51
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Ekesan Ş, York DM. Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution. Nucleic Acids Res 2019; 47:10282-10295. [PMID: 31511899 PMCID: PMC6821293 DOI: 10.1093/nar/gkz773] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/20/2019] [Accepted: 09/03/2019] [Indexed: 02/01/2023] Open
Abstract
We perform molecular dynamics simulations, based on recent crystallographic data, on the 8-17 DNAzyme at four states along the reaction pathway to determine the dynamical ensemble for the active state and transition state mimic in solution. A striking finding is the diverse roles played by Na+ and Pb2+ ions in the electrostatically strained active site that impact all four fundamental catalytic strategies, and share commonality with some features recently inferred for naturally occurring hammerhead and pistol ribozymes. The active site Pb2+ ion helps to stabilize in-line nucleophilic attack, provides direct electrostatic transition state stabilization, and facilitates leaving group departure. A conserved guanine residue is positioned to act as the general base, and is assisted by a bridging Na+ ion that tunes the pKa and facilitates in-line fitness. The present work provides insight into how DNA molecules are able to solve the RNA-cleavage problem, and establishes functional relationships between the mechanism of these engineered DNA enzymes with their naturally evolved RNA counterparts. This adds valuable information to our growing body of knowledge on general mechanisms of phosphoryl transfer reactions catalyzed by RNA, proteins and DNA.
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Affiliation(s)
- Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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52
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Hwang K, Mou Q, Lake RJ, Xiong M, Holland B, Lu Y. Metal-Dependent DNAzymes for the Quantitative Detection of Metal Ions in Living Cells: Recent Progress, Current Challenges, and Latest Results on FRET Ratiometric Sensors. Inorg Chem 2019; 58:13696-13708. [PMID: 31364355 PMCID: PMC7176321 DOI: 10.1021/acs.inorgchem.9b01280] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Many different metal ions are involved in various biological functions including metallomics and trafficking, and yet there are currently effective sensors for only a few metal ions, despite the first report of metal sensors for calcium more than 40 years ago. To expand upon the number of metal ions that can be probed in biological systems, we and other laboratories employ the in vitro selection method to obtain metal-specific DNAzymes with high specificity for a metal ion and then convert these DNAzymes into fluorescent sensors for these metal ions using a catalytic beacon approach. In this Forum Article, we summarize recent progress made in developing these DNAzyme sensors to probe metal ions in living cells and in vivo, including several challenges that we were able to overcome for this application, such as DNAzyme delivery, spatiotemporal control, and signal amplification. Furthermore, we have identified a key remaining challenge for the quantitative detection of metal ions in living cells and present a new design and the results of a Förster resonance energy transfer (FRET)-based DNAzyme sensor for the ratiometric quantification of Zn2+ in HeLa cells. By converting existing DNAzyme sensors into a ratiometric readout without compromising the fundamental catalytic function of the DNAzymes, this FRET-based ratiometric DNAzyme design can readily be applied to other DNAzyme sensors as a major advance in the field to develop much more quantitative metal-ion probes for biological systems.
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Affiliation(s)
- Kevin Hwang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Quanbing Mou
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Ryan J. Lake
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Mengyi Xiong
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Brandalynn Holland
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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53
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Verdonck L, Buyst D, de Vries AM, Gheerardijn V, Madder A, Martins JC. Tethered imidazole mediated duplex stabilization and its potential for aptamer stabilization. Nucleic Acids Res 2019; 46:11671-11686. [PMID: 30418582 PMCID: PMC6294506 DOI: 10.1093/nar/gky1062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/01/2018] [Indexed: 12/15/2022] Open
Abstract
Previous investigations of the impact of an imidazole-tethered thymidine in synthetic DNA duplexes, monitored using UV and NMR spectroscopy, revealed a base context dependent increase in thermal stability of these duplexes and a striking correlation with the imidazolium pKa. Unrestrained molecular dynamics (MD) simulations demonstrated the existence of a hydrogen bond between the imidazolium and the Hoogsteen side of a nearby guanosine which, together with electrostatic interactions, form the basis of the so-called pKa-motif responsible for these duplex-stabilizing and pKa-modulating properties. Here, the robustness and utility of this pKa-motif was explored by introducing multiple imidazole-tethered thymidines at different positions on the same dsDNA duplex. For all constructs, sequence based expectations as to pKa-motif formation were supported by MD simulations and experimentally validated using NOESY. Based on the analysis of the pKa values and melting temperatures, guidelines are formulated to assist in the rational design of oligonucleotides modified with imidazolium-tethered thymidines for increased thermal stability that should be generally applicable, as demonstrated through a triply modified construct. In addition, a proof-of-principle study demonstrating enhanced stability of the l-argininamide binding aptamer modified with an imidazole-tethered thymidine in the presence and absence of ligand, demonstrates its potential for the design of more stable aptamers.
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Affiliation(s)
- Lars Verdonck
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium.,Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Dieter Buyst
- Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium.,NMR Expertise Centre, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Anne-Mare de Vries
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium.,Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Vicky Gheerardijn
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - José C Martins
- Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
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54
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A Novel Small RNA-Cleaving Deoxyribozyme with a Short Binding Arm. Sci Rep 2019; 9:8224. [PMID: 31160698 PMCID: PMC6546695 DOI: 10.1038/s41598-019-44750-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/17/2019] [Indexed: 01/12/2023] Open
Abstract
Deoxyribozymes capable of catalyzing sequence-specific RNA cleavage have found broad applications in biotechnology, DNA computing and environmental sensing. Among these, deoxyribozyme 8–17 is the most common small DNA motif capable of catalyzing RNA cleavage. However, the extent to which other DNA molecules with similar catalytic motifs exist remains elusive. Here we report a novel RNA-cleaving deoxyribozyme called 10–12opt that functions with an equally small catalytic motif and an unusually short binding arm. This deoxyribozyme contains a 14-nucleotide catalytic core that preferentially catalyzes RNA cleavage at UN dinucleotide junctions (kobs = 0.9 h−1 for UU cleavage). Surprisingly, the left binding arm contains only three nucleotides and forms two canonical base pairs with the RNA substrate. Mutational analysis reveals that a riboguanosine residue 3-nucleotide downstream of cleavage site must not form canonical base pairing for the optimal catalysis, and this nucleobase likely participates in catalysis with its carbonyl O6 atom. Furthermore, we demonstrate that deoxyribozyme 10–12opt can be utilized to cleave certain microRNA sequences which are not preferentially cleaved by 8–17. Together, these results suggest that this novel RNA-cleaving deoxyribozyme forms a distinct catalytic structure than 8–17 and that sequence space may contain additional examples of DNA molecules that can cleave RNA at site-specific locations.
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55
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Zhang Z, Liu J. Molecular Imprinting with Functional DNA. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805246. [PMID: 30761744 DOI: 10.1002/smll.201805246] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/01/2019] [Indexed: 06/09/2023]
Abstract
Molecular imprinting refers to templated polymerization with rationally designed monomers, and this is a general method to prepare stable and cost-effective ligands. This attractive concept however suffers from low affinity, low specificity, and limited signaling mechanisms for binding. Acrydite-modified DNA oligonucleotides can be readily copolymerized into acrylic polymers. With molecular recognition and catalytic functions, such functional DNAs are recently shown to enhance the performance of molecularly imprinted polymers (MIPs) in a few ways. First, DNA aptamers are used as macromonomers to enhance binding affinity and specificity of MIPs. Second, DNA can help produce optical signals to follow binding events. Third, imprinting can also improve the performance of catalytic DNA by enhancing its activity and specificity toward the template substrate. Finally, MIP is shown to help aptamer selection. Bulk imprinting, nanoparticle imprinting, and surface imprinting are all demonstrated with DNA. Since both DNA and synthetic polymers are cost effective and stable, their hybrid materials still possess such properties while enhancing the function of each component. This review covers recent developments on the abovementioned aspects of DNA-containing MIPs, a field just emerged in the last five years, and future research directions are discussed toward the end.
