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Li X, Chang Y, Wu Y, Liu M. A DNAzymes-in-droplets assay for Burkholderia gladioli pathovar cocovenenans with single-bacterium sensitivity. Chem Sci 2024; 15:2996-3002. [PMID: 38404397 PMCID: PMC10882462 DOI: 10.1039/d3sc05874c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/15/2024] [Indexed: 02/27/2024] Open
Abstract
Foodborne pathogens pose a serious risk to human health, and the simple and rapid detection of such bacteria in complex food matrices remains challenging. Herein, we present the selection and characterization of a novel RNA-cleaving fluorogenic DNAzyme, named RFD-BC1, with exceptional specificity for Burkholderia gladioli pv. cocovenenans (B. cocovenenans), a pathogen strongly associated with fatal food poisoning cases. RFD-BC1 was activated by a protein secreted specifically by whole viable B. cocovenenans and displayed an optimum pH distinct from the selection pH, with a rate constant of approximately 0.01 min-1 at pH 5.0. Leveraging this newly discovered DNAzyme, we developed a novel system, termed DNAzymes-in-droplets (DID), that integrates droplet microfluidics to achieve the rapid and selective detection of live B. cocovenenans with single-cell sensitivity. We believe that the approach described herein holds promise for combating specific bacterial pathogens in food samples, offering significant potential for broader applications in food safety and public health.
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Affiliation(s)
- Xiaoqian Li
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
| | - Yunping Wu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
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2
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Pospieszna-Markiewicz I, Fik-Jaskółka MA, Hnatejko Z, Patroniak V, Kubicki M. Synthesis and Characterization of Lanthanide Metal Ion Complexes of New Polydentate Hydrazone Schiff Base Ligand. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238390. [PMID: 36500479 PMCID: PMC9736465 DOI: 10.3390/molecules27238390] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/11/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022]
Abstract
The new homodinuclear complexes of the general formula [Ln2L3(NO3)3] (where HL is newly synthesized 2-((2-(benzoxazol-2-yl)-2-methylhydrazono)methyl)phenol and Ln = Sm3+ (1), Eu3+ (2), Tb3+ (3a, 3b), Dy3+ (4), Ho3+ (5), Er3+ (6), Tm3+ (7), Yb3+ (8)), have been synthesized from the lanthanide(III) nitrates with the polydentate hydrazone Schiff base ligand. The flexibility of this unsymmetrical Schiff base ligand containing N2O binding moiety, attractive for lanthanide metal ions, allowed for a self-assembly of these complexes. The compounds were characterized by spectroscopic data (ESI-MS, IR, UV/Vis, luminescence) and by the X-ray structure determination of the single crystals, all of which appeared to be different solvents. The analytical data suggested 2:3 metal:ligand stoichiometry in these complexes, and this was further confirmed by the structural results. The metal cations are nine-coordinated, by nitrogen and oxygen donor atoms. The complexes are two-centered, with three oxygen atoms in bridging positions. There are two types of structures, differing by the sources of terminal (non-bridging) coordination centers (group A: two ligands, one nitro anion/one ligand, two nitro anions, group B: three ligands, three anions).
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3
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Ru XM, Yang ZY, Ran SY. Lanthanide ions induce DNA compaction with ionic specificity. Int J Biol Macromol 2022; 210:292-299. [DOI: 10.1016/j.ijbiomac.2022.04.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 11/05/2022]
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4
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Yum JH, Sugiyama H, Park S. Harnessing DNA as a Designable Scaffold for Asymmetric Catalysis: Recent Advances and Future Perspectives. CHEM REC 2022; 22:e202100333. [PMID: 35312235 DOI: 10.1002/tcr.202100333] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/27/2022]
Abstract
Since the first report of DNAzyme by in vitro selection in 1994, catalytic DNA has investigated extensively, and their application has expanded continually in virtue of rapid advances in molecular biology and biotechnology. Nowadays, DNA is in the second prime time by way of DNA-based hybrid catalysts and DNA metalloenzymes in which helical chirality of DNA serves to asymmetric catalysis. DNA-based hybrid catalysts are attractive system to respond the demand of the times to pursuit green and sustainable society beyond traditional catalytic systems that value reaction efficiency. Herein, we highlight the recent advances and perspective of DNA-based hybrid catalysts with various aspects of DNA as a versatile scaffold for asymmetric synthesis. We hope that scientists in a variety of fields will be encouraged to join and promote remarkable evolution of this interesting research.
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Affiliation(s)
- Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Soyoung Park
- Immunology Frontier Research Center (iFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871, Japan.,Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita, 565-0871, Japan
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5
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Xu T, Zhang C, Xia K, Li W, Cao Y, Gu H. Small DNAs that Bind Nickel(II) Specifically and Tightly. Anal Chem 2021; 93:14912-14917. [PMID: 34734709 DOI: 10.1021/acs.analchem.1c04034] [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
Metal recognition by nucleic acids provides an intriguing route for biosensing of metal. Toward this goal, a key prerequisite is the acquisition of nucleic acids that can selectively respond to specific metals. Herein, we report for the first time the discovery of two small DNAs that can specifically bind Ni2+ and discriminate against similar ions, particularly, Co2+. Their minimal effective constructs are 60-70 nucleotides (nt) in length with Ni2+ binding even at harsh denaturing conditions of 8 M urea and 50 mM EDTA. Using isothermal titration calorimetry (ITC), we estimated the dissociation constant (KD) of a representative DNA to be 24.0 ± 4.5 μM, with a 9:1 stoichiometry of Ni2+ bound to DNA. As being engineered into nanosized particles, these DNAs can act like nanosponges to specifically adsorb Ni2+ from artificial wastewater, demonstrating their potential as a novel molecular tool for high-quality nickel enrichment and detection.
