1
|
Dantu SC, Khalil M, Bria M, Saint-Pierre C, Orio M, Gasparutto D, Sicoli G. Cleaving DNA with DNA: Cooperative Tuning of Structure and Reactivity Driven by Copper Ions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306710. [PMID: 38419268 DOI: 10.1002/advs.202306710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/15/2024] [Indexed: 03/02/2024]
Abstract
A copper-dependent self-cleaving DNA (DNAzyme or deoyxyribozyme) previously isolated by in vitro selection has been analyzed by a combination of Molecular Dynamics (MD) simulations and advanced Electron Paramagnetic Resonance (Electron Spin Resonance) EPR/ESR spectroscopy, providing insights on the structural and mechanistic features of the cleavage reaction. The modeled 46-nucleotide deoxyribozyme in MD simulations forms duplex and triplex sub-structures that flank a highly conserved catalytic core. The DNA self-cleaving construct can also form a bimolecular complex that has a distinct substrate and enzyme domains. The highly dynamic structure combined with an oxidative site-specific cleavage of the substrate are two key-aspects to elucidate. By combining EPR/ESR spectroscopy with selectively isotopically labeled nucleotides it has been possible to overcome the major drawback related to the "metal-soup" scenario, also known as "super-stoichiometric" ratios of cofactors versus substrate, conventionally required for the DNA cleavage reaction within those nucleic acids-based enzymes. The focus on the endogenous paramagnetic center (Cu2+) here described paves the way for analysis on mixtures where several different cofactors are involved. Furthermore, the insertion of cleavage reaction within more complex architectures is now a realistic perspective towards the applicability of EPR/ESR spectroscopic studies.
Collapse
Affiliation(s)
- Sarath Chandra Dantu
- Department of Computer Science, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Mahdi Khalil
- LASIRE, CNRS UMR 8516, University of Lille, C4 building, Avenue Paul Langevin, Villeneuve d'Ascq, F-59655, France
| | - Marc Bria
- Michle-Eugène Chevreul Institute, FR 2638, Avenue Paul Langevin, Villeneuve d'Ascq, F-59655, France
| | - Christine Saint-Pierre
- Université Grenoble Alpes, CEA, CNRS, UMR 5819 SyMMES-CREAB, Avenue des Martyrs, Grenoble, F-38000, France
| | - Maylis Orio
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, UMR CNRS 7313, Marseille, 13397, France
| | - Didier Gasparutto
- Université Grenoble Alpes, CEA, CNRS, UMR 5819 SyMMES-CREAB, Avenue des Martyrs, Grenoble, F-38000, France
| | - Giuseppe Sicoli
- LASIRE, CNRS UMR 8516, University of Lille, C4 building, Avenue Paul Langevin, Villeneuve d'Ascq, F-59655, France
| |
Collapse
|
2
|
Han Q, Zhang X, Jia Y, Guo S, Zhu J, Luo S, Na N, Ouyang J. Synthesis and Characteristics of Self‐Assembled Multifunctional Ln
3+
‐DNA Hybrid Coordination Polymers. Chemistry 2022; 28:e202200281. [DOI: 10.1002/chem.202200281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Qingzhi Han
- Key Laboratory of Theoretical and Computational Photochemistry College of Chemistry Beijing Normal University Beijing 100875 China
| | - Xinlian Zhang
- Key Laboratory of Theoretical and Computational Photochemistry College of Chemistry Beijing Normal University Beijing 100875 China
| | - Yijing Jia
- Key Laboratory of Theoretical and Computational Photochemistry College of Chemistry Beijing Normal University Beijing 100875 China
| | - Shaoshi Guo
- Key Laboratory of Theoretical and Computational Photochemistry College of Chemistry Beijing Normal University Beijing 100875 China
| | - Jiale Zhu
- Key Laboratory of Theoretical and Computational Photochemistry College of Chemistry Beijing Normal University Beijing 100875 China
| | - Shirui Luo
- Key Laboratory of Theoretical and Computational Photochemistry College of Chemistry Beijing Normal University Beijing 100875 China
| | - Na Na
- Key Laboratory of Theoretical and Computational Photochemistry College of Chemistry Beijing Normal University Beijing 100875 China
| | - Jin Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry College of Chemistry Beijing Normal University Beijing 100875 China
| |
Collapse
|
3
|
Martinon TLM, Pierre VC. Luminescent Lanthanide Probes for Inorganic and Organic Phosphates. Chem Asian J 2022; 17:e202200495. [PMID: 35750633 PMCID: PMC9388549 DOI: 10.1002/asia.202200495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/19/2022] [Indexed: 11/09/2022]
Abstract
Inorganic and organic phosphates-including orthophosphate, nucleotides, and DNA-are some of the most fundamental anions in cellular biology, regulating numerous processes of both medical and environmental significance. The characteristic long lifetimes of emitting lanthanides, including the brighter europium(III) and terbium(III), make them ideally suited for the development of molecular probes for the detection of phosphates directly in complex aqueous media. Moreover, given their high oxophilicity and the exquisite sensitivity of their quantum yields to their hydration number, those luminescent lanthanides are perfect for the detection of phosphates. Herein we discuss the principles that have guided the recent developments of molecular probes selective for inorganic or organic phosphates and how these lanthanide complexes facilitate the study of numerous biological processes.