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Affiliation(s)
- Zijie 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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56
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Gu L, Yan W, Wu H, Fan S, Ren W, Wang S, Lyu M, Liu J. Selection of DNAzymes for Sensing Aquatic Bacteria: Vibrio Anguillarum. Anal Chem 2019; 91:7887-7893. [DOI: 10.1021/acs.analchem.9b01707] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | | | | | - Wei Ren
- Key Laboratory of Marine Biology, Nanjing Agricultural University, Nanjing, Jiangsu 210000, P. R. China
| | | | | | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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57
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Peeters B, Daems D, Van der Donck T, Delport F, Lammertyn J. Real-Time FO-SPR Monitoring of Solid-Phase DNAzyme Cleavage Activity for Cutting-Edge Biosensing. ACS APPLIED MATERIALS & INTERFACES 2019; 11:6759-6768. [PMID: 30682241 DOI: 10.1021/acsami.8b18756] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA nanotechnology has a great potential in biosensor design including nanostructuring of the biosensor surface through DNA origami, target recognition by means of aptamers, and DNA-based signal amplification strategies. In this paper, we use DNA nanotechnology to describe for the first time the concept of real-time solid-phase monitoring of DNAzyme cleavage activity for the detection of specific single-stranded DNA (ssDNA) with a fiber optic surface plasmon resonance (FO-SPR) biosensor. Hereto, we first developed a robust ligation strategy for the functionalization of the FO-SPR biosensing surface with ssDNA-tethered gold nanoparticles, serving as the substrate for the DNAzyme. Next, we established a relation between the SPR signal change, due to the cleavage activity of the 10-23 DNAzyme, and the concentration of the DNAzyme, showing faster cleavage kinetics for higher DNAzyme concentrations. Finally, we implemented this generic concept for biosensing of ssDNA target in solution. Hereto, we designed a DNAzyme-inhibitor complex, consisting of an internal loop structure complementary to the ssDNA target, that releases active DNAzyme molecules in a controlled way as a function of the target concentration. We demonstrated reproducible target detection with a theoretical limit of detection of 1.4 nM, proving that the presented ligation strategy is key to a universal DNAzyme-based FO-SPR biosensing concept with promising applications in the medical and agrofood sector.
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Affiliation(s)
- Bernd Peeters
- Department of Biosystems, Biosensors Group , KU Leuven , Willem de Croylaan 42 , B-3001 Leuven , Belgium
| | - Devin Daems
- Department of Biosystems, Biosensors Group , KU Leuven , Willem de Croylaan 42 , B-3001 Leuven , Belgium
| | - Tom Van der Donck
- Department of Materials Engineering , KU Leuven , Kasteelpark Arenberg 44 , B-3001 Leuven , Belgium
| | - Filip Delport
- FOx Biosystems NV , Veldstraat 120 , B-9140 Temse , Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group , KU Leuven , Willem de Croylaan 42 , B-3001 Leuven , Belgium
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58
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Khachigian LM. Deoxyribozymes as Catalytic Nanotherapeutic Agents. Cancer Res 2019; 79:879-888. [DOI: 10.1158/0008-5472.can-18-2474] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/24/2018] [Accepted: 12/14/2018] [Indexed: 11/16/2022]
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59
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Lichtor PA, Chen Z, Elowe NH, Chen JC, Liu DR. Side chain determinants of biopolymer function during selection and replication. Nat Chem Biol 2019; 15:419-426. [PMID: 30742124 PMCID: PMC6430648 DOI: 10.1038/s41589-019-0229-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/12/2019] [Indexed: 12/21/2022]
Abstract
The chemical functionalities within biopolymers determine their physical properties and biological activities. The relationship between the side-chains available to a biopolymer population and the potential functions of the resulting polymers, however, has proven difficult to study experimentally. Using seven sets of chemically diverse charged, polar, and nonpolar side-chains, we performed cycles of artificial translation, in vitro selections for binding to either PCSK9 or IL-6 protein, and replication on libraries of random side-chain-functionalized nucleic acid polymers. Polymer sequence convergence, bulk population target binding, affinity of individual polymers, and head-to-head competition among post-selection libraries collectively indicate that polymer libraries with nonpolar side-chains outperformed libraries lacking these side-chains. The presence of nonpolar groups, resembling functionality present in proteins but missing from natural nucleic acids, thus may be strong determinants of binding activity. This factor may contribute to the apparent evolutionary advantage of proteins over their nucleic acid precursors for some molecular recognition tasks.
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Affiliation(s)
- Phillip A Lichtor
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Zhen Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Nadine H Elowe
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jonathan C Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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60
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Steinmetzger C, Palanisamy N, Gore KR, Höbartner C. A Multicolor Large Stokes Shift Fluorogen-Activating RNA Aptamer with Cationic Chromophores. Chemistry 2019; 25:1931-1935. [PMID: 30485561 DOI: 10.1002/chem.201805882] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Indexed: 12/31/2022]
Abstract
Large Stokes shift (LSS) fluorescent proteins (FPs) exploit excited state proton transfer pathways to enable fluorescence emission from the phenolate intermediate of their internal 4-hydroxybenzylidene imidazolone (HBI) chromophore. An RNA aptamer named Chili mimics LSS FPs by inducing highly Stokes-shifted emission from several new green and red HBI analogues that are non-fluorescent when free in solution. The ligands are bound by the RNA in their protonated phenol form and feature a cationic aromatic side chain for increased RNA affinity and reduced magnesium dependence. In combination with oxidative functionalization at the C2 position of the imidazolone, this strategy yielded DMHBO+ , which binds to the Chili aptamer with a low-nanomolar KD . Because of its highly red-shifted fluorescence emission at 592 nm, the Chili-DMHBO+ complex is an ideal fluorescence donor for Förster resonance energy transfer (FRET) to the rhodamine dye Atto 590 and will therefore find applications in FRET-based analytical RNA systems.
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Affiliation(s)
- Christian Steinmetzger
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Navaneethan Palanisamy
- International Max Planck Research School Molecular Biology, University of Göttingen, Germany.,Present address: BIOSS Center for Biological Signaling Studies, University of Freiburg, Germany
| | - Kiran R Gore
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany.,Present address: Department of Chemistry, University of Mumbai, India
| | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.,International Max Planck Research School Molecular Biology, University of Göttingen, Germany.,Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
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61
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Damase TR, Allen PB. Designed and Evolved Nucleic Acid Nanotechnology: Contrast and Complementarity. Bioconjug Chem 2019; 30:2-12. [PMID: 30561987 DOI: 10.1021/acs.bioconjchem.8b00810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this review, we explore progress on DNA aptamers (evolved DNA), DNA circuits (designed DNA), and the newest projects that integrate both. Designed DNA nanotechnology includes static nanostructures, dynamic nanodevices, and reaction networks (sometimes called DNA circuits). DNA circuits are dynamic DNA reactions that perform computations and sequence-specific amplification. Directed evolution can be used to produce DNA that can recognize specific targets. Aptamers are evolved nucleic acids; they are produced artificially with an in vitro selection process. DNA aptamers are molecular recognition elements made of single-stranded DNA (ssDNA) with the potential to interact with proteins, small molecules, viruses, and even cells. Designed molecular structures can incorporate aptamers for applications with immediate practical impact.
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Affiliation(s)
- Tulsi Ram Damase
- Department of Chemistry , University of Idaho , 001 Renfrew Hall, 875 Perimeter Drive , Moscow , Idaho 83844-2343 , United States
| | - Peter B Allen
- Department of Chemistry , University of Idaho , 001 Renfrew Hall, 875 Perimeter Drive , Moscow , Idaho 83844-2343 , United States
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62
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Dayeh DM, Cantara WA, Kitzrow JP, Musier-Forsyth K, Nakanishi K. Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA. Nucleic Acids Res 2018; 46:e98. [PMID: 29897478 PMCID: PMC6144825 DOI: 10.1093/nar/gky496] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/20/2018] [Accepted: 05/22/2018] [Indexed: 12/26/2022] Open
Abstract
The recent identification and development of RNA-guided enzymes for programmable cleavage of target nucleic acids offers exciting possibilities for both therapeutic and biotechnological applications. However, critical challenges such as expensive guide RNAs and inability to predict the efficiency of target recognition, especially for highly-structured RNAs, remain to be addressed. Here, we introduce a programmable RNA restriction enzyme, based on a budding yeast Argonaute (AGO), programmed with cost-effective 23-nucleotide (nt) single-stranded DNAs as guides. DNA guides offer the advantage that diverse sequences can be easily designed and purchased, enabling high-throughput screening to identify optimal recognition sites in the target RNA. Using this DNA-induced slicing complex (DISC) programmed with 11 different guide DNAs designed to span the sequence, sites of cleavage were identified in the 352-nt human immunodeficiency virus type 1 5'-untranslated region. This assay, coupled with primer extension and capillary electrophoresis, allows detection and relative quantification of all DISC-cleavage sites simultaneously in a single reaction. Comparison between DISC cleavage and RNase H cleavage reveals that DISC not only cleaves solvent-exposed sites, but also sites that become more accessible upon DISC binding. This study demonstrates the advantages of the DISC system for programmable cleavage of highly-structured, functional RNAs.