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Affiliation(s)
- Tianbin Xu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200032, China.,Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 200433, China
| | - Canyu Zhang
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200032, China.,Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 200433, China
| | - Kai Xia
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200032, China.,Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 200433, China
| | - Wei Li
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200032, China.,Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 200433, China
| | - Yichun Cao
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200032, China.,Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 200433, China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200032, China.,Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 200433, China
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7
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Zhang C, Li Q, Xu T, Li W, He Y, Gu H. New DNA-hydrolyzing DNAs isolated from an ssDNA library carrying a terminal hybridization stem. Nucleic Acids Res 2021; 49:6364-6374. [PMID: 34057476 PMCID: PMC8216280 DOI: 10.1093/nar/gkab439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023] Open
Abstract
DNA-hydrolyzing DNAs represent an attractive type of DNA-processing catalysts distinctive from the protein-based restriction enzymes. The innate DNA property has enabled them to readily join DNA-based manipulations to promote the development of DNA biotechnology. A major in vitro selection strategy to identify these DNA catalysts relies tightly on the isolation of linear DNAs processed from a circular single-stranded (ss) DNA sequence library by self-hydrolysis. Herein, we report that by programming a terminal hybridization stem in the library, other than the previously reported classes (I & II) of deoxyribozymes, two new classes (III & IV) were identified with the old selection strategy to site-specifically hydrolyze DNA in the presence of Zn2+. Their representatives own a catalytic core consisting of ∼20 conserved nucleotides and a half-life of ∼15 min at neutral pH. In a bimolecular construct, class III exhibits unique broad generality on the enzyme strand, which can be potentially harnessed to engineer DNA-responsive DNA hydrolyzers for detection of any target ssDNA sequence. Besides the new findings, this work should also provide an improved approach to select for DNA-hydrolyzing deoxyribozymes that use various molecules and ions as cofactors.
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Affiliation(s)
- Canyu Zhang
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China.,Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 201399, China
| | - Qingting Li
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China
| | - Tianbin Xu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China
| | - Wei Li
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China
| | - Yungang He
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China.,Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 201399, China
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8
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Huang PJJ, Liu J. In vitro selection and application of lanthanide-dependent DNAzymes. Methods Enzymol 2021; 651:373-396. [PMID: 33888210 DOI: 10.1016/bs.mie.2021.01.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Highly sensitive and selective detection of lanthanide ions is a major analytical challenge. In recent years, the use of DNA for this purpose has been pursued. For such highly charged cations, it is difficult to select their aptamers due to strong nonspecific binding. On the other hand, the use of catalytic DNA or DNAzymes has an advantage to overcome this problem, especially DNAzymes with RNA-cleaving activity. In this chapter, a few such DNAzymes are introduced and methods for in vitro selection of lanthanide-dependent RNA-cleaving DNAzymes are described in detail, including the selection protocols, the DNA sequences used, the characterization of selected DNAzymes and their conversion into biosensors. All of the experiments use only fluorophore-labeled DNA, and radioisotope labeling is completely avoided. The resulting DNAzymes can distinguish lanthanides from non-lanthanide metals, tell the difference between light and heavy lanthanides, and can be used together to discriminate individual lanthanides.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada.
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9
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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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10
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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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11
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Safdar S, Lammertyn J, Spasic D. RNA-Cleaving NAzymes: The Next Big Thing in Biosensing? Trends Biotechnol 2020; 38:1343-1359. [PMID: 32473751 DOI: 10.1016/j.tibtech.2020.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023]
Abstract
Nucleic acid enzymes (NAzymes) are nucleic acid molecules with catalytic activity. A subset, the RNA-cleaving NAzyme, is characterized by its substrate of choice: an RNA unit. These enzymes have been used for diverse applications, including biosensor development, akin to their protein counterparts. Owing to their function as both biorecognition elements and signal generators, robust bioassays based entirely on NAzyme molecules have been developed. Additionally, unique mechanisms for integration with other biorecognition elements and signal generation methods have been explored to realize ultrasensitive, specific, and user-friendly biosensors. Furthermore, NAzyme-based bioassays have already broken into the in vitro diagnostics market, with more promise in the pipeline.
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Affiliation(s)
- Saba Safdar
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium.
| | - Dragana Spasic
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium
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12
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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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Chan EJ, Harrowfield JM, Skelton BW, Sobolev AN, White AH. Structural Systematics of Lanthanide(III) Picrate Solvates: Molecular, Mononuclear Ln(pic)3(trimethylphosphate)3 Arrays. Aust J Chem 2020. [DOI: 10.1071/ch19176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Adducts of the form Ln(pic)3(tmp)3 (Ln=lanthanide(iii); pic=picrate=2,4,6-trinitrophenoxide; tmp=trimethylphosphate, (MeO)3PO) have been prepared for extremal Ln=La, Lu and some intermediate members, also Y, and characterised by single crystal X-ray structure determinations as unsolvated, mononuclear, molecular species. The lanthanide atom has nine-coordinate, tri-capped trigonal prismatic stereochemistry in all cases, the picrate components behaving as O,O′-bidentate ligands chelating through the phenoxy- and an adjacent O-nitro oxygen atom, thus: [Ln(tmp-O)3(pic-O,O′)3]. Two isomeric forms are found, one mer in which the three unidentate tmp-O ligands coordinate in cis-sites spanning the upper and lower triangles and a capping site of the coordination sphere, and fac, in which all three unidentate ligands occupy the mutually cis-sites of one triangular face. The mer isomer has been described as an isomorphous series in a monoclinic P21/c, Z 4, form, for Ln=La, Ce, Pr, Nd, Sm, Gd, Lu, and Y, presumptively accessible for the full gamut of Ln. The fac-isomer also crystallises in a monoclinic P21/c form, Z 8, two independent molecules of similar stereochemistry here comprising the asymmetric unit and described for Ln=Eu, Lu(isomorphous); it has also been described in a triclinic P, Z 2 form for Ln=La.
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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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Targeting a viral DNA sequence with a deoxyribozyme in a preparative scale. Biochimie 2019; 165:161-169. [PMID: 31377192 DOI: 10.1016/j.biochi.2019.07.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 07/28/2019] [Indexed: 01/13/2023]
Abstract
Deoxyribozymes are synthetic and single stranded DNAs that are capable of catalysis of a variety of reactions, including cleavage of DNA substrates. Deoxyribozymes are usually characterized by analytical single-turnover kinetic assays, however, for many applications e.g. characterization of the reaction products, semi-preparative and preparative reactions are required. At such scales, there is a lack of comprehensive analysis and conditions that supports high amount of products in an appropriate time-scale are vaguely guessed by researchers. In this report, catalytic activity of an oxidizing DNA-cleaving deoxyribozyme, F-8(X), was comprehensively inspected in semi-preparative (10 μM substrate) scale. A 60 nucleotides long synthetic DNA sequence was selected as the target DNA for this study. The DNA sequence was originated from a single stranded DNA virus. Investigations revealed high yield in the presence of optimal concentration of oxidizing agents. The optimal conditions have been applied for scale-up of the reaction to preparative (40 μM substrate) and multi-turnover reactions to achieve highest amount of product in a cost-, time- and labor-effective manner. Such a comprehensive analysis of a deoxyribozyme's activity in semi-preparative scale provides a platform for expanded applications of DNA catalysts as a tool in chemical biology.
