooxidase Driven by Visible Light. ChemCatChem 2019. [DOI: 10.1002/cctc.201901481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Longlong Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Xingyu Tong
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Ting Ye
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Heng Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Qingqing Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Chenxiao Yan
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Yali Yu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Yifan Fei
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
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27
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Banno A, Higashi S, Shibata A, Ikeda M. A stimuli-responsive DNAzyme displaying Boolean logic-gate responses. Chem Commun (Camb) 2019; 55:1959-1962. [PMID: 30681683 DOI: 10.1039/c8cc09345h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Introducing a desired stimuli-responsive function into catalytically active biomacromolecules is potentially useful in developing molecular tools for various bio-applications. In this paper, we discuss the development of a stimuli-responsive DNAzyme (catalytic deoxyribozyme) capable of displaying Boolean logic-gate responses.
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Affiliation(s)
- Ayaka Banno
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
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