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Affiliation(s)
- Daniel M Dayeh
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - William A Cantara
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
| | - Jonathan P Kitzrow
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
| | - Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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63
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Xu Q, Zhang Y, Xiang D, Li CC, Zhang CY. A universal DNAzyme-based bioluminescent sensor for label-free detection of biomolecules. Anal Chim Acta 2018; 1043:81-88. [PMID: 30392672 DOI: 10.1016/j.aca.2018.08.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/27/2018] [Accepted: 08/30/2018] [Indexed: 12/28/2022]
Abstract
We demonstrate for the first time the development of a universal DNAzyme-based bioluminescent sensor for label-free detection of various biomolecules including DNAzyme and DNA. The presence of DNAzyme may induce the cyclic cleavage of riboadenosine (rA)-containing substrates, and the subsequent digestion of the cleaved substrates by exonuclease III (Exo III) releases abundant AMPs to initiate cyclic AMP pyrophosphorylation-ATP depyrophosphorylation for the generation of an enhanced bioluminescence signal. This sensor can real-time monitor the DNAzyme activity with a detection limit of 3.16 × 10-12 M. Moreover, the DNAzyme may be divided into two subunits for sensitive detection of target DNA. In the presence of target DNA, the two separated subunits may assemble into an active DNAzyme which can catalyze the cyclic cleavage of substrates and initiate the digestion of cleaved substrates by Exo III for the generation of an enhanced bioluminescence signal. This sensor can sensitively detect target DNA with a detection limit of 3.31 × 10-12 M. Importantly, this bioluminescent sensor can achieve a zero-background signal, and its output signal originates from the release of AMP for the generation of self-illuminating light emission without the requirement of either the external labels or the reporting reagents.
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Affiliation(s)
- Qinfeng Xu
- College of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Dongxue Xiang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Chen-Chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China.
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64
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Potaczek DP, Unger SD, Zhang N, Taka S, Michel S, Akdağ N, Lan F, Helfer M, Hudemann C, Eickmann M, Skevaki C, Megremis S, Sadewasser A, Alashkar Alhamwe B, Alhamdan F, Akdis M, Edwards MR, Johnston SL, Akdis CA, Becker S, Bachert C, Papadopoulos NG, Garn H, Renz H. Development and characterization of DNAzyme candidates demonstrating significant efficiency against human rhinoviruses. J Allergy Clin Immunol 2018; 143:1403-1415. [PMID: 30114391 DOI: 10.1016/j.jaci.2018.07.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 07/16/2018] [Accepted: 07/20/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Infections with human rhinoviruses (RVs) are responsible for millions of common cold episodes and the majority of asthma exacerbations, especially in childhood. No drugs specifically targeting RVs are available. OBJECTIVE We sought to identify specific anti-RV molecules based on DNAzyme technology as candidates to a clinical study. METHODS A total of 226 candidate DNAzymes were designed against 2 regions of RV RNA genome identified to be sufficiently highly conserved between virus strains (ie, the 5'-untranslated region and cis-acting replication element) by using 3 test strains: RVA1, RVA16, and RVA29. All DNAzymes were screened for their cleavage efficiency against in vitro-expressed viral RNA. Those showing any catalytic activity were subjected to bioinformatic analysis of their reverse complementarity to 322 published RV genomic sequences. Further molecular optimization was conducted for the most promising candidates. Cytotoxic and off-target effects were excluded in HEK293 cell-based systems. Antiviral efficiency was analyzed in infected human bronchial BEAS-2B cells and ex vivo-cultured human sinonasal tissue. RESULTS Screening phase-generated DNAzymes characterized by either good catalytic activity or by high RV strain coverage but no single molecule represented a satisfactory combination of those 2 features. Modifications in length of the binding domains of 2 lead candidates, Dua-01(-L12R9) and Dua-02(-L10R11), improved their cleavage efficiency to an excellent level, with no loss in eminent strain coverage (about 98%). Both DNAzymes showed highly favorable cytotoxic/off-target profiles. Subsequent testing of Dua-01-L12R9 in BEAS-2B cells and sinonasal tissue demonstrated its significant antiviral efficiency. CONCLUSIONS Effective and specific management of RV infections with Dua-01-L12R9 might be useful in preventing asthma exacerbations, which should be verified by clinical trials.
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Affiliation(s)
- Daniel P Potaczek
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), and the inVIVO Planetary Health, Group of the Worldwide Universities Network (WUN), Marburg, Germany; PreDicta Consortium; John Paul II Hospital, Krakow, Poland
| | - Sebastian D Unger
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), and the inVIVO Planetary Health, Group of the Worldwide Universities Network (WUN), Marburg, Germany; PreDicta Consortium
| | - Nan Zhang
- PreDicta Consortium; Upper Airway Research Laboratory, Department of Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium
| | - Styliani Taka
- PreDicta Consortium; Allergy and Clinical Immunology Unit, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | - Sven Michel
- Secarna Pharmaceuticals GmbH, Planegg, Germany
| | - Nesibe Akdağ
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), and the inVIVO Planetary Health, Group of the Worldwide Universities Network (WUN), Marburg, Germany; PreDicta Consortium
| | - Feng Lan
- PreDicta Consortium; Upper Airway Research Laboratory, Department of Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium
| | | | - Christoph Hudemann
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), and the inVIVO Planetary Health, Group of the Worldwide Universities Network (WUN), Marburg, Germany; PreDicta Consortium
| | - Markus Eickmann
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Chrysanthi Skevaki
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), and the inVIVO Planetary Health, Group of the Worldwide Universities Network (WUN), Marburg, Germany; PreDicta Consortium
| | - Spyridon Megremis
- PreDicta Consortium; Division of Infection, Inflammation and Respiratory Medicine, University of Manchester, London, United Kingdom
| | | | - Bilal Alashkar Alhamwe
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), and the inVIVO Planetary Health, Group of the Worldwide Universities Network (WUN), Marburg, Germany; PreDicta Consortium
| | - Fahd Alhamdan
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), and the inVIVO Planetary Health, Group of the Worldwide Universities Network (WUN), Marburg, Germany; PreDicta Consortium
| | - Mübeccel Akdis
- PreDicta Consortium; Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland; Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Michael R Edwards
- PreDicta Consortium; Airway Disease Infection Section, National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom; Medical Research Council (MRC) and Asthma UK Centre in Allergic Mechanisms of Asthma, London, United Kingdom
| | - Sebastian L Johnston
- PreDicta Consortium; Airway Disease Infection Section, National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom; Medical Research Council (MRC) and Asthma UK Centre in Allergic Mechanisms of Asthma, London, United Kingdom
| | - Cezmi A Akdis
- PreDicta Consortium; Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland; Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Stephan Becker
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Claus Bachert
- PreDicta Consortium; Upper Airway Research Laboratory, Department of Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium
| | - Nikolaos G Papadopoulos
- PreDicta Consortium; Allergy and Clinical Immunology Unit, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece; Division of Infection, Inflammation and Respiratory Medicine, University of Manchester, London, United Kingdom
| | - Holger Garn
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), and the inVIVO Planetary Health, Group of the Worldwide Universities Network (WUN), Marburg, Germany; PreDicta Consortium
| | - Harald Renz
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), and the inVIVO Planetary Health, Group of the Worldwide Universities Network (WUN), Marburg, Germany; PreDicta Consortium.
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Manochehry S, McConnell EM, Tram KQ, Macri J, Li Y. Colorimetric Detection of Uranyl Using a Litmus Test. Front Chem 2018; 6:332. [PMID: 30140672 PMCID: PMC6095041 DOI: 10.3389/fchem.2018.00332] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/16/2018] [Indexed: 01/10/2023] Open
Abstract
Ingestion of water containing toxic contaminants above levels deemed safe for human consumption can occur unknowingly since numerous common contaminants in drinking water are colorless and odorless. Uranyl is particularly problematic as it has been found at dangerous levels in sources of drinking water. Detection of this heavy metal-ion species in drinking water currently requires sending a sample to a laboratory where trained personnel use equipment to perform the analysis and turn-around times can be long. A pH-responsive colorimetric biosensor was developed to enable detection of uranyl in water which coupled the uranyl-specific 39E DNAzyme as a recognition element, and an enzyme capable of producing a pH change as the reporter element. The rapid colorimetric assay presented herein can detect uranyl in lake and well water at concentrations relevant for environmental monitoring, as demonstrated by the detection of uranyl at levels below the limits set for drinking water by major regulatory agencies including the World Health Organization (30 μg/L). This simple and inexpensive DNAzyme-based assay enabled equipment-free visual detection of 15 μg/L uranyl, using both solution-based and paper-based pH-dependent visualization strategies.