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He Y, Lopez A, Zhang Z, Chen D, Yang R, Liu J. Nucleotide and DNA coordinated lanthanides: From fundamentals to applications. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.02.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Ma L, Liu J. An in Vitro-Selected DNAzyme Mutant Highly Specific for Na + under Slightly Acidic Conditions. Chembiochem 2018; 20:537-542. [PMID: 29989277 DOI: 10.1002/cbic.201800322] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Indexed: 12/19/2022]
Abstract
Sodium is one of the most common metal ions in biology; however, DNA-based sodium probes have only been reported recently. A Na+ -specific RNA-cleaving DNAzyme named NaA43 is active with Na+ alone. In this work, we were using Co(NH3 )6 3+ as the intended metal cofactor for in vitro selection, but obtained a mutant of the NaA43 DNAzyme. The mutant was named NaH1, and differs from NaA43 by only two nucleotides. NaA43 has an optimal pH of 7.0, whereas the optimal pH for NaH1 is 6.0. This difference might be due to our selection having been performed at pH 6.0. NaH1 also displays an excellent selectivity for sodium relative to other competing monovalent ions, as well as a fast catalytic rate of (0.11±0.01) min-1 with 50 mm Na+ . At low Na+ concentrations, the selected DNAzyme exhibited a higher cleavage rate than NaA43 and thus a tighter apparent Kd of (12.0±1.6) mm Na+ . Furthermore, the NaH1 DNAzyme was engineered into a fluorescent Na+ biosensor by attaching a fluorophore/quencher pair to the DNAzyme with a detection limit of 223 μm Na+ . Preliminary work on detection of Na+ in serum was demonstrated as well. This study provides a useful mutant that works in a slightly acidic environment, which might be useful for sensing Na+ in acidic in vivo environments.
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Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
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19
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Du X, Zhong X, Li W, Li H, Gu H. Retraining and Optimizing DNA-Hydrolyzing Deoxyribozymes for Robust Single- and Multiple-Turnover Activities. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01466] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xinyu Du
- Fudan University Shanghai Cancer Center, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xin Zhong
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Wei Li
- Fudan University Shanghai Cancer Center, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Hua Li
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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20
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Xu L, Zhang Z, Fang X, Liu Y, Liu B, Liu J. Robust Hydrogels from Lanthanide Nucleotide Coordination with Evolving Nanostructures for a Highly Stable Protein Encapsulation. ACS APPLIED MATERIALS & INTERFACES 2018; 10:14321-14330. [PMID: 29644845 DOI: 10.1021/acsami.7b18005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Metal coordination with organic ligands often produce crystalline metal-organic frameworks and sometimes amorphous nanoparticles. In this work, we explore a different type of material from the same chemistry: hydrogels. Lanthanides are chosen as the metal component because of their important technological applications and continuously tunable properties. Adenosine monophosphate (AMP) and lanthanides form two types of coordination materials: the lighter lanthanides from La3+ to Tb3+ form nanoparticles, whereas the rest heavier ones initially form nanoparticles but later spontaneously transform to hydrogels. This slow sol-to-gel transition is accompanied by heat release, as indicated by isothermal titration calorimetry. The transition is also accompanied by a morphology change from nanoparticles to nanofibers, as indicated by transmission electron microscopy. These gels are insensitive to ionic strength or temperature with excellent stability. Gelation is unique to AMP because other nucleotides or other adenine derivatives only yield nanoparticles or soluble products. Entrapment of guest molecules such as glucose oxidase is also explored, where the hydrogels allow a better enzyme activity and stability compared to nanoparticles. Further applications of lanthanide coordinated hydrogels might include biosensors, imaging agents, and drug delivery.
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Affiliation(s)
- Li Xu
- School of Chemistry and Chemical Engineering , Guangdong Pharmaceutical University , Zhongshan 528458 , P. R. China
- Department of Chemistry and Waterloo Institute for Nanotechnology , University of Waterloo , 200 University Avenue West , Waterloo , Ontario , Canada N2L 3G1
| | - Zijie Zhang
- Department of Chemistry and Waterloo Institute for Nanotechnology , University of Waterloo , 200 University Avenue West , Waterloo , Ontario , Canada N2L 3G1
| | - Xiaoqiang Fang
- School of Chemistry and Chemical Engineering , Guangdong Pharmaceutical University , Zhongshan 528458 , P. R. China
| | - Yibo Liu
- Department of Chemistry and Waterloo Institute for Nanotechnology , University of Waterloo , 200 University Avenue West , Waterloo , Ontario , Canada N2L 3G1
| | - Biwu Liu
- Department of Chemistry and Waterloo Institute for Nanotechnology , University of Waterloo , 200 University Avenue West , Waterloo , Ontario , Canada N2L 3G1
| | - Juewen Liu
- Department of Chemistry and Waterloo Institute for Nanotechnology , University of Waterloo , 200 University Avenue West , Waterloo , Ontario , Canada N2L 3G1
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21
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Abstract
The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an 'RNA world', notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pK a values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.
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22
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Zhang Z, Morishita K, Lin WTD, Huang PJJ, Liu J. Nucleotide coordination with 14 lanthanides studied by isothermal titration calorimetry. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.06.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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Abstract
Nucleic acid enzymes require metal ions for activity, and many recently discovered enzymes can use multiple metals, either binding to the scissile phosphate or also playing an allosteric role.
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Affiliation(s)
- Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences
- Central South University
- Changsha
- China
| | - Juewen Liu
- Department of Chemistry
- Water Institute, and Waterloo Institute for Nanotechnology
- University of Waterloo
- Waterloo
- Canada
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24
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Yuan Y, Zhao Y, Chen L, Wu J, Chen G, Li S, Zou J, Chen R, Wang J, Jiang F, Tang Z. Selective tumor cell death induced by irradiated riboflavin through recognizing DNA G-T mismatch. Nucleic Acids Res 2017; 45:8676-8683. [PMID: 28911109 PMCID: PMC5587794 DOI: 10.1093/nar/gkx602] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 07/04/2017] [Indexed: 12/04/2022] Open
Abstract
Riboflavin (vitamin B2) has been thought to be a promising antitumoral agent in photodynamic therapy, though the further application of the method was limited by the unclear molecular mechanism. Our work reveals that riboflavin was able to recognize G–T mismatch specifically and induce single-strand breaks in duplex DNA targets efficiently under irradiation. In the presence of riboflavin, the photo-irradiation could induce the death of tumor cells that are defective in mismatch repair system selectively, highlighting the G–T mismatch as potential drug target for tumor cells. Moreover, riboflavin is a promising leading compound for further drug design due to its inherent specific recognition of the G–T mismatch.