Collapse
Affiliation(s)
- Thibaut L M Martinon
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Valérie C Pierre
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| |
Collapse
|
4
|
Abstract
This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.
Collapse
Affiliation(s)
- Erin M McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
| | | | | | | | | | | |
Collapse
|
5
|
Huang PJJ, Liu J. In vitro selection and application of lanthanide-dependent DNAzymes. Methods Enzymol 2021; 651:373-396. [PMID: 33888210 DOI: 10.1016/bs.mie.2021.01.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Highly sensitive and selective detection of lanthanide ions is a major analytical challenge. In recent years, the use of DNA for this purpose has been pursued. For such highly charged cations, it is difficult to select their aptamers due to strong nonspecific binding. On the other hand, the use of catalytic DNA or DNAzymes has an advantage to overcome this problem, especially DNAzymes with RNA-cleaving activity. In this chapter, a few such DNAzymes are introduced and methods for in vitro selection of lanthanide-dependent RNA-cleaving DNAzymes are described in detail, including the selection protocols, the DNA sequences used, the characterization of selected DNAzymes and their conversion into biosensors. All of the experiments use only fluorophore-labeled DNA, and radioisotope labeling is completely avoided. The resulting DNAzymes can distinguish lanthanides from non-lanthanide metals, tell the difference between light and heavy lanthanides, and can be used together to discriminate individual lanthanides.
Collapse
Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada.
| |
Collapse
|
6
|
Saran R, Huang Z, Liu J. Phosphorothioate nucleic acids for probing metal binding, biosensing and nanotechnology. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213624] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
7
|
Ullmann S, Hahn P, Mini P, Tuck KL, Kahnt A, Abel B, Gutierrez Suburu ME, Strassert CA, Kersting B. Mixed-ligand lanthanide complexes supported by ditopic bis(imino-methyl)-phenol/calix[4]arene macrocycles: synthesis, structures, and luminescence properties of [Ln 2(L 2)(MeOH) 2] (Ln = La, Eu, Tb, Yb). Dalton Trans 2020; 49:11179-11191. [PMID: 32748924 DOI: 10.1039/d0dt02303e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The lanthanide binding ability of a macrocyclic ligand H6L2 comprising two bis(iminomethyl)phenol and two calix[4]arene units has been studied. H6L2 is a ditopic ligand which provides dinuclear neutral complexes of composition [Ln2(L2)(MeOH)2] (Ln = La (1), Eu (2), Tb (3), and Yb (4)) in very good yield. X-ray crystal structure analyses for 2 and 3 show that (L2)6- accommodates two seven coordinated lanthanide ions in a distorted monocapped trigonal prismatic/octahedral coordination environment. UV-vis spectroscopic titrations performed with La3+, Eu3+, Tb3+ and Yb3+ ions in mixed MeOH/CH2Cl2 solution (I = 0.01 M NBu4PF6) reveal that a 2 : 1 (metal : ligand) stoichiometry is present in solution, with log K11 and K21 values ranging from 5.25 to 6.64. The ratio α = K11/K21 of the stepwise formation constants for the mononuclear (L2 + M = ML2, log K11) and the dinuclear complexes (ML2 + M = M2L2, log K21) was found to be invariably smaller than unity indicating that the binding of the first Ln3+ ion augments the binding of the second Ln3+ ion. The present complexes are less luminescent than other seven-coordinated Eu and Tb complexes, which can be traced to vibrational relaxation of excited EuIII and TbIII states by the coligated MeOH and H2O molecules and/or low-lying ligand-to-metal charge-transfer (LMCT) states.