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Affiliation(s)
- Sepehr Manochehry
- Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamilton, ON, Canada
| | - Erin M. McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamilton, ON, Canada
| | - Kha Q. Tram
- Department of Chemistry and Chemical Biology, McMaster UniversityHamilton, ON, Canada
| | - Joseph Macri
- Department of Pathology and Molecular Medicine, McMaster UniversityHamilton, ON, Canada
- Hamilton Regional Laboratory Medicine ProgramHamilton, ON, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamilton, ON, Canada
- Department of Chemistry and Chemical Biology, McMaster UniversityHamilton, ON, Canada
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66
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Hartmann AK, Cairns-Gibson DF, Santiana JJ, Tolentino MQ, Barber HM, Rouge JL. Enzymatically Ligated DNA-Surfactants: Unmasking Hydrophobically Modified DNA for Intracellular Gene Regulation. Chembiochem 2018; 19:1734-1739. [PMID: 29862626 DOI: 10.1002/cbic.201800302] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Indexed: 01/07/2023]
Abstract
Herein, we describe the characterization of a novel self-assembling and intracellular disassembling nanomaterial for nucleic acid delivery and targeted gene knockdown. By using a recently developed nucleic acid nanocapsule (NAN) formed from surfactants and conjugated DNAzyme (DNz) ligands, it is shown that DNz-NAN can enable cellular uptake of the DNAzyme and result in 60 % knockdown of a target gene without the use of transfection agents. The DNAzyme also exhibits activity without chemical modification, which we attribute to the underlying nanocapsule design and release of hydrophobically modified nucleic acids as a result of enzymatically triggered disassembly of the NAN. Fluorescence-based experiments indicate that the surfactant-conjugated DNAzymes are better able to access a fluorescent mRNA target within a mock lipid bilayer system than the free DNAzyme, highlighting the advantage of the hydrophobic surfactant modification to the nucleic acid ligands. In vitro characterization of DNz-NAN's substrate-cleavage kinetics, stability in biological serum, and persistence of knockdown against a proinflammatory transcription factor, GATA-3, are presented.
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Affiliation(s)
- Alyssa K Hartmann
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
| | | | - Joshua J Santiana
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
| | - Mark Q Tolentino
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
| | - Halle M Barber
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
| | - Jessica L Rouge
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
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67
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Grzechnik P, Szczepaniak SA, Dhir S, Pastucha A, Parslow H, Matuszek Z, Mischo HE, Kufel J, Proudfoot NJ. Nuclear fate of yeast snoRNA is determined by co-transcriptional Rnt1 cleavage. Nat Commun 2018; 9:1783. [PMID: 29725044 PMCID: PMC5934358 DOI: 10.1038/s41467-018-04094-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/04/2018] [Indexed: 01/30/2023] Open
Abstract
Small nucleolar RNA (snoRNA) are conserved and essential non-coding RNA that are transcribed by RNA Polymerase II (Pol II). Two snoRNA classes, formerly distinguished by their structure and ribonucleoprotein composition, act as guide RNA to target RNA such as ribosomal RNA, and thereby introduce specific modifications. We have studied the 5'end processing of individually transcribed snoRNA in S. cerevisiae to define their role in snoRNA biogenesis and functionality. Here we show that pre-snoRNA processing by the endonuclease Rnt1 occurs co-transcriptionally with removal of the m7G cap facilitating the formation of box C/D snoRNA. Failure of this process causes aberrant 3'end processing and mislocalization of snoRNA to the cytoplasm. Consequently, Rnt1-dependent 5'end processing of box C/D snoRNA is critical for snoRNA-dependent methylation of ribosomal RNA. Our results reveal that the 5'end processing of box C/D snoRNA defines their distinct pathway of maturation.
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Affiliation(s)
- Pawel Grzechnik
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Sylwia A Szczepaniak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089, Warsaw, Poland
| | - Somdutta Dhir
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Anna Pastucha
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Hannah Parslow
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Zaneta Matuszek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Hannah E Mischo
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Nicholas J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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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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69
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Cepeda-Plaza M, McGhee CE, Lu Y. Evidence of a General Acid-Base Catalysis Mechanism in the 8-17 DNAzyme. Biochemistry 2018; 57:1517-1522. [PMID: 29389111 PMCID: PMC5879137 DOI: 10.1021/acs.biochem.7b01096] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
DNAzymes are catalytic DNA molecules that can perform a variety of reactions. Although advances have been made in obtaining DNAzymes via in vitro selection and many of them have been developed into sensors and imaging agents for metal ions, bacteria, and other molecules, the structural features responsible for these enzymatic reactions are still not well understood. Previous studies of the 8-17 DNAzyme have suggested conserved guanines close to the phosphodiester transfer site may play a role in the catalytic reaction. To identify the specific guanine and functional group of the guanine responsible for the reaction, we herein report the effects of replacing G1.1 and G14 (G; p Ka,N1 = 9.4) with analogues with a different p Ka at the N1 position, such as inosine (G14I; p Ka,N1 = 8.7), 2,6-diaminopurine (G14diAP; p Ka,N1 = 5.6), and 2-aminopurine (G14AP; p Ka,N1 = 3.8) on pH-dependent reaction rates. A comparison of the pH dependence of the reaction rates of these DNAzymes demonstrated that G14 in the bulge loop next to the cleavage site, is involved in proton transfer at the catalytic site. In contrast, we did not find any evidence of G1.1 being involved in acid-base catalysis. These results support general acid-base catalysis as a feasible strategy used in DNA catalysis, as in RNA and protein enzymes.
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Affiliation(s)
- Marjorie Cepeda-Plaza
- Department of Chemical Sciences, School of Exact Sciences, Universidad Andres Bello, República 275, Santiago, Chile
| | - Claire E. McGhee
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801
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70
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Liu M, Yin Q, McConnell EM, Chang Y, Brennan JD, Li Y. DNAzyme Feedback Amplification: Relaying Molecular Recognition to Exponential DNA Amplification. Chemistry 2018; 24:4473-4479. [PMID: 29240289 DOI: 10.1002/chem.201705338] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Indexed: 01/10/2023]
Abstract
Technologies capable of linking DNA amplification to molecular recognition are very desirable for ultrasensitive biosensing applications. We have developed a simple but powerful isothermal DNA amplification method, termed DNAzyme feedback amplification (DFA), that is capable of relaying molecular recognition to exponential DNA amplification. The method incorporates both an RNA-cleaving DNAzyme (RCD) and rolling circle amplification (RCA) carried out by a special DNA polymerase using a circular DNA template. DFA begins with a stimulus-dependent RCA reaction, producing tandemly linked RCDs in long-chain DNA products. These RCDs cleave an RNA-containing DNA sequence to form additional primers that hybridize to the circular DNA molecule, giving rise to DNA assemblies that act as the new inputs for RCA. The RCA reaction and the cleavage event keep on feeding each other autonomously, resulting in exponential growth of repetitive DNA sequences that can be easily detected. This method can be used for the detection of both nucleic acid based targets and non-nucleic acid analytes. In this article, we discuss the conceptual framework of the feedback amplification approach, the essential features of this method as well as remaining challenges and possible solutions.
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Affiliation(s)
- Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, P. R. China
| | - Qingxin Yin
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, P. R. China
| | - Erin M McConnell
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, P. R. China
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.,Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada
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Inability of DNAzymes to cleave RNA in vivo is due to limited Mg[Formula: see text] concentration in cells. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 47:333-343. [PMID: 29248953 DOI: 10.1007/s00249-017-1270-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 11/18/2017] [Indexed: 10/18/2022]
Abstract
Sequence specific cleavage of RNA can be achieved by hammerhead ribozymes as well as DNAzymes. They comprise a catalytic core sequence flanked by regions that form double strands with complementary RNA. While different types of ribozymes have been discovered in natural organisms, DNAzymes derive from in vitro selection. Both have been used for therapeutic down-regulation of harmful proteins by reducing drastically the corresponding mRNA concentration. A priori DNAzymes appear advantageous because of the higher haemolytic stability and better cost effectiveness when compared to RNA. In the present work the 10-23 DNAzyme was applied to knockdown expression of the prion protein (PrP), the sole causative agent of transmissible spongiform encephalopathies. We selected accessible target sequences on the PrP mRNA based on a sequential folding algorithm. Very high effectivity of DNAzymes was found for cleavage of RNA in vitro, but activity in neuroblastoma cells was very low. However, siRNA directed to the identical target sequences reduced expression of PrP in the same cell type. According to our analysis, three Mg[Formula: see text] bind cooperatively to the DNAzyme to exert full activity. However, free ATP binds the Mg[Formula: see text] ions more strongly and already stoichiometric amounts of Mg[Formula: see text] and ATP inhibited the activity of DNAzymes drastically. In contrast, natural ribozymes form three-dimensional structures close to the cleavage site that stabilize the active conformation at much lower Mg[Formula: see text] concentrations. For DNAzymes, however, a similar stabilization is not known and therefore DNAzymes need higher free Mg[Formula: see text] concentrations than that available inside the cell.