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Affiliation(s)
- Yi Yuan
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China.,College of pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, PR China
| | - Yongyun Zhao
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Lianqi Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Jiasi Wu
- College of pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, PR China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Sheng Li
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Jiawei Zou
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Rong Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Jian Wang
- College of pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, PR China
| | - Fan Jiang
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
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25
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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26
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Lee Y, Klauser PC, Brandsen BM, Zhou C, Li X, Silverman SK. DNA-Catalyzed DNA Cleavage by a Radical Pathway with Well-Defined Products. J Am Chem Soc 2016; 139:255-261. [PMID: 27935689 DOI: 10.1021/jacs.6b10274] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe an unprecedented DNA-catalyzed DNA cleavage process in which a radical-based reaction pathway cleanly results in excision of most atoms of a specific guanosine nucleoside. Two new deoxyribozymes (DNA enzymes) were identified by in vitro selection from N40 or N100 random pools initially seeking amide bond hydrolysis, although they both cleave simple single-stranded DNA oligonucleotides. Each deoxyribozyme generates both superoxide (O2-• or HOO•) and hydrogen peroxide (H2O2) and leads to the same set of products (3'-phosphoglycolate, 5'-phosphate, and base propenal) as formed by the natural product bleomycin, with product assignments by mass spectrometry and colorimetric assay. We infer the same mechanistic pathway, involving formation of the C4' radical of the guanosine nucleoside that is subsequently excised. Consistent with a radical pathway, glutathione fully suppresses catalysis. Conversely, adding either superoxide or H2O2 from the outset strongly enhances catalysis. The mechanism of generation and involvement of superoxide and H2O2 by the deoxyribozymes is not yet defined. The deoxyribozymes do not require redox-active metal ions and function with a combination of Zn2+ and Mg2+, although including Mn2+ increases the activity, and Mn2+ alone also supports catalysis. In contrast to all of these observations, unrelated DNA-catalyzed radical DNA cleavage reactions require redox-active metals and lead to mixtures of products. This study reports an intriguing example of a well-defined, DNA-catalyzed, radical reaction process that cleaves single-stranded DNA and requires only redox-inactive metal ions.
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Affiliation(s)
- Yujeong Lee
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Paul C Klauser
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Benjamin M Brandsen
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Cong Zhou
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Xinyi Li
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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27
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Xie JQ, Zhang Y, Cai SL, Li FZ, Feng FM. Catalytic Capacity of Diaza-Crown Ether Lanthanum Complexes with Varied Ligands for Phosphate Ester Hydrolysis in Different Media. PROGRESS IN REACTION KINETICS AND MECHANISM 2016. [DOI: 10.3184/146867816x14710833328904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Two diaza-crown ether compounds, 1,4,10,13-tetraoxa-7,16-diazacyclooctadecane (L0) and its derivative with double acetamide side arms 2,2'-(1,4,10,13-teteaoxa-7,16-diazacyclooctadecane-7,16-diyl)diacetamide (L), and the corresponding two lanthanum complexes were synthesised and characterised. The catalytic capacity of the lanthanum complexes was investigated for the hydrolysis of bis(4-nitrophenyl) phosphate ester (BNPP) in aqueous solution and in CTAB micelles. Kinetic studies show that the catalytic efficiency of complex LaL is obviously higher than that of complex LaL0, and introducing acetamide into the ring of the diaza-crown ether can improve the catalytic ability of the complexes for BNPP hydrolysis. A rate enhancement of about two times was observed for the complex–micelle in contrast with the complex–water system for BNPP catalytic hydrolysis. The optimal pH for the catalytic reaction in the two kinds of media systems show an approximately 0.4 pH unit difference. The two complexes possess higher thermostability, and are more stable in the micelle than in aqueous solution. Based on the results and their analysis, a catalytic mechanism with cooperation of acetamide is proposed.
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Affiliation(s)
- Jia-qing Xie
- College of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, P.R. China
| | - Ya Zhang
- Chongqing Environmental Monitoring Center, Chongqing 401147, P.R. China
| | - Shu-lan Cai
- College of Chemistry and Pharmaceutical Engineering, Sichuan University of Science & Engineering, Zigong, Sichuan 643000, P.R. China
| | - Fang-zhen Li
- College of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, P.R. China
| | - Fa-mei Feng
- College of Chemistry and Pharmaceutical Engineering, Sichuan University of Science & Engineering, Zigong, Sichuan 643000, P.R. China
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28
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Jabeen F, Najam-ul-Haq M, Ashiq MN, Rainer M, Huck CW, Bonn GK. Gadolinium oxide: Exclusive selectivity and sensitivity in the enrichment of phosphorylated biomolecules. J Sep Sci 2016; 39:4175-4182. [DOI: 10.1002/jssc.201600651] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/20/2016] [Accepted: 08/20/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Fahmida Jabeen
- Division of Analytical Chemistry, Institute of Chemical Sciences; Bahauddin Zakariya University; Multan Pakistan
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University; Innsbruck Austria
| | - Muhammad Najam-ul-Haq
- Division of Analytical Chemistry, Institute of Chemical Sciences; Bahauddin Zakariya University; Multan Pakistan
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University; Innsbruck Austria
| | - Muhammad Naeem Ashiq
- Division of Analytical Chemistry, Institute of Chemical Sciences; Bahauddin Zakariya University; Multan Pakistan
| | - Matthias Rainer
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University; Innsbruck Austria
| | - Christian W. Huck
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University; Innsbruck Austria
| | - Guenther K. Bonn
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University; Innsbruck Austria
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29
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Cai SL, Feng FM, Liu FA. Function of the Metallomicelle from an Aza-Crown Ether Complex with an Acetamide Branch as a Highly Potent Promoter of Phosphate Diester Hydrolytic Cleavage. J DISPER SCI TECHNOL 2016. [DOI: 10.1080/01932691.2015.1088451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Ma L, Liu B, Huang PJJ, Zhang X, Liu J. DNA Adsorption by ZnO Nanoparticles near Its Solubility Limit: Implications for DNA Fluorescence Quenching and DNAzyme Activity Assays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:5672-80. [PMID: 27166701 DOI: 10.1021/acs.langmuir.6b00906] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Zinc oxide (ZnO) is a highly important material, and Zn(2+) is a key metal ion in biology. ZnO and Zn(2+) interconvert via dissolution and hydrolysis/condensation. In this work, we explore their interactions with DNA, which is important for biointerface, analytical, and bioinorganic chemistry. Fluorescently labeled DNA oligonucleotides were adsorbed by a low concentration (around 5 μg/mL) of ZnO nanoparticles, near the solubility limit. Right after mixing, fluorescence quenching occurred, indicating DNA adsorption. Then, fluorescence recovered, attributable to ZnO dissolution. The dissolution rate followed A5 > T5 > C5. Dissolution was slower with longer DNA. The adsorption affinity was also measured by a displacement assay to be G5 > C5 > T5 > A5, suggesting that tightly adsorbed DNA can retard ZnO dissolution. Electrostatic interactions are important for DNA adsorption because ZnO is positively charged at neutral pH, and a high salt concentration inhibits DNA adsorption. Next, in situ formation of ZnO from Zn(2+) was studied. First, titrating Zn(2+) into a fluorescently labeled oligonucleotide at pH 7.5 resulted in an abrupt fluorescence quenching beyond 0.2 mM Zn(2+). At pH 6, quenching occurred linearly with the Zn(2+) concentration, suggesting the effect of Zn(2+) precipitation at pH 7.5. Second, a Zn(2+)-dependent DNA-cleaving DNAzyme was studied. This DNAzyme was inhibited at higher than 2 mM Zn(2+), attributable to Zn(2+) precipitation and adsorption of the DNAzyme. This paper has established the interplay between DNA, Zn(2+), and ZnO. This understanding can avoid misinterpretation of DNA assay results and adds knowledge to DNA immobilization.