Collapse
Affiliation(s)
- Steve Ullmann
- Institut für Anorganische Chemie, Universität Leipzig, Johannisallee 29, 04103 Leipzig, Germany.
| | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Ma L, Liu J. Catalytic Nucleic Acids: Biochemistry, Chemical Biology, Biosensors, and Nanotechnology. iScience 2020; 23:100815. [PMID: 31954323 PMCID: PMC6962706 DOI: 10.1016/j.isci.2019.100815] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/11/2019] [Accepted: 12/26/2019] [Indexed: 01/06/2023] Open
Abstract
Since the initial discovery of ribozymes in the early 1980s, catalytic nucleic acids have been used in different areas. Compared with protein enzymes, catalytic nucleic acids are programmable in structure, easy to modify, and more stable especially for DNA. We take a historic view to summarize a few main interdisciplinary areas of research on nucleic acid enzymes that may have broader impacts. Early efforts on ribozymes in the 1980s have broken the notion that all enzymes are proteins, supplying new evidence for the RNA world hypothesis. In 1994, the first catalytic DNA (DNAzyme) was reported. Since 2000, the biosensor applications of DNAzymes have emerged and DNAzymes are particularly useful for detecting metal ions, a challenging task for enzymes and antibodies. Combined with nanotechnology, DNAzymes are key building elements for switches allowing dynamic control of materials assembly. The search for new DNAzymes and ribozymes is facilitated by developments in DNA sequencing and computational algorithms, further broadening our fundamental understanding of their biochemistry.
Collapse
Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
| |
Collapse
|
9
|
Huang PJ, Rochambeau D, Sleiman HF, Liu J. Target Self‐Enhanced Selectivity in Metal‐Specific DNAzymes. Angew Chem Int Ed Engl 2020; 59:3573-3577. [PMID: 31867832 DOI: 10.1002/anie.201915675] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
| | - Donatien Rochambeau
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Juewen Liu
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
| |
Collapse
|
10
|
Huang PJ, Rochambeau D, Sleiman HF, Liu J. Target Self‐Enhanced Selectivity in Metal‐Specific DNAzymes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915675] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
| | - Donatien Rochambeau
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Juewen Liu
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
| |
Collapse
|
11
|
Le Vay K, Salibi E, Song EY, Mutschler H. Nucleic Acid Catalysis under Potential Prebiotic Conditions. Chem Asian J 2020; 15:214-230. [PMID: 31714665 PMCID: PMC7003795 DOI: 10.1002/asia.201901205] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/05/2019] [Indexed: 01/25/2023]
Abstract
Catalysis by nucleic acids is indispensable for extant cellular life, and it is widely accepted that nucleic acid enzymes were crucial for the emergence of primitive life 3.5-4 billion years ago. However, geochemical conditions on early Earth must have differed greatly from the constant internal milieus of today's cells. In order to explore plausible scenarios for early molecular evolution, it is therefore essential to understand how different physicochemical parameters, such as temperature, pH, and ionic composition, influence nucleic acid catalysis and to explore to what extent nucleic acid enzymes can adapt to non-physiological conditions. In this article, we give an overview of the research on catalysis of nucleic acids, in particular catalytic RNAs (ribozymes) and DNAs (deoxyribozymes), under extreme and/or unusual conditions that may relate to prebiotic environments.