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72
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Liu M, Chang D, Li Y. Discovery and Biosensing Applications of Diverse RNA-Cleaving DNAzymes. Acc Chem Res 2017; 50:2273-2283. [PMID: 28805376 DOI: 10.1021/acs.accounts.7b00262] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA-based enzymes, or DNAzymes, are not known to exist in Nature but can be isolated from random-sequence DNA pools using test tube selection techniques. Since the report of the first DNAzyme in 1994, many catalytic DNA molecules for catalyzing wide-ranging chemical transformations have been isolated and studied. Our laboratory has a keen interest in searching for diverse DNAzymes capable of cleaving RNA-containing substrates, determining their sequence requirements and structural properties, and examining their potential as biosensors. This Account begins with the description of an accidental discovery on the sequence adaptability of a small DNAzyme known as "8-17", when we performed 16 parallel selections to search for DNAzymes that targeted each and every possible dinucleotide junction of RNA for cleavage. DNAzyme 8-17 dominated all the selection pools targeting purine-containing junctions. In-depth sequence analysis revealed that 8-17 could manifest itself in many sequence options defined by the requirement of four absolutely conserved nucleotides. This study also exposed the fact that 8-17 had poor activity toward pyrimidine-pyrimidine junctions. With this information in hand, we proceeded to the discovery of diverse non-8-17 DNAzymes that exhibited robust catalytic activity under physiological conditions. These DNAzymes were found to universally interact with their substrates through two Watson-Crick binding arms and have a catalytic core of varying length and secondary-structure complexity. RNA-cleaving DNAzymes were also isolated to function at acidic conditions (pH 3-5), and these molecules exhibited intriguing pH profiles, with the highest activity precisely matching the pH used for their selection. Interestingly, these DNAzymes appear to use non-Watson-Crick interactions in defining their structures. More recently, we have embarked on the development of ligand-responsive RNA-cleaving fluorogenic DNAzymes that can recognize specific bacterial pathogens, such as Escherichia coli and Clostridium difficile, using a method that does not require a priori identification of a specific biomarker. Instead, the crude extracellular mixture as a whole is used as the target to drive the DNAzyme isolation. High recognition specificity can be achieved with a double-selection approach in which a DNA library is negatively selected against the cellular mixture prepared from unintended bacteria, followed by positive selection against the same mixture derived from a specific species or strain of bacterial pathogen. Finally, we have shown that DNAzymes' compatibility with DNA replication can benefit the design of amplification mechanisms that uniquely link the action of RNA-cleaving DNAzymes to rolling circle amplification, an isothermal DNA amplification technique. These methods are well suited for translating the target-binding and cleavage activity of an analyte-activated RNA-cleaving DNAzyme into the production of massive amounts of DNA amplicons to achieve ultrahigh detection sensitivity. Given the high chemical stability of DNA, our ability to discover catalytic DNA sequences by simultaneously evaluating as many as 1016 different DNA sequences, the accessibility to diverse RNA-cleaving DNAzymes in a single DNA pool, and the availability of methods for designing simple biosensors that incorporate RNA-cleaving DNAzymes, we believe we are moving closer to employing RNA-cleaving DNAzymes for exciting applications, such as point of care diagnostics or field detection of environmental toxins.
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Affiliation(s)
- Meng Liu
- Department
of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute
of Infectious Disease Research, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
- Biointerfaces
Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
- School
of Environmental Science and Technology, Key Laboratory of Industrial
Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian 116024, China
| | - Dingran Chang
- Department
of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute
of Infectious Disease Research, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Yingfu Li
- Department
of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute
of Infectious Disease Research, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
- Biointerfaces
Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
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Sondhi D, Stiles KM, De BP, Crystal RG. Genetic Modification of the Lung Directed Toward Treatment of Human Disease. Hum Gene Ther 2017; 28:3-84. [PMID: 27927014 DOI: 10.1089/hum.2016.152] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genetic modification therapy is a promising therapeutic strategy for many diseases of the lung intractable to other treatments. Lung gene therapy has been the subject of numerous preclinical animal experiments and human clinical trials, for targets including genetic diseases such as cystic fibrosis and α1-antitrypsin deficiency, complex disorders such as asthma, allergy, and lung cancer, infections such as respiratory syncytial virus (RSV) and Pseudomonas, as well as pulmonary arterial hypertension, transplant rejection, and lung injury. A variety of viral and non-viral vectors have been employed to overcome the many physical barriers to gene transfer imposed by lung anatomy and natural defenses. Beyond the treatment of lung diseases, the lung has the potential to be used as a metabolic factory for generating proteins for delivery to the circulation for treatment of systemic diseases. Although much has been learned through a myriad of experiments about the development of genetic modification of the lung, more work is still needed to improve the delivery vehicles and to overcome challenges such as entry barriers, persistent expression, specific cell targeting, and circumventing host anti-vector responses.
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Affiliation(s)
- Dolan Sondhi
- Department of Genetic Medicine, Weill Cornell Medical College , New York, New York
| | - Katie M Stiles
- Department of Genetic Medicine, Weill Cornell Medical College , New York, New York
| | - Bishnu P De
- Department of Genetic Medicine, Weill Cornell Medical College , New York, New York
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medical College , New York, New York
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75
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Liu M, Zhang Q, Chang D, Gu J, Brennan JD, Li Y. A DNAzyme Feedback Amplification Strategy for Biosensing. Angew Chem Int Ed Engl 2017; 56:6142-6146. [PMID: 28370773 DOI: 10.1002/anie.201700054] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/05/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
| | - Qiang Zhang
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - John D. Brennan
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
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76
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Dolot R, Sobczak M, Mikołajczyk B, Nawrot B. Synthesis, crystallization and preliminary crystallographic analysis of a 52-nucleotide DNA/2'-OMe-RNA oligomer mimicking 10-23 DNAzyme in the complex with a substrate. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:292-301. [PMID: 28323518 DOI: 10.1080/15257770.2016.1276291] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
A 52-nucleotide DNA/2'-OMe-RNA oligomer mimicking 10-23 DNAzyme in the complex with its substrate was synthesized, purified and crystallized by the hanging-drop method using 0.8 M sodium potassium tartrate as a precipitant. A data set to 1.21 Å resolution was collected from a monocrystal at 100 K using synchrotron radiation on a beamline BL14.1 at BESSY. The crystal belonged to the P21 group with unit-cell a = 49.42, b = 24.69, c = 50.23, β = 118.48.
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Affiliation(s)
- Rafał Dolot
- a Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences , Department of Bioorganic Chemistry , Łódź , Poland
| | - Milena Sobczak
- a Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences , Department of Bioorganic Chemistry , Łódź , Poland
| | - Barbara Mikołajczyk
- a Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences , Department of Bioorganic Chemistry , Łódź , Poland
| | - Barbara Nawrot
- a Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences , Department of Bioorganic Chemistry , Łódź , Poland
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77
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Tauber PA, Pickl WF. Pharmacological targeting of allergen-specific T lymphocytes. Immunol Lett 2017; 189:27-39. [PMID: 28322861 DOI: 10.1016/j.imlet.2017.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 03/15/2017] [Indexed: 12/18/2022]
Abstract
Allergic disorders are the result of a complex pathophysiology, involving major cellular lineages and a multitude of humoral factors of the innate and adaptive immune system, and have the tendency to involve multiple organs. Consequently, even standard pharmacological treatment of allergies is rarely specific but usually targets more than one pathway/cellular system at a time. Accordingly, many of the classic anti-allergic drugs have a critical impact also on T helper cells, which are pivotal not only during the sensitization but also the maintenance phase of allergic diseases. Recent years have seen a dramatic increase of novel drugs with the potency to interfere, more or less specifically, with T lymphocyte function, which might, possibly together with classic anti-allergic drugs, help harnessing one of the central cellular players in allergic responses. A major theme in the years to come will be a thoughtful combination of previously established with recently developed treatment modalities.
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Affiliation(s)
- Peter A Tauber
- Institute of Immunology, Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
| | - Winfried F Pickl
- Institute of Immunology, Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria.
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78
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Defrancq E, Messaoudi S. Palladium-Mediated Labeling of Nucleic Acids. Chembiochem 2017; 18:426-431. [PMID: 28000981 DOI: 10.1002/cbic.201600599] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Indexed: 11/11/2022]
Abstract
New applications of Pd-catalyzed coupling reactions (Suzuki-Miyaura, Sonogashira, and Stille-Migita coupling) for post-conjugation of nucleic acids have been developed recently. Breakthroughs in this area might now pave the way for the development of sophisticated DNA probes, which might be of great interest in chemical biology, nanotechnology, and bioanalysis, as well as in diagnostic domains.