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Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Biwu Liu
- 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
| | - Xu Zhang
- 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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31
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Catalytic DNA: Scope, Applications, and Biochemistry of Deoxyribozymes. Trends Biochem Sci 2016; 41:595-609. [PMID: 27236301 DOI: 10.1016/j.tibs.2016.04.010] [Citation(s) in RCA: 243] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 04/27/2016] [Accepted: 04/29/2016] [Indexed: 11/23/2022]
Abstract
The discovery of natural RNA enzymes (ribozymes) prompted the pursuit of artificial DNA enzymes (deoxyribozymes) by in vitro selection methods. A key motivation is the conceptual and practical advantages of DNA relative to proteins and RNA. Early studies focused on RNA-cleaving deoxyribozymes, and more recent experiments have expanded the breadth of catalytic DNA to many other reactions. Including modified nucleotides has the potential to widen the scope of DNA enzymes even further. Practical applications of deoxyribozymes include their use as sensors for metal ions and small molecules. Structural studies of deoxyribozymes are only now beginning; mechanistic experiments will surely follow. Following the first report 21 years ago, the field of deoxyribozymes has promise for both fundamental and applied advances in chemistry, biology, and other disciplines.
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32
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Huang PJJ, Vazin M, Lin JJ, Pautler R, Liu J. Distinction of Individual Lanthanide Ions with a DNAzyme Beacon Array. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00239] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Po-Jung Jimmy Huang
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Mahsa Vazin
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Jennifer J. Lin
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Rachel Pautler
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Juewen Liu
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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33
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Camden AJ, Walsh SM, Suk SH, Silverman SK. DNA Oligonucleotide 3'-Phosphorylation by a DNA Enzyme. Biochemistry 2016; 55:2671-6. [PMID: 27063020 DOI: 10.1021/acs.biochem.6b00151] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
T4 polynucleotide kinase is widely used for 5'-phosphorylation of DNA and RNA oligonucleotide termini, but no natural protein enzyme is capable of 3'-phosphorylation. Here, we report the in vitro selection of deoxyribozymes (DNA enzymes) capable of DNA oligonucleotide 3'-phosphorylation, using a 5'-triphosphorylated RNA transcript (pppRNA) as the phosphoryl donor. The basis of selection was the capture, during each selection round, of the 3'-phosphorylated DNA substrate terminus by 2-methylimidazole activation of the 3'-phosphate (forming 3'-MeImp) and subsequent splint ligation with a 5'-amino DNA oligonucleotide. Competing and precedented DNA-catalyzed reactions were DNA phosphodiester hydrolysis or deglycosylation, each also leading to a 3'-phosphate but at a different nucleotide position within the DNA substrate. One oligonucleotide 3'-kinase deoxyribozyme, obtained from an N40 random pool and named 3'Kin1, can 3'-phosphorylate nearly any DNA oligonucleotide substrate for which the 3'-terminus has the sequence motif 5'-NKR-3', where N denotes any oligonucleotide sequence, K = T or G, and R = A or G. These results establish the viabilty of in vitro selection for identifying DNA enzymes that 3'-phosphorylate DNA oligonucleotides.
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Affiliation(s)
- Alison J Camden
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Shannon M Walsh
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Sarah H Suk
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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34
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Hwang K, Hosseinzadeh P, Lu Y. Biochemical and Biophysical Understanding of Metal Ion Selectivity of DNAzymes. Inorganica Chim Acta 2016; 452:12-24. [PMID: 27695134 DOI: 10.1016/j.ica.2016.04.017] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This review summarizes research into the metal-binding properties of catalytic DNAzymes, towards the goal of understanding the structural properties leading to metal ion specificity. Progress made and insight gained from a range of biochemical and biophysical techniques are covered, and promising directions for future investigations are discussed.
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Affiliation(s)
- Kevin Hwang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Parisa Hosseinzadeh
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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35
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Huang PJJ, Vazin M, Liu J. In Vitro Selection of a DNAzyme Cooperatively Binding Two Lanthanide Ions for RNA Cleavage. Biochemistry 2016; 55:2518-25. [PMID: 27054549 DOI: 10.1021/acs.biochem.6b00132] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Trivalent lanthanide ions (Ln(3+)) were recently employed to select RNA-cleaving DNAzymes, and three new DNAzymes have been reported so far. In this work, dysprosium (Dy(3+)) was used with a library containing 50 random nucleotides. After six rounds of in vitro selection, a new DNAzyme named Dy10a was obtained and characterized. Dy10a has a bulged hairpin structure cleaving a RNA/DNA chimeric substrate. Dy10a is highly active in the presence of the five Ln(3+) ions in the middle of the lanthanide series (Sm(3+), Eu(3+), Gd(3+), Tb(3+), and Dy(3+)), while its activity descends on the two sides. The cleavage rate reaches 0.6 min(-1) at pH 6 with just 200 nM Sm(3+), which is the fastest among all known Ln(3+)-dependent enzymes. Dy10a binds two Ln(3+) ions cooperatively. When a phosphorothioate (PS) modification is introduced at the cleavage junction, the activity decreases by >2500-fold for both the Rp and Sp diastereomers, and thiophilic Cd(2+) cannot rescue the activity. The pH-rate profile has a slope of 0.37 between pH 4.2 and 5.2, and the slope was even lower at higher pH. On the basis of these data, a model of metal binding is proposed. Finally, a catalytic beacon sensor that can detect Ho(3+) down to 1.7 nM is constructed.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
| | - Mahsa Vazin
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
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Zhou W, Ding J, Liu J. An Efficient Lanthanide-Dependent DNAzyme Cleaving 2'-5'-Linked RNA. Chembiochem 2016; 17:890-4. [PMID: 26957420 DOI: 10.1002/cbic.201500690] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Indexed: 12/29/2022]
Abstract
RNA can form two types of linkage. In addition to the predominant 3'-5' linkage, 2'-5'-linked RNA is also important in biology, medicine, and prebiotic studies. Here, in vitro selection was used to isolate a DNAzyme that specifically cleaves 2'-5' RNA by using Ce(3+) as the metal cofactor, but leaves the 3'-5' counterpart intact. This Ce5 DNAzyme requires trivalent light lanthanide ions and shows a rate of 0.16 min(-1) in the presence of 10 μm Ce(3+) ; the activity decreases with heavier lanthanide ions. This is the fastest DNAzyme reported for this reaction, and it might enable applications in chemical biology. As a proof-of-concept, using this DNAzyme, the reactions between phosphorothioate-modified RNA and strongly thiophilic metals (Hg(2+) and Tl(3+) ) were studied as a function of pH.