Collapse
Affiliation(s)
- Kristian Le Vay
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Elia Salibi
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Emilie Y. Song
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Hannes Mutschler
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| |
Collapse
|
12
|
He Y, Chen D, Huang PJJ, Zhou Y, Ma L, Xu K, Yang R, Liu J. Misfolding of a DNAzyme for ultrahigh sodium selectivity over potassium. Nucleic Acids Res 2019; 46:10262-10271. [PMID: 30215808 PMCID: PMC6212836 DOI: 10.1093/nar/gky807] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/08/2018] [Indexed: 02/07/2023] Open
Abstract
Herein, the excellent Na+ selectivity of a few RNA-cleaving DNAzymes was exploited, where Na+ can be around 3000-fold more effective than K+ for promoting catalysis. By using a double mutant based on the Ce13d DNAzyme, and by lowering the temperature, increased 2-aminopurine (2AP) fluorescence was observed with addition of both Na+ and K+. The fluorescence increase was similar for these two metals at below 10 mM, after which K+ took a different pathway. Since 2AP probes its local base stacking environment, K+ can be considered to induce misfolding. Binding of both Na+ and K+ was specific, since single base mutations could fully inhibit 2AP fluorescence for both metals. The binding thermodynamics was measured by temperature-dependent experiments revealing enthalpy-driven binding for both metals and less coordination sites compared to G-quadruplex DNA. Cleavage activity assays indicated a moderate cleavage activity with 10 mM K+, while further increase of K+ inhibited the activity, also supporting its misfolding of the DNAzyme. For comparison, a G-quadruplex DNA was also studied using the same system, where Na+ and K+ led to the same final state with only around 8-fold difference in Kd. This study provides interesting insights into strategies for discriminating Na+ and K+.
Collapse
Affiliation(s)
- Yanping He
- State Key Laboratory of Precision Measurement Technology and Instruments, University of Tianjin, Tianjin 300072, China.,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Da Chen
- State Key Laboratory of Precision Measurement Technology and Instruments, University of Tianjin, Tianjin 300072, China
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Yibo Zhou
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Kexin Xu
- State Key Laboratory of Precision Measurement Technology and Instruments, University of Tianjin, Tianjin 300072, China
| | - Ronghua Yang
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| |
Collapse
|
13
|
He Y, Lopez A, Zhang Z, Chen D, Yang R, Liu J. Nucleotide and DNA coordinated lanthanides: From fundamentals to applications. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.02.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
14
|
Roy B, Roy TS, Rahaman SA, Das K, Bandyopadhyay S. A Minimalist Approach for Distinguishing Individual Lanthanide Ions Using Multivariate Pattern Analysis. ACS Sens 2018; 3:2166-2174. [PMID: 30239190 DOI: 10.1021/acssensors.8b00767] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To discriminate among the 14 trivalent lanthanide ions, curcumin, a naturally occurring, nontoxic, off-the-shelf, commercially available compound containing a single fluorophore, was chosen as a probe in the water media at pH 6.8 and pH 8.2. By measuring the emission and absorption spectra of the probe, under the different pH conditions, and by performing linear discriminant analysis on the data, 14 Ln3+ ions were discriminated. Additionally, an easy tool for the nonspecialists was developed with easily available household substances, using a smartphone app, which added an extra advantage to this single probe. This probe possesses advantageous features in terms of low-cost and instant on-site detection of the lanthanide ions.
Collapse
Affiliation(s)
- Biswajit Roy
- Department of Chemical Sciences and ‡Department of Mathematical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, Nadia 741246, India
| | | | - Sk. Atiur Rahaman
- Department of Chemical Sciences and ‡Department of Mathematical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, Nadia 741246, India
| | | | - Subhajit Bandyopadhyay
- Department of Chemical Sciences and ‡Department of Mathematical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, Nadia 741246, India
| |
Collapse
|
15
|
Ma L, Liu J. An in Vitro-Selected DNAzyme Mutant Highly Specific for Na + under Slightly Acidic Conditions. Chembiochem 2018; 20:537-542. [PMID: 29989277 DOI: 10.1002/cbic.201800322] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Indexed: 12/19/2022]
Abstract
Sodium is one of the most common metal ions in biology; however, DNA-based sodium probes have only been reported recently. A Na+ -specific RNA-cleaving DNAzyme named NaA43 is active with Na+ alone. In this work, we were using Co(NH3 )6 3+ as the intended metal cofactor for in vitro selection, but obtained a mutant of the NaA43 DNAzyme. The mutant was named NaH1, and differs from NaA43 by only two nucleotides. NaA43 has an optimal pH of 7.0, whereas the optimal pH for NaH1 is 6.0. This difference might be due to our selection having been performed at pH 6.0. NaH1 also displays an excellent selectivity for sodium relative to other competing monovalent ions, as well as a fast catalytic rate of (0.11±0.01) min-1 with 50 mm Na+ . At low Na+ concentrations, the selected DNAzyme exhibited a higher cleavage rate than NaA43 and thus a tighter apparent Kd of (12.0±1.6) mm Na+ . Furthermore, the NaH1 DNAzyme was engineered into a fluorescent Na+ biosensor by attaching a fluorophore/quencher pair to the DNAzyme with a detection limit of 223 μm Na+ . Preliminary work on detection of Na+ in serum was demonstrated as well. This study provides a useful mutant that works in a slightly acidic environment, which might be useful for sensing Na+ in acidic in vivo environments.