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Affiliation(s)
- Eric Defrancq
- Université Grenoble Alpes, CNRS, Département de Chimie Moléculaire, UMR 5250, B. P. 53, 38041, Grenoble Cedex 9, France
| | - Samir Messaoudi
- Université Paris-Sud, CNRS, BioCIS-UMR 8076, Laboratoire CoSMIT, Equipe Labellisée Ligue Contre Le Cancer, LabEx LERMIT, Faculté de Pharmacie, 5 rue J.-B. Clément, Châtenay-Malabry, 92296, France
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79
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Zhang Z, Liu B, Liu J. Molecular Imprinting for Substrate Selectivity and Enhanced Activity of Enzyme Mimics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1602730. [PMID: 27925383 DOI: 10.1002/smll.201602730] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/26/2016] [Indexed: 06/06/2023]
Abstract
Using molecular imprinting, a peroxidase-mimicking DNAzyme has achieved substrate specificity with enhanced activity in a nanoscale gel for three different substrates.
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Affiliation(s)
- Zijie Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada
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80
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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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81
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Kim J, Lee JB. Giant Catalytic DNA Particles for Simple and Intuitive Detection of Pb(2.). NANOSCALE RESEARCH LETTERS 2016; 11:244. [PMID: 27169418 PMCID: PMC4864767 DOI: 10.1186/s11671-016-1462-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/03/2016] [Indexed: 06/05/2023]
Abstract
DNAzymes have been extensively studied as biosensors because of their unique functionality of cleaving substrate in the presence of metal ion cofactors. However, there are only a few reports on visual detection using gold nanoparticles. Here, we synthesized the DNAzyme microparticle (DzMP) (~1 μm) via rolling circle amplification for detection of Pb(2+) without the help of other materials. Then, the substrate strands were labeled with two different fluorophores (6-carboxyfluorescein and Cy5) to visualize the DzMPs and to monitor the separation of substrate strands. Because of their large size, the decline in the number of fluorescent particles in the presence of Pb(2+) could be successfully demonstrated by a fluorescence microscopy, presenting a new platform for heavy metal detection.
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Affiliation(s)
- Jieun Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, 130-743, South Korea
| | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, 130-743, South Korea.
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82
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Zhang W, Feng Q, Chang D, Tram K, Li Y. In vitro selection of RNA-cleaving DNAzymes for bacterial detection. Methods 2016; 106:66-75. [DOI: 10.1016/j.ymeth.2016.03.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 12/23/2022] Open
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83
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Direct and precise length measurement of single, stretched DNA fragments by dynamic molecular combing and STED nanoscopy. Anal Bioanal Chem 2016; 408:6453-9. [DOI: 10.1007/s00216-016-9764-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/25/2016] [Accepted: 07/04/2016] [Indexed: 11/25/2022]
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84
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Programming a topologically constrained DNA nanostructure into a sensor. Nat Commun 2016; 7:12074. [PMID: 27337657 PMCID: PMC4931013 DOI: 10.1038/ncomms12074] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 05/27/2016] [Indexed: 01/21/2023] Open
Abstract
Many rationally engineered DNA nanostructures use mechanically interlocked topologies to connect individual DNA components, and their physical connectivity is achieved through the formation of a strong linking duplex. The existence of such a structural element also poses a significant topological constraint on functions of component rings. Herein, we hypothesize and confirm that DNA catenanes with a strong linking duplex prevent component rings from acting as the template for rolling circle amplification (RCA). However, by using an RNA-containing DNA [2] catenane with a strong linking duplex, we show that a stimuli-responsive RNA-cleaving DNAzyme can linearize one component ring, and thus enable RCA, producing an ultra-sensitive biosensing system. As an example, a DNA catenane biosensor is engineered to detect the model bacterial pathogen Escherichia coli through binding of a secreted protein, with a detection limit of 10 cells ml−1, thus establishing a new platform for further applications of mechanically interlocked DNA nanostructures. DNA nanostructures with interlocked topologies will tend to display different behaviour to the linear counterparts. Here, the authors show a DNA catenane that is inactive for rolling circle amplification but is activated upon cleavage of one ring, and exploit this for the development of a biosensing system.
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85
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Gwak R, Kim H, Yoo SM, Lee SY, Lee GJ, Lee MK, Rhee CK, Kang T, Kim B. Precisely Determining Ultralow level UO2(2+) in Natural Water with Plasmonic Nanowire Interstice Sensor. Sci Rep 2016; 6:19646. [PMID: 26791784 PMCID: PMC4726367 DOI: 10.1038/srep19646] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/15/2015] [Indexed: 01/01/2023] Open
Abstract
Uranium is an essential raw material in nuclear energy generation; however, its use raises concerns about the possibility of severe damage to human health and the natural environment. In this work, we report an ultrasensitive uranyl ion (UO22+) detection method in natural water that uses a plasmonic nanowire interstice (PNI) sensor combined with a DNAzyme-cleaved reaction. UO22+ induces the cleavage of DNAzymes into enzyme strands and released strands, which include Raman-active molecules. A PNI sensor can capture the released strands, providing strong surface-enhanced Raman scattering signal. The combination of a PNI sensor and a DNAzyme-cleaved reaction significantly improves the UO22+ detection performance, resulting in a detection limit of 1 pM and high selectivity. More importantly, the PNI sensor operates perfectly, even in UO22+-contaminated natural water samples. This suggests the potential usefulness of a PNI sensor in practical UO22+-sensing applications. We anticipate that diverse toxic metal ions can be detected by applying various ion-specific DNA-based ligands to PNI sensors.
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Affiliation(s)
- Raekeun Gwak
- KAIST, Department of Chemistry, Daejeon 34141, Korea
| | - Hongki Kim
- KAIST, Department of Chemistry, Daejeon 34141, Korea
| | - Seung Min Yoo
- KAIST, Department of Chemical and Biomolecular Engineering, Daejeon 34141, Korea
| | - Sang Yup Lee
- KAIST, Department of Chemical and Biomolecular Engineering, Daejeon 34141, Korea
| | - Gyoung-Ja Lee
- KAERI, Nuclear Materials Development Division, Daejeon 34057, Korea
| | - Min-Ku Lee
- KAERI, Nuclear Materials Development Division, Daejeon 34057, Korea
| | - Chang-Kyu Rhee
- KAERI, Nuclear Materials Development Division, Daejeon 34057, Korea
| | - Taejoon Kang
- KRIBB, BioNanotechnology Research Center and BioNano Health Guard Research Center, Daejeon 34141, Korea.,UST, Major of Nanobiotechnology and Bioinformatics, Daejeon 34113, Korea
| | - Bongsoo Kim
- KAIST, Department of Chemistry, Daejeon 34141, Korea
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86
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Kasprowicz A, Stokowa-Sołtys K, Wrzesiński J, Jeżowska-Bojczuk M, Ciesiołka J. In vitro selection of deoxyribozymes active with Cd(2+) ions resulting in variants of DNAzyme 8-17. Dalton Trans 2016; 44:8138-49. [PMID: 25836771 DOI: 10.1039/c5dt00187k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In vitro selection was performed to search for RNA-cleaving DNAzymes catalytically active with Cd(2+) ions from the oligonucleotide combinatorial library with a 23-nucleotide random region. All the selected, catalytically active variants turned out to belong to the 8-17 type DNAzyme. Three DNAzymes were prepared in shortened, cis-acting versions which were subjected to a detailed study of the kinetic properties and metal ion preferences. Although the selection protocol was designed for Cd(2+)-dependent DNAzymes, the variants showed broader metal ion specificity. They preferred Cd(2+) but were also active with Mn(2+) and Zn(2+), suggesting that binding of the catalytic ion does not require an extremely specific coordination pattern. The unexpected decrease of the catalytic activity of the variants along with the temperature increase suggested that some changes occurred in their structures or the rate-limiting step of the reaction was changed. Two elements of the catalytic core of DNAzyme 1/VIIWS, the nucleotide at position 12 and the three-base-pair hairpin motif, were mutated. The presence of a purine residue at position 12 was crucial for the catalytic activity but the changes at that position had a relatively small influence on the metal ion preferences of this variant. The middle base pair of the three-base-pair hairpin was changed from A-T to C-G interaction. The catalytic activity of the mutated variant was increased with Zn(2+), decreased with Mn(2+), and was not changed in the presence of Cd(2+) ions. Clearly, this base pair was important for defining the metal ion preferences of the DNAzyme 1/VIIWS.