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Affiliation(s)
- Wenhu Zhou
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, China.,Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Jinsong Ding
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, China
| | - Juewen Liu
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, China. .,Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.
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Feng FM, Cai SL, Liu FA. Phosphate Diester Cleavage Promoted by the Metallomicelles of Ce(III) Complexes of Aza-Crown Ether with Different Numbers of Nitrogen Atoms. J DISPER SCI TECHNOL 2016. [DOI: 10.1080/01932691.2015.1024320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Zhou W, Zhang Y, Huang PJJ, Ding J, Liu J. A DNAzyme requiring two different metal ions at two distinct sites. Nucleic Acids Res 2015; 44:354-63. [PMID: 26657636 PMCID: PMC4705669 DOI: 10.1093/nar/gkv1346] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 11/18/2015] [Indexed: 12/21/2022] Open
Abstract
Most previously reported RNA-cleaving DNAzymes require only a single divalent metal ion for catalysis. We recently reported a general trivalent lanthanide-dependent DNAzyme named Ce13d. This work shows that Ce13d requires both Na+ and a trivalent lanthanide (e.g. Ce3+), simultaneously. This discovery is facilitated by the sequence similarity between Ce13d and a recently reported Na+-specific DNAzyme, NaA43. The Ce13d cleavage rate linearly depends on the concentration of both metal ions. Sensitized Tb3+ luminescence and DMS footprinting experiments indicate that the guanines in the enzyme loop are important for Na+-binding. The Na+ dissociation constants of Ce13d measured from the cleavage activity assay, Tb3+ luminescence and DMS footprinting are 24.6, 16.3 and 47 mM, respectively. Mutation studies indicate that the role of Ce3+ might be replaced by G23 in NaA43. Ce3+ functions by stabilizing the transition state phosphorane, thus promoting cleavage. G23 competes favorably with low concentration Ce3+ (below 1 μM). The G23-to-hypoxanthine mutation suggests the N1 position of the guanine as a hydrogen bond donor. Together, Ce13d has two distinct metal binding sites, each fulfilling a different role. DNAzymes can be quite sophisticated in utilizing metal ions for catalysis and molecular recognition, similar to protein metalloenzymes.
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Affiliation(s)
- Wenhu Zhou
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yupei Zhang
- 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
| | - Jinsong Ding
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Juewen Liu
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Hollenstein M. DNA Catalysis: The Chemical Repertoire of DNAzymes. Molecules 2015; 20:20777-804. [PMID: 26610449 PMCID: PMC6332124 DOI: 10.3390/molecules201119730] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 12/24/2022] Open
Abstract
Deoxyribozymes or DNAzymes are single-stranded catalytic DNA molecules that are obtained by combinatorial in vitro selection methods. Initially conceived to function as gene silencing agents, the scope of DNAzymes has rapidly expanded into diverse fields, including biosensing, diagnostics, logic gate operations, and the development of novel synthetic and biological tools. In this review, an overview of all the different chemical reactions catalyzed by DNAzymes is given with an emphasis on RNA cleavage and the use of non-nucleosidic substrates. The use of modified nucleoside triphosphates (dN*TPs) to expand the chemical space to be explored in selection experiments and ultimately to generate DNAzymes with an expanded chemical repertoire is also highlighted.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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40
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Yu L, Li FZ, Xie JQ, Cai S. DNA Cleavage Activity: Comparison of two Lanthanum Complexes Based on Aza-Crown Ethers with Different Numbers of Nitrogen Atoms. PROGRESS IN REACTION KINETICS AND MECHANISM 2015. [DOI: 10.3184/146867815x14420468512656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Based on the unique characteristics of lanthanum ion and aza-crown ethers, the lanthanum complexes of two aza-crown ether (L1: 1,10-Dioxa-4,7,13,16-tetraazacyclo-octadecane and L2: 1,4,10,13-tetraoxa-7,16-diazacyclooctadecane) were designed and synthesised. The interaction between these two complexes and DNA was measured by UV-Vis spectroscopy and gel electrophoresis. Moreover, a series of experiments of cleavage of pUC19 DNA were conducted to illustrate the acidity, time and concentration effects. The results indicated that the two metal complexes can accelerate the breakage of DNA from its supercoiled form (form I) to the nicked form (form II) at near-physiological conditions, and the optimum acidity of DNA catalytic cleavage is pH=6.5 and pH=7.0 for LaL1 and LaL2, respectively. Furthermore, the LaL1 exhibited better cleavage activity than LaL2 under the same conditions, thus supercoiled DNA was thoroughly cleaved to the nicked form under the appropriate conditions. The hydrolytic mechanism was verified by applying several oxygen-scavengers to the DNA catalytic cleavage.