Collapse
Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| |
Collapse
|
16
|
Augspurger EE, Rana M, Yigit MV. Chemical and Biological Sensing Using Hybridization Chain Reaction. ACS Sens 2018; 3:878-902. [PMID: 29733201 DOI: 10.1021/acssensors.8b00208] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.
Collapse
|
17
|
Serendipitous Discovery of a Guanine-rich DNA Molecule with a Highly Stable Structure in Urea. Sci Rep 2018; 8:1935. [PMID: 29386529 PMCID: PMC5792554 DOI: 10.1038/s41598-018-20248-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/15/2018] [Indexed: 11/16/2022] Open
Abstract
We have made an accidental discovery of an unusual, single-stranded, guanine-rich DNA molecule that is capable of adopting a folded structure in 7 M urea (7MU) known to denature nucleic acid structures. The folding of this molecule requires Na+ and Mg2+ and the folded structure remains stable when subjected to denaturing (7MU) polyacrylamide gel electrophoresis. Results from sequence mutagenesis, DNA methylation, and circular dichroism spectroscopy studies suggest that this molecule adopts an intramolecular guanine-quadruplex structure with 5 layers of guanine tetrads. Our finding indicates that DNA has the ability to create extremely stable structural folds despite its limited chemical repertoire, making it possible to develop DNA-based systems for unconventional applications.
Collapse
|
18
|
Zhang Z, Morishita K, Lin WTD, Huang PJJ, Liu J. Nucleotide coordination with 14 lanthanides studied by isothermal titration calorimetry. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.06.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
19
|
Abstract
Nucleic acid enzymes require metal ions for activity, and many recently discovered enzymes can use multiple metals, either binding to the scissile phosphate or also playing an allosteric role.
Collapse
Affiliation(s)
- Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences
- Central South University
- Changsha
- China
| | - Juewen Liu
- Department of Chemistry
- Water Institute, and Waterloo Institute for Nanotechnology
- University of Waterloo
- Waterloo
- Canada
| |
Collapse
|
20
|
Zhou W, Saran R, Ding J, Liu J. Two Completely Different Mechanisms for Highly Specific Na + Recognition by DNAzymes. Chembiochem 2017; 18:1828-1835. [PMID: 28658518 DOI: 10.1002/cbic.201700184] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Indexed: 02/06/2023]
Abstract
Our view of the interaction between Na+ and nucleic acids was changed by a few recently discovered Na+ -specific RNA-cleaving DNAzymes. In addition to nonspecific electrostatic interactions, highly specific recognition is also possible. Herein, two such DNAzymes, named EtNa and Ce13d, are compared to elucidate their mechanisms of Na+ binding. Mutation studies indicate that they have different sequence requirements. Phosphorothioate (PS) substitution at the scissile phosphate drops the activity of EtNa 140-fold, and it cannot be rescued by thiophilic Cd2+ or Mn2+ , whereas the activity of PS-modified Ce13d can be rescued. Na+ -dependent activity assays indicate that two Na+ ions bind cooperatively in EtNa, and each Na+ likely interacts with a nonbridging oxygen atom in the scissile phosphate, whereas Ce13d binds only one Na+ ion in a well-defined Na+ aptamer, and this Na+ ion does not directly interact with the scissile phosphate. Both DNAzymes display a normal pH-rate profile, with a single deprotonation reaction required for catalysis. For EtNa, Na+ fails to protect the conserved nucleotides from dimethyl sulfate attack, and no specific Na+ binding is detected by 2-aminopurine fluorescence, both of which are different from those observed for Ce13d. This work suggests that EtNa binds Na+ mainly through its scissile phosphate without significant involvement of the nucleotides in the enzyme strand, whereas Ce13d has a well-defined aptamer for Na+ binding. Therefore, DNA has at least two distinct ways to achieve highly selective Na+ binding.
