1
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Fang Z, Pazienza LT, Zhang J, Tam CP, Szostak JW. Catalytic Metal Ion-Substrate Coordination during Nonenzymatic RNA Primer Extension. J Am Chem Soc 2024; 146:10632-10639. [PMID: 38579124 PMCID: PMC11027144 DOI: 10.1021/jacs.4c00323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/22/2024] [Accepted: 03/22/2024] [Indexed: 04/07/2024]
Abstract
Nonenzymatic template-directed RNA copying requires catalysis by divalent metal ions. The primer extension reaction involves the attack of the primer 3'-hydroxyl on the adjacent phosphate of a 5'-5'-imidazolium-bridged dinucleotide substrate. However, the nature of the interaction of the catalytic metal ion with the reaction center remains unclear. To explore the coordination of the catalytic metal ion with the imidazolium-bridged dinucleotide substrate, we examined catalysis by oxophilic and thiophilic metal ions with both diastereomers of phosphorothioate-modified substrates. We show that Mg2+ and Cd2+ exhibit opposite preferences for the two phosphorothioate substrate diastereomers, indicating a stereospecific interaction of the divalent cation with one of the nonbridging phosphorus substituents. High-resolution X-ray crystal structures of the products of primer extension with phosphorothioate substrates reveal the absolute stereochemistry of this interaction and indicate that catalysis by Mg2+ involves inner-sphere coordination with the nonbridging phosphate oxygen in the pro-SP position, while thiophilic cadmium ions interact with sulfur in the same position, as in one of the two phosphorothioate substrates. These results collectively suggest that during nonenzymatic RNA primer extension with a 5'-5'-imidazolium-bridged dinucleotide substrate the interaction of the catalytic Mg2+ ion with the pro-SP oxygen of the reactive phosphate plays a crucial role in the metal-catalyzed SN2(P) reaction.
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Affiliation(s)
- Ziyuan Fang
- Department
of Chemistry, Howard Hughes Medical Institute,
The University of Chicago, Chicago, Illinois 60637, United States
| | - Lydia T. Pazienza
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Howard Hughes Medical Institute,
Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jian Zhang
- Department
of Chemistry, Howard Hughes Medical Institute,
The University of Chicago, Chicago, Illinois 60637, United States
| | - Chun Pong Tam
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Howard Hughes Medical Institute,
Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jack W. Szostak
- Department
of Chemistry, Howard Hughes Medical Institute,
The University of Chicago, Chicago, Illinois 60637, United States
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2
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Saran R, Piccolo KA, He Y, Kang Y, Huang PJJ, Wei C, Chen D, Dieckmann T, Liu J. Thioflavin T fluorescence and NMR spectroscopy suggesting a non-G-quadruplex structure for a sodium binding aptamer embedded in DNAzymes. CAN J CHEM 2021. [DOI: 10.1139/cjc-2021-0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Recently, a Na+-binding aptamer was reported to be embedded in a few RNA-cleaving DNAzymes, including NaA43, Ce13d, and NaH1. The Na+ aptamer consists of multiple GG stretches, which is a prerequisite for the formation of G-quadruplex (G4) structures. These DNAzymes require Na+ for activity but show no activity in the presence of K+ or other metal ions. Given that DNA can selectively bind K+ by forming a G4 structure, this work aims to answer whether this Na+ aptamer also uses a G4 to bind Na+. Through comparative ThT fluorescence spectrometry studies, while a control G4 DNA exhibited notable fluorescence enhancement up to 5 mM K+ with a Kd of 0.28 ± 0.06 mM, the Ce13d DNAzyme fluorescence was negligibly perturbed with similar concentrations of K+. Opposed to this, Ce13d displayed specific remarkable fluorescence decrease with low millimolar concentrations of Na+. NMR experiments at two different pH values suggest that Ce13d adopts a significantly different conformation or equilibrium of conformations in the presence of Na+ versus K+ and has a more stable structure in the presence of Na+. Additionally, absence of characteristic G4 peaks in one-dimensional 1H NMR suggest that G4 is not responsible for the Na+ binding. This hypothesis is confirmed by the absence of characteristic peaks in the CD spectra of this sequence. Therefore, we concluded that the aptamer must be selective for Na+ and that it binds Na+ using a structural element that does not contain G4.
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Affiliation(s)
- Runjhun Saran
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Kyle A. Piccolo
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Yanping He
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- State Key Laboratory of Precision Measurement Technology and Instruments, Tianjin University, Tianjin 300072, P.R. China
| | - Yongqiang Kang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Shanxi University, Taiyuan 030006, P.R. China
| | - Po-Jung Jimmy Huang
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Chunying Wei
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Shanxi University, Taiyuan 030006, P.R. China
| | - Da Chen
- State Key Laboratory of Precision Measurement Technology and Instruments, Tianjin University, Tianjin 300072, P.R. China
| | - Thorsten Dieckmann
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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3
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Moon WJ, Huang PJJ, Liu J. Probing Metal-Dependent Phosphate Binding for the Catalysis of the 17E DNAzyme. Biochemistry 2021; 60:1909-1918. [PMID: 34106684 DOI: 10.1021/acs.biochem.1c00091] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The RNA-cleaving 17E DNAzyme exhibits different levels of cleavage activity in the presence of various divalent metal ions, with Pb2+ giving the fastest cleavage. In this study, the metal-phosphate interaction is probed to understand the trend of activity with different metal ions. For the first-row transition metals, the lowest activity shown by Ni2+ correlates with the inhibition by the inorganic phosphate and its water ligand exchange rate, suggesting inner-sphere metal coordination. Cleavage activity with the two stereoisomers of the phosphorothioate-modified substrates, Rp and Sp, indicated that