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Affiliation(s)
- Lan Yu
- College of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, P.R. China
| | - Fang-zhen Li
- College of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, P.R. China
| | - Jia-qing Xie
- College of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, P.R. China
| | - Shulan Cai
- College of Chemistry & Pharmaceutical Engineering, Sichuan University of Science & Engineering, Zigong, Sichuan, P.R. China, 643000
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Yu L, Li FZ, Wu JY, Xie JQ, Li S. Development of the aza-crown ether metal complexes as artificial hydrolase. J Inorg Biochem 2015; 154:89-102. [PMID: 26460062 DOI: 10.1016/j.jinorgbio.2015.09.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 09/05/2015] [Accepted: 09/30/2015] [Indexed: 01/13/2023]
Abstract
Hydrolases play a crucial role in the biochemical process, which can catalyze the hydrolysis of various compounds like carboxylic esters, phosphoesters, amides, nucleic acids, peptides, and so on. The design of artificial hydrolases has attracted extensive attention due to their scientific significance and potential applications in the field of gene medicine and molecular biology. Numerous macrocyclic metal complexes have been used as artificial hydrolase in the catalytic hydrolysis of the organic substrate. Aza-crown ether for this comment is a special class of the macrocyclic ligand containing both the nitrogen atoms and oxygen atoms in the ring. The studies showed that the aza-crown complexes exhibited high activity of hydrolytic enzyme. However, the aza-crown ether metal complex as artificial hydrolase is still very limited because of its difficulty in synthesis. This review summarizes the development of the aza-crown ether metal complexes as the artificial hydrolase, including the synthesis and catalysis of the transition metal complexes and lanthanide metal complexes of aza-crown ethers. The purpose of this review is to highlight: (1) the relationship between the structure and hydrolytic activity of synthetic hydrolase; (2) the synergistic effect of metal sites and ligands in the course of organic compound hydrolysis; and (3) the design strategies of the aza-crown ethers as hydrolase.
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Affiliation(s)
- Lan Yu
- College of Chemistry and Chemical Engineering,Chongqing University of Technology, Chongqing 400054, PR China
| | - Fang-zhen Li
- College of Chemistry and Chemical Engineering,Chongqing University of Technology, Chongqing 400054, PR China
| | - Jiao-yi Wu
- College of Chemistry and Molecular Engineering, Peking University, Peking 100871, PR China
| | - Jia-qing Xie
- College of Chemistry and Chemical Engineering,Chongqing University of Technology, Chongqing 400054, PR China
| | - Shuo Li
- College of Chemistry and Chemical Engineering,Chongqing University of Technology, Chongqing 400054, PR China.
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Vazin M, Huang PJJ, Matuszek Ż, Liu J. Biochemical Characterization of a Lanthanide-Dependent DNAzyme with Normal and Phosphorothioate-Modified Substrates. Biochemistry 2015; 54:6132-8. [DOI: 10.1021/acs.biochem.5b00691] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mahsa Vazin
- Department of Chemistry,
Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Po-Jung Jimmy Huang
- Department of Chemistry,
Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Żaneta Matuszek
- Department of Chemistry,
Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Juewen Liu
- Department of Chemistry,
Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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Abstract
Catalysis is a fundamental chemical concept, and many kinds of catalysts have considerable practical value. Developing entirely new catalysts is an exciting challenge. Rational design and screening have provided many new small-molecule catalysts, and directed evolution has been used to optimize or redefine the function of many protein enzymes. However, these approaches have inherent limitations that prompt the pursuit of different kinds of catalysts using other experimental methods. Nature evolved RNA enzymes, or ribozymes, for key catalytic roles that in modern biology are limited to phosphodiester cleavage/ligation and amide bond formation. Artificial DNA enzymes, or deoxyribozymes, have great promise for a broad range of catalytic activities. They can be identified from unbiased (random) sequence populations as long as the appropriate in vitro selection strategies can be implemented for their identification. Notably, in vitro selection is different in key conceptual and practical ways from rational design, screening, and directed evolution. This Account describes the development by in vitro selection of DNA catalysts for many different kinds of covalent modification reactions of peptide and protein substrates, inspired in part by our earlier work with DNA-catalyzed RNA ligation reactions. In one set of studies, we have sought DNA-catalyzed peptide backbone cleavage, with the long-term goal of artificial DNA-based proteases. We originally anticipated that amide hydrolysis should be readily achieved, but in vitro selection instead surprisingly led to deoxyribozymes for DNA phosphodiester hydrolysis; this was unexpected because uncatalyzed amide bond hydrolysis is 10(5)-fold faster. After developing a suitable selection approach that actively avoids DNA hydrolysis, we were able to identify deoxyribozymes for hydrolysis of esters and aromatic amides (anilides). Aliphatic amide cleavage remains an ongoing focus, including via inclusion of chemically modified DNA nucleotides in the catalyst, which we have recently found to enable this cleavage reaction. In numerous other efforts, we have investigated DNA-catalyzed peptide side chain modification reactions. Key successes include nucleopeptide formation (attachment of oligonucleotides to peptide side chains) and phosphatase and kinase activities (removal and attachment of phosphoryl groups to side chains). Through all of these efforts, we have learned the importance of careful selection design, including the frequent need to develop specific "capture" reactions that enable the selection process to provide only those DNA sequences that have the desired catalytic functions. We have established strategies for identifying deoxyribozymes that accept discrete peptide and protein substrates, and we have obtained data to inform the key choice of random region length at the outset of selection experiments. Finally, we have demonstrated the viability of modular deoxyribozymes that include a small-molecule-binding aptamer domain, although the value of such modularity is found to be minimal, with implications for many selection endeavors. Advances such as those summarized in this Account reveal that DNA has considerable catalytic abilities for biochemically relevant reactions, specifically including covalent protein modifications. Moreover, DNA has substantially different, and in many ways better, characteristics than do small molecules or proteins for a catalyst that is obtained "from scratch" without demanding any existing information on catalyst structure or mechanism. Therefore, prospects are very strong for continued development and eventual practical applications of deoxyribozymes for peptide and protein modification.
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Affiliation(s)
- Scott K. Silverman
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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Abstract
Lanthanides represent a group of very important but challenging analytes for biosensor development. These 15 elements are very similar in their chemical properties. So far, limited success has been realized using the rational ligand design approach. My laboratory has successfully accomplished the task of carrying out combinatorial selection to isolate lanthanide-dependent RNA-cleaving DNAzymes. We report two new DNAzymes, each discovered in a different selection condition and both are highly specific to lanthanides. When both DNAzymes are used together, it is possible to identify the last few heavy lanthanides. Upon introducing a phosphorothioate modification, one of the abovementioned DNAzymes becomes highly active with many toxic heavy metals. With the selection of more DNAzymes with different activity patterns cross the lanthanide series, a sensor array might be produced for identifying each ion. This article is a minireview of the current developments on this topic and some of the historical aspects. It reflects the main content of the Fred Beamish Award presentation delivered at the 2014 Canadian Society for Chemistry Conference in Vancouver. Future directions in this area are also discussed.