Collapse
Affiliation(s)
- Wenhu Zhou
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.,Xiangya School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China
| | - Runjhun Saran
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Jinsong Ding
- Xiangya School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China
| | - Juewen Liu
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| |
Collapse
|
21
|
Wu Z, Fan H, Satyavolu NSR, Wang W, Lake R, Jiang JH, Lu Y. Imaging Endogenous Metal Ions in Living Cells Using a DNAzyme-Catalytic Hairpin Assembly Probe. Angew Chem Int Ed Engl 2017; 56:8721-8725. [PMID: 28557357 PMCID: PMC5814595 DOI: 10.1002/anie.201703540] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/03/2017] [Indexed: 12/16/2022]
Abstract
DNAzymes are a promising platform for metal ion detection, and a few DNAzyme-based sensors have been reported to detect metal ions inside cells. However, these methods required an influx of metal ions to increase their concentrations for detection. To address this major issue, the design of a catalytic hairpin assembly (CHA) reaction to amplify the signal from photocaged Na+ -specific DNAzyme to detect endogenous Na+ inside cells is reported. Upon light activation and in the presence of Na+ , the NaA43 DNAzyme cleaves its substrate strand and releases a product strand, which becomes an initiator that trigger the subsequent CHA amplification reaction. This strategy allows detection of endogenous Na+ inside cells, which has been demonstrated by both fluorescent imaging of individual cells and flow cytometry of the whole cell population. This method can be generally applied to detect other endogenous metal ions and thus contribute to deeper understanding of the role of metal ions in biological systems.
Collapse
Affiliation(s)
- Zhenkun Wu
- State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics Institute of Chemical Biology and Nanomedicine and College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Huanhuan Fan
- State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics Institute of Chemical Biology and Nanomedicine and College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | | | - WenJing Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- State Key Laboratory of Analytical Chemistry for Life Science and School of Chemistry & Chemical Engineering, Nanjing University, N, anjing, 210093, P. R. China
| | - Ryan Lake
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Jian-Hui Jiang
- State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics Institute of Chemical Biology and Nanomedicine and College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| |
Collapse
|
22
|
Wu Z, Fan H, Satyavolu NSR, Wang W, Lake R, Jiang JH, Lu Y. Imaging Endogenous Metal Ions in Living Cells Using a DNAzyme-Catalytic Hairpin Assembly Probe. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703540] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zhenkun Wu
- State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics Institute of Chemical Biology and Nanomedicine and College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
- Department of Chemistry; University of Illinois at Urbana-Champaign; Urbana Illinois 61801 USA
| | - Huanhuan Fan
- State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics Institute of Chemical Biology and Nanomedicine and College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
- Department of Chemistry; University of Illinois at Urbana-Champaign; Urbana Illinois 61801 USA
| | | | - WenJing Wang
- Department of Chemistry; University of Illinois at Urbana-Champaign; Urbana Illinois 61801 USA
- State Key Laboratory of Analytical Chemistry for Life Science and School of Chemistry & Chemical Engineering; Nanjing University, N; anjing 210093 P. R. China
| | - Ryan Lake
- Department of Chemistry; University of Illinois at Urbana-Champaign; Urbana Illinois 61801 USA
| | - Jian-Hui Jiang
- State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics Institute of Chemical Biology and Nanomedicine and College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Yi Lu
- Department of Chemistry; University of Illinois at Urbana-Champaign; Urbana Illinois 61801 USA
| |
Collapse
|
23
|
Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
24
|
Wang W, Satyavolu NSR, Wu Z, Zhang JR, Zhu JJ, Lu Y. Near-Infrared Photothermally Activated DNAzyme-Gold Nanoshells for Imaging Metal Ions in Living Cells. Angew Chem Int Ed Engl 2017; 56:6798-6802. [PMID: 28471018 PMCID: PMC5861726 DOI: 10.1002/anie.201701325] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/30/2017] [Indexed: 12/31/2022]
Abstract
DNAzymes have enjoyed success as metal ion sensors outside cells. Their susceptibility to metal-dependent cleavage during delivery into cells has limited their intracellular applications. To overcome this limitation, a near-infrared (NIR) photothermal activation method is presented for controlling DNAzyme activity in living cells. The system consists of a three-stranded DNAzyme precursor (TSDP), the hybridization of which prevents the DNAzyme from being active. After conjugating the TSDP onto gold nanoshells and upon NIR illumination, the increased temperature dehybridizes the TSDP to release the active DNAzyme, which then carries out metal-ion-dependent cleavage, resulting in releasing the cleaved product containing a fluorophore. Using this construct, detecting Zn2+ in living HeLa cells is demonstrated. This method has expanded the DNAzyme versatility for detecting metal ions in biological systems under NIR light that exhibits lower phototoxicity and higher tissue penetration ability.