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Affiliation(s)
- Aleksandra Kasprowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
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87
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Räz MH, Hollenstein M. Probing the effect of minor groove interactions on the catalytic efficiency of DNAzymes 8-17 and 10-23. MOLECULAR BIOSYSTEMS 2016; 11:1454-61. [PMID: 25854917 DOI: 10.1039/c5mb00102a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNAzymes (Dz) 8-17 and 10-23 are two widely studied and well-characterized RNA-cleaving DNA catalysts. In an effort to further improve the understanding of the fragile interactions and dynamics of the enzymatic mechanism, this study examines the catalytic efficiency of minimally modified DNAzymes. Five single mutants of Dz8-17 and Dz10-23 were prepared by replacing the adenine residues in the corresponding catalytic cores with 3-deazaadenine units. Kinetic assays were used to assess the effect on the catalytic activity and thereby identify the importance of hydrogen bonding that arises from the N3 atoms. The results suggest that modifications at A15 and A15.0 of Dz8-17 have a significant influence and show a reduction in catalytic activity. Modification at each location in Dz10-23 results in a decrease of the observed rate constants, with A12 appearing to be the most affected with a reduction of ∼80% of kobs and ∼25% of the maximal cleavage rate compared to the wild-type DNAzyme. On the other hand, modification of A12 in Dz8-17 showed an ∼130% increase in kobs, thus unraveling a new potential site for the introduction of chemical modifications. A pH-profile analysis showed that the chemical cleavage step is rate-determining, regardless of the presence and/or location of the mutation. These findings point towards the importance of the N3-nitrogens of certain adenine nucleotides located within the catalytic cores of the DNAzymes for efficient catalytic activity and further suggest that they might directly partake in maintaining the appropriate tertiary structure. Therefore, it appears that minor groove interactions constitute an important feature of DNAzymes as well as ribozymes.
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Affiliation(s)
- Michael H Räz
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
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88
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Wang MQ, Dong J, Zhang H, Tang Z. Characterization of deoxyribozymes with site-specific oxidative cleavage activity against DNA obtained by in vitro selection. Org Biomol Chem 2016; 14:2347-51. [DOI: 10.1039/c6ob00148c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have generated a new class of deoxyribozymes that required Mn2+ and Cu2+ to catalyze a site-specific oxidative cleavage of DNA.
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Affiliation(s)
- Ming-Qi Wang
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Juan Dong
- Natural Products Research Center
- Chengdu Institution of Biology
- Chinese Academy of Science
- Chengdu 610041
- P. R. China
| | - Huafan Zhang
- Natural Products Research Center
- Chengdu Institution of Biology
- Chinese Academy of Science
- Chengdu 610041
- 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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89
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Purath U, Ibrahim R, Zeitvogel J, Renz H, Runkel F, Schmidts T, Dobler D, Werfel T, Müller A, Garn H. Efficacy of T-cell transcription factor-specific DNAzymes in murine skin inflammation models. J Allergy Clin Immunol 2015; 137:644-647.e8. [PMID: 26560045 DOI: 10.1016/j.jaci.2015.09.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 08/07/2015] [Accepted: 09/02/2015] [Indexed: 10/22/2022]
Affiliation(s)
| | - Rouba Ibrahim
- Medical Faculty, Institute of Laboratory Medicine and Pathobiochemistry - Molecular Diagnostics, Philipps University Marburg, Marburg, Germany
| | - Jana Zeitvogel
- Clinic for Dermatology, Allergology and Venerology, Division of Immunodermatology and Allergy Research, Hannover Medical School, Hannover, Germany
| | - Harald Renz
- Medical Faculty, Institute of Laboratory Medicine and Pathobiochemistry - Molecular Diagnostics, Philipps University Marburg, Marburg, Germany
| | - Frank Runkel
- Institute of Bioprocessengineering and Biopharmaceutical Technology, Technische Hochschule Mittelhessen, Giessen, Germany
| | - Thomas Schmidts
- Institute of Bioprocessengineering and Biopharmaceutical Technology, Technische Hochschule Mittelhessen, Giessen, Germany
| | - Dorota Dobler
- Institute of Bioprocessengineering and Biopharmaceutical Technology, Technische Hochschule Mittelhessen, Giessen, Germany
| | - Thomas Werfel
- Clinic for Dermatology, Allergology and Venerology, Division of Immunodermatology and Allergy Research, Hannover Medical School, Hannover, Germany
| | - Anke Müller
- Sterna Biologicals GmbH & Co. KG, Marburg, Germany
| | - Holger Garn
- Medical Faculty, Institute of Laboratory Medicine and Pathobiochemistry - Molecular Diagnostics, Philipps University Marburg, Marburg, Germany.
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90
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Sequence Mutation and Structural Alteration Transform a Noncatalytic DNA Sequence into an Efficient RNA-Cleaving DNAzyme. J Mol Evol 2015; 81:245-53. [DOI: 10.1007/s00239-015-9712-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 10/29/2015] [Indexed: 01/16/2023]
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91
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Sequence-specific RNA Photocleavage by Single-stranded DNA in Presence of Riboflavin. Sci Rep 2015; 5:15039. [PMID: 26461456 PMCID: PMC4602204 DOI: 10.1038/srep15039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 08/24/2015] [Indexed: 02/07/2023] Open
Abstract
Constant efforts have been made to develop new method to realize sequence-specific RNA degradation, which could cause inhibition of the expression of targeted gene. Herein, by using an unmodified short DNA oligonucleotide for sequence recognition and endogenic small molecue, vitamin B2 (riboflavin) as photosensitizer, we report a simple strategy to realize the sequence-specific photocleavage of targeted RNA. The DNA strand is complimentary to the target sequence to form DNA/RNA duplex containing a G•U wobble in the middle. The cleavage reaction goes through oxidative elimination mechanism at the nucleoside downstream of U of the G•U wobble in duplex to obtain unnatural RNA terminal, and the whole process is under tight control by using light as switch, which means the cleavage could be carried out according to specific spatial and temporal requirements. The biocompatibility of this method makes the DNA strand in combination with riboflavin a promising molecular tool for RNA manipulation.
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92
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Taylor AI, Holliger P. Directed evolution of artificial enzymes (XNAzymes) from diverse repertoires of synthetic genetic polymers. Nat Protoc 2015; 10:1625-42. [PMID: 26401917 DOI: 10.1038/nprot.2015.104] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes the directed evolution of artificial endonuclease and ligase enzymes composed of synthetic genetic polymers (XNAzymes), using 'cross-chemistry selective enrichment by exponential amplification' (X-SELEX). The protocol is analogous to (deoxy)ribozyme selections, but it enables the development of fully substituted catalysts. X-SELEX is initiated by the synthesis of diverse repertoires (here 10(14) different sequences), using xeno nucleic acid (XNA) polymerases, on DNA templates primed with DNA, RNA or XNA oligonucleotides that double as substrates, allowing selection for XNA-catalyzed cleavage or ligation. XNAzymes are reverse-transcribed into cDNA using XNA-dependent DNA polymerases, and then PCR-amplified to generate templates for subsequent rounds or deep sequencing. We describe methods developed for four XNA chemistries, arabino nucleic acids (ANAs), 2'-fluoroarabino nucleic acids (FANAs), hexitol nucleic acids (HNAs) and cyclohexene nucleic acids (CeNAs), which require ∼1 week per round, and typically 10-20 rounds; in principle, these methods are scalable and applicable to a wide range of novel XNAzyme chemistries, substrates and reactions.
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Affiliation(s)
| | - Philipp Holliger
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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93
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Fasoli J, Corn RM. Surface Enzyme Chemistries for Ultrasensitive Microarray Biosensing with SPR Imaging. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:9527-9536. [PMID: 25641598 PMCID: PMC4564839 DOI: 10.1021/la504797z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/30/2015] [Indexed: 06/01/2023]
Abstract
The sensitivity and selectivity of surface plasmon resonance imaging (SPRI) biosensing with nucleic acid microarrays can be greatly enhanced by exploiting various nucleic acid ligases, nucleases, and polymerases that manipulate the surface-bound DNA and RNA. We describe here various examples from each of these different classes of surface enzyme chemistries that have been incorporated into novel detection strategies that either drastically enhance the sensitivity of or create uniquely selective methods for the SPRI biosensing of proteins and nucleic acids. A dual-element generator-detector microarray approach that couples a bioaffinity adsorption event on one microarray element to nanoparticle-enhanced SPRI measurements of nucleic acid hybridization adsorption on a different microarray element is used to quantitatively detect DNA, RNA, and proteins at femtomolar concentrations. Additionally, this dual-element format can be combined with the transcription and translation of RNA from surface-bound double-stranded DNA (dsDNA) templates for the on-chip multiplexed biosynthesis of aptamer and protein microarrays in a microfluidic format; these microarrays can be immediately used for real-time SPRI bioaffinity sensing measurements.