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Affiliation(s)
- Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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45
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Huang PJJ, Vazin M, Matuszek Ż, Liu J. A new heavy lanthanide-dependent DNAzyme displaying strong metal cooperativity and unrescuable phosphorothioate effect. Nucleic Acids Res 2014; 43:461-9. [PMID: 25488814 PMCID: PMC4288186 DOI: 10.1093/nar/gku1296] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In vitro selection of RNA-cleaving DNAzymes was performed using three heavy lanthanide ions (Ln3+): Ho3+, Er3+ and Tm3+. The resulting sequences were aligned together and about half of the library contained a new family of DNAzyme. These DNAzymes have a simple loop structure, and they are active only with the seven heavy Ln3+. Among the tested non-lanthanide ions, only Y3+ induced cleavage and even Pb2+ failed to cleave, suggesting a very high specificity. A representative DNAzyme, Tm7, has a sigmoidal metal binding curve with a Hill coefficient of 3, indicating that three metal ions are involved in the catalytic step. Its pH-rate profile has a slope of 1, suggesting a single deprotonation step is involved in the rate-limiting step. Tm7 has a cleavage rate of 1.6 min−1 at pH 7.8 with 10 μM Er3+. Phosphorothioate substitution at the cleavage junction completely inhibits the activity, which cannot be rescued by Cd2+ alone, or by a mixture of Er3+ and Cd2+, suggesting that two interacting metal ions are involved in direct bonding to both non-bridging oxygen atoms. A new model involving three lanthanide ions is proposed based on this study. A biosensor is engineered using Tm7 to detect Dy3+ down to 14 nM.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Ontario, Canada N2L 3G1
| | - Mahsa Vazin
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Ontario, Canada N2L 3G1
| | - Żaneta Matuszek
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Ontario, Canada N2L 3G1
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Ontario, Canada N2L 3G1
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46
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Huang PJJ, Vazin M, Liu J. In vitro selection of a new lanthanide-dependent DNAzyme for ratiometric sensing lanthanides. Anal Chem 2014; 86:9993-9. [PMID: 25199650 DOI: 10.1021/ac5029962] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Developing biosensors for lanthanides is an important but challenging analytical task. To address this problem, in vitro selection of RNA-cleaving DNAzymes was carried out using a library containing a region of 35 random nucleotides in the presence of Lu(3+), since Lu(3+) was reported to be the most efficient lanthanide for RNA cleavage. The resulting DNA sequences can be aligned to a single family with two conserved stretches of nucleotides. One of the representative DNAzymes (named Lu12) was further studied. Lu12 is more active with smaller lanthanides and has the lowest activity in the presence of the largest lanthanide (lutetium). Its cleavage rate is 0.12 min(-1) in the presence of 10 μM Nd(3+) at pH 6.0. This is a new DNAzyme, and a catalytic beacon sensor is designed by attaching a fluorophore/quencher pair, detecting Nd(3+) down to 0.4 nM (72 parts-per-trillion). This DNAzyme is highly selective for lanthanides as well, showing cleavage only with two nonlanthanide ions: Y(3+) and Pb(2+). We previously reported a DNAzyme named Ce13d, which has similar responses to all the trivalent lanthanides. Combining these two allows for a ratiometric assay that identifies a few large lanthanides.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Ave West, Waterloo, Ontario Canada , N2L 3G1
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Lin WTD, Huang PJJ, Pautler R, Liu J. The group trend of lanthanides binding to DNA and DNAzymes with a complex but symmetric pattern. Chem Commun (Camb) 2014; 50:11859-62. [DOI: 10.1039/c4cc05551a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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48
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Wang M, Zhang H, Zhang W, Zhao Y, Yasmeen A, Zhou L, Yu X, Tang Z. In vitro selection of DNA-cleaving deoxyribozyme with site-specific thymidine excision activity. Nucleic Acids Res 2014; 42:9262-9. [PMID: 25030901 PMCID: PMC4132718 DOI: 10.1093/nar/gku592] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Single-nucleotide polymorphisms, either inherited or due to spontaneous DNA damage, are associated with numerous diseases. Developing tools for site-specific nucleotide modification may one day provide a way to alter disease polymorphisms. Here, we describe the in vitro selection and characterization of a new deoxyribozyme called F-8, which catalyzes nucleotide excision specifically at thymidine. Cleavage by F-8 generates 3'- and 5'-phosphate ends recognized by DNA modifying enzymes, which repair the targeted deoxyribonucleotide while maintaining the integrity of the rest of the sequence. These results illustrate the potential of DNAzymes as tools for DNA manipulation.
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Affiliation(s)
- Mingqi Wang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China Department of Chemistry, Key Laboratory of Green Chemistry and Technology (Ministry of Education), Sichuan University, Chengdu 610064, P.R. China
| | - Huafan Zhang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Wei Zhang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Yongyun Zhao
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Afshan Yasmeen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Li Zhou
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Xiaoqi Yu
- Department of Chemistry, Key Laboratory of Green Chemistry and Technology (Ministry of Education), Sichuan University, Chengdu 610064, P.R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
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49
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Urata S, Miyahata T, Matsuura H, Kitamura Y, Ihara T. Alteration of DNAzyme Activity by Silver Ion. CHEM LETT 2014. [DOI: 10.1246/cl.140197] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shoma Urata
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
| | - Takaaki Miyahata
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
| | - Hirotaka Matsuura
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
| | - Yusuke Kitamura
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
- CREST, Japan Science and Technology Agency
| | - Toshihiro Ihara
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
- CREST, Japan Science and Technology Agency
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50
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Wang F, Liu J. Platinated DNA oligonucleotides: new probes forming ultrastable conjugates with graphene oxide. NANOSCALE 2014; 6:7079-7084. [PMID: 24844813 DOI: 10.1039/c4nr00867g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Metal containing polymers have expanded the property of polymers by involving covalently associated metal complexes. DNA is a special block copolymer. While metal ions are known to influence DNA, little is explored on its polymer property when strong metal complexes are associated. In this work, we study cisplatin modified DNA as a new polymer and probe. Out of the complexes formed between cisplatin-A15, HAuCl4-A15, Hg(2+)-T15 and Ag(+)-C15, only the cisplatin adduct is stable under the denaturing gel electrophoresis condition. Each Pt-nucleobase bond gives a positive charge and thus makes DNA a zwitterionic polymer. This allows ultrafast adsorption of DNA by graphene oxide (GO) and the adsorbed complex is highly stable. Non-specific DNA, protein, surfactants and thiolated compounds cannot displace platinated DNA from GO, while non-modified DNA is easily displaced in most cases. The stable GO/DNA conjugate is further tested for surface hybridization. This is the first demonstration of using metallated DNA as a polymeric material for interfacing with nanoscale materials.
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Affiliation(s)
- Feng Wang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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