Collapse
Affiliation(s)
- Wenjing Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- State Key Laboratory of Analytical for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210093, P.R. China
| | | | - Zhenkun Wu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- State Key Laboratory of Chemo/BioSensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, P.R. China
| | - Jian-Rong Zhang
- State Key Laboratory of Analytical for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210093, P.R. China
- School of Chemistry and Life Science, Nanjing University, Jinling College, Nanjing, Jiangsu, 210089, P.R. China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210093, P.R. China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
25
|
Wang W, Satyavolu NSR, Wu Z, Zhang JR, Zhu JJ, Lu Y. Near-Infrared Photothermally Activated DNAzyme-Gold Nanoshells for Imaging Metal Ions in Living Cells. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701325] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wenjing Wang
- Department of Chemistry; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
- State Key Laboratory of Analytical for Life Science; School of Chemistry & Chemical Engineering; Nanjing University; Nanjing Jiangsu 210093 P.R. China
| | | | - Zhenkun Wu
- Department of Chemistry; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
- State Key Laboratory of Chemo/BioSensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha Hunan 410082 P.R. China
| | - Jian-Rong Zhang
- State Key Laboratory of Analytical for Life Science; School of Chemistry & Chemical Engineering; Nanjing University; Nanjing Jiangsu 210093 P.R. China
- School of Chemistry and Life Science; Nanjing University, Jinling College; Nanjing Jiangsu 210089 P.R. China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical for Life Science; School of Chemistry & Chemical Engineering; Nanjing University; Nanjing Jiangsu 210093 P.R. China
| | - Yi Lu
- Department of Chemistry; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| |
Collapse
|
26
|
Saran R, Kleinke K, Zhou W, Yu T, Liu J. A Silver-Specific DNAzyme with a New Silver Aptamer and Salt-Promoted Activity. Biochemistry 2017; 56:1955-1962. [PMID: 28345892 DOI: 10.1021/acs.biochem.6b01131] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Most RNA-cleaving DNAzymes require a metal ion to interact with the scissile phosphate for activity. Therefore, few unmodified DNAzymes work with thiophilic metals because of their low affinity for phosphate. Recently, an Ag+-specific Ag10c DNAzyme was reported via in vitro selection. Herein, Ag10c is characterized to rationalize the role of the strongly thiophilic Ag+. Systematic mutation studies indicate that Ag10c is a highly conserved DNAzyme and its Ag+ binding is unrelated to C-Ag+-C interaction. Its activity is enhanced by increasing Na+ concentrations in buffer. At the same metal concentration, activity decreases in the following order: Li+ > Na+ > K+. Ag10c binds one Na+ ion and two Ag+ ions for catalysis. The pH-rate profile has a slope of ∼1, indicating a single deprotonation step. Phosphorothioate substitution at the scissile phosphate suggests that Na+ interacts with the pro-Rp oxygen of the phosphate, and dimethyl sulfate footprinting indicates that the DNAzyme loop is a silver aptamer binding two Ag+ ions. Therefore, Ag+ exerts its function allosterically, while the scissile phosphate interacts with Na+, Li+, Na+, or Mg2+. This work suggests the possibility of isolating thiophilic metal aptamers based on DNAzyme selection, and it also demonstrates a new Ag+ aptamer.
Collapse
Affiliation(s)
- Runjhun Saran
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Kimberly Kleinke
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Wenhu Zhou
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Tianmeng Yu
- 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
| |
Collapse
|
27
|
Abstract
DNAzymes are catalytically active DNA molecules that are obtained via in vitro selection. RNA-cleaving DNAzymes have attracted significant attention for both therapeutic and diagnostic applications due to their excellent programmability, stability, and activity. They can be designed to cleave a specific mRNA to down-regulate gene expression. At the same time, DNAzymes can sense a broad range of analytes. By combining these two functions, theranostic DNAzymes are obtained. This review summarizes the progress of DNAzyme for theranostic applications. First, in vitro selection of DNAzymes is briefly introduced, and some representative DNAzymes related to biological applications are summarized. Then, the applications of DNAzyme for RNA cleaving are reviewed. DNAzymes have been used to cleave RNA for treating various diseases, such as viral infection, cancer, inflammation and atherosclerosis. Several formulations have entered clinical trials. Next, the use of DNAzymes for detecting metal ions, small molecules and nucleic acids related to disease diagnosis is summarized. Finally, the theranostic applications of DNAzyme are reviewed. The challenges to be addressed include poor DNAzyme activity under biological conditions, mRNA accessibility, delivery, and quantification of gene expression. Possible solutions to overcome these challenges are discussed, and future directions of the field are speculated.
Collapse
|
28
|
Zhou W, Saran R, Huang PJJ, Ding J, Liu J. An Exceptionally Selective DNA Cooperatively Binding Two Ca2+Ions. Chembiochem 2017; 18:518-522. [PMID: 28087991 DOI: 10.1002/cbic.201600708] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Wenhu Zhou
- School of Pharmaceutical Sciences; Central South University; 172 Tongzipo Road Changsha Hunan 410013 China
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo ON N2L 3G1 Canada
| | - Runjhun Saran
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo ON N2L 3G1 Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo ON N2L 3G1 Canada
| | - Jinsong Ding
- School of Pharmaceutical Sciences; Central South University; 172 Tongzipo Road Changsha Hunan 410013 China
| | - Juewen Liu
- School of Pharmaceutical Sciences; Central South University; 172 Tongzipo Road Changsha Hunan 410013 China
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo ON N2L 3G1 Canada
| |
Collapse
|
29
|
Zhou W, Ding J, Liu J. A highly specific sodium aptamer probed by 2-aminopurine for robust Na+ sensing. Nucleic Acids Res 2016; 44:10377-10385. [PMID: 27655630 PMCID: PMC5137442 DOI: 10.1093/nar/gkw845] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/10/2016] [Accepted: 09/13/2016] [Indexed: 12/12/2022] Open
Abstract
Sodium is one of the most abundant metals in the environment and in biology, playing critical ecological and physiological roles. Na+ is also the most common buffer salt for nucleic acids research, while its specific interaction with DNA has yet to be fully studied. Herein, we probe a highly selective and robust Na+ aptamer using 2-aminopurine (2AP), a fluorescent adenine analog. This aptamer has two DNA strands derived from the Ce13d DNAzyme. By introducing a 2AP at the cleavage site of the substrate strand, Na+ induces ∼40% fluorescence increase. The signaling is improved by a series of rational mutations, reaching >600% with the C10A20 double mutant. This fluorescence enhancement suggests relaxed base stacking near the 2AP label upon Na+ binding. By replacing a non-conserved adenine in the enzyme strand by 2AP, Na+-dependent fluorescence quenching is observed, suggesting that the enzyme loop folds into a more compact structure upon Na+ binding. The fluorescence changes allow for Na+ detection. With an optimized sequence, a detection limit of 0.4 mM Na+ is achieved, reaching saturated signal in less than 10 s. The sensor response is insensitive to ionic strength, which is critical for Na+ detection.
Collapse
Affiliation(s)
- Wenhu Zhou
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China.,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jinsong Ding
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Juewen Liu
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China .,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
30
|
Huang PJJ, Vazin M, Lin JJ, Pautler R, Liu J. Distinction of Individual Lanthanide Ions with a DNAzyme Beacon Array. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00239] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Po-Jung Jimmy Huang
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Mahsa Vazin
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Jennifer J. Lin
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Rachel Pautler
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Juewen Liu
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| |
Collapse
|