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94
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Zhou Z, Xiao L, Xiang Y, Zhou J, Tong A. A general approach for rational design of fluorescent DNA aptazyme sensors based on target-induced unfolding of DNA hairpins. Anal Chim Acta 2015; 889:179-86. [PMID: 26343441 DOI: 10.1016/j.aca.2015.06.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/16/2015] [Accepted: 06/18/2015] [Indexed: 01/03/2023]
Abstract
DNA aptazymes are allosteric DNAzymes activated by the targets of DNA aptamers. They take the advantages of both aptamers and DNAzymes, which can recognize specific targets with high selectivity and catalyze multiple-turnover reactions for signal amplification, respectively, and have shown their great promise in many analytical applications. So far, however, the available examples of DNA aptazyme sensors are still limited in utilizing only several DNAzymes and DNA aptamers, most likely due to the lack of a general and simple approach for rational design. Herein, we have developed such a general approach for designing fluorescent DNA aptazyme sensors. In this approach, aptamers and DNAzymes are connected at the ends to avoid any change in their original sequences, therefore enabling the general use of different aptamers and DNAzymes in the design. Upon activation of the aptazymes by the targets of interest, the rate of fluorescence enhancement via the cleavage of a dually labeled substrate by the active aptazymes is then monitored for target quantification. Two DNAzymes and two aptamers are used as examples for the design of three fluorescent aptazyme sensors, and they all show high selectivity and sensitivity for the detection of their targets. More DNA aptazyme sensors for a broader range of targets could be developed by this general approach as long as suitable DNAzymes and aptamers are used.
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Affiliation(s)
- Zhaojuan Zhou
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China; Beijing Third Class Tobacco Supervision Station, Beijing, 101121, China
| | - Lu Xiao
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Jun Zhou
- Beijing Third Class Tobacco Supervision Station, Beijing, 101121, China.
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China.
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95
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Bone SM, Lima NE, Todd AV. DNAzyme switches for molecular computation and signal amplification. Biosens Bioelectron 2015; 70:330-7. [DOI: 10.1016/j.bios.2015.03.057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/21/2015] [Accepted: 03/23/2015] [Indexed: 12/20/2022]
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96
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Tram K, Xia J, Gysbers R, Li Y. An Efficient Catalytic DNA that Cleaves L-RNA. PLoS One 2015; 10:e0126402. [PMID: 25946137 PMCID: PMC4422682 DOI: 10.1371/journal.pone.0126402] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 04/01/2015] [Indexed: 12/22/2022] Open
Abstract
Many DNAzymes have been isolated from synthetic DNA pools to cleave natural RNA (D-RNA) substrates and some have been utilized for the design of aptazyme biosensors for bioanalytical applications. Even though these biosensors perform well in simple sample matrices, they do not function effectively in complex biological samples due to ubiquitous RNases that can efficiently cleave D-RNA substrates. To overcome this issue, we set out to develop DNAzymes that cleave L-RNA, the enantiomer of D-RNA, which is known to be completely resistant to RNases. Through in vitro selection we isolated three L-RNA-cleaving DNAzymes from a random-sequence DNA pool. The most active DNAzyme exhibits a catalytic rate constant ~3 min-1 and has a structure that contains a kissing loop, a structural motif that has never been observed with D-RNA-cleaving DNAzymes. Furthermore we have used this DNAzyme and a well-known ATP-binding DNA aptamer to construct an aptazyme sensor and demonstrated that this biosensor can achieve ATP detection in biological samples that contain RNases. The current work lays the foundation for exploring RNA-cleaving DNAzymes for engineering biosensors that are compatible with complex biological samples.
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Affiliation(s)
- Kha Tram
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Jiaji Xia
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Rachel Gysbers
- Department of Biochemistry and Biomedical Sciences and Origins Institute, McMaster University, Hamilton, Ontario, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, and Origins Institute, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
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97
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Homburg U, Renz H, Timmer W, Hohlfeld JM, Seitz F, Lüer K, Mayer A, Wacker A, Schmidt O, Kuhlmann J, Turowska A, Roller J, Kutz K, Schlüter G, Krug N, Garn H. Safety and tolerability of a novel inhaled GATA3 mRNA targeting DNAzyme in patients with TH2-driven asthma. J Allergy Clin Immunol 2015; 136:797-800. [PMID: 25842286 DOI: 10.1016/j.jaci.2015.02.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 02/03/2015] [Accepted: 02/06/2015] [Indexed: 11/18/2022]
Affiliation(s)
| | - Harald Renz
- Institute of Laboratory Medicine and Pathobiochemistry-Molecular Diagnostics, Medical Faculty, Philipps University Marburg, Universities of Giessen and Marburg Lung Center (UGMLC), Marburg, Germany
| | | | - Jens M Hohlfeld
- Department of Clinical Airway Research, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | | | - Katrin Lüer
- Department of Clinical Airway Research, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Alexandra Mayer
- CRS Clinical Research Services Mannheim GmbH, Mannheim, Germany
| | - Anja Wacker
- Engelhard Arzneimittel GmbH, Niederdorfelden, Germany
| | | | | | | | | | | | | | - Norbert Krug
- Department of Clinical Airway Research, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Holger Garn
- Institute of Laboratory Medicine and Pathobiochemistry-Molecular Diagnostics, Medical Faculty, Philipps University Marburg, Universities of Giessen and Marburg Lung Center (UGMLC), Marburg, Germany.
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98
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Gao L, Li LL, Wang X, Wu P, Cao Y, Liang B, Li X, Lin Y, Lu Y, Guo X. Graphene-DNAzyme Junctions: A Platform for Direct Metal Ion Detection with Ultrahigh Sensitivity. Chem Sci 2015; 6:2469-2473. [PMID: 26417425 PMCID: PMC4583199 DOI: 10.1039/c4sc03612c] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/04/2015] [Indexed: 02/06/2023] Open
Abstract
Many metal ions are present in biology and in the human body in trace amounts. Despite numerous efforts, metal sensors with ultrahigh sensitivity (< a few picomolar) are rarely achieved. Here, we describe a platform method that integrates a Cu2+-dependent DNAzyme into graphene-molecule junctions and its application for direct detection of paramagnetic Cu2+ with femtomolar sensitivity and high selectivity. Since DNAzymes specific for other metal ions can be obtained through in vitro selection, the method demonstrated here can be applied to the detection of a broad range of other metal ions.
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Affiliation(s)
- Li Gao
- Center for Nanochemistry , Beijing National Laboratory for Molecular Sciences , State Key Laboratory for Structural Chemistry of Unstable and Stable Species , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China .
| | - Le-Le Li
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , USA .
| | - Xiaolong Wang
- Center for Nanochemistry , Beijing National Laboratory for Molecular Sciences , State Key Laboratory for Structural Chemistry of Unstable and Stable Species , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China .
| | - Peiwen Wu
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , USA .
| | - Yang Cao
- Center for Nanochemistry , Beijing National Laboratory for Molecular Sciences , State Key Laboratory for Structural Chemistry of Unstable and Stable Species , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China .
| | - Bo Liang
- Adesso Advanced Materials Wuxi Co., Ltd. , Huihong Industrial Park , 18 Xishi Road, New District , Wuxi , Jiangsu Province 214000 , P. R. China
| | - Xin Li
- Adesso Advanced Materials Wuxi Co., Ltd. , Huihong Industrial Park , 18 Xishi Road, New District , Wuxi , Jiangsu Province 214000 , P. R. China
| | - Yuanwei Lin
- Center for Nanochemistry , Beijing National Laboratory for Molecular Sciences , State Key Laboratory for Structural Chemistry of Unstable and Stable Species , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China .
| | - Yi Lu
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , USA .
| | - Xuefeng Guo
- Center for Nanochemistry , Beijing National Laboratory for Molecular Sciences , State Key Laboratory for Structural Chemistry of Unstable and Stable Species , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China .
- Department of Materials Science and Engineering , College of Engineering , Peking University , Beijing 100871 , P. R. China
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99
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Wu P, Yu Y, McGhee CE, Tan LH, Lu Y. Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic acid-functionalized nanomaterials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:7849-72. [PMID: 25205057 PMCID: PMC4275547 DOI: 10.1002/adma.201304891] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 06/02/2014] [Indexed: 05/22/2023]
Abstract
In this review, we summarize recent progress in the application of synchrotron-based spectroscopic techniques for nucleic acid research that takes advantage of high-flux and high-brilliance electromagnetic radiation from synchrotron sources. The first section of the review focuses on the characterization of the structure and folding processes of nucleic acids using different types of synchrotron-based spectroscopies, such as X-ray absorption spectroscopy, X-ray emission spectroscopy, X-ray photoelectron spectroscopy, synchrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering. In the second section, the characterization of nucleic acid-based nanostructures, nucleic acid-functionalized nanomaterials and nucleic acid-lipid interactions using these spectroscopic techniques is summarized. Insights gained from these studies are described and future directions of this field are also discussed.
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Affiliation(s)
- Peiwen Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yang Yu
- Center of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Claire E. McGhee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Li Huey Tan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Center of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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100
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Tram K, Kanda P, Salena BJ, Huan S, Li Y. Translating Bacterial Detection by DNAzymes into a Litmus Test. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407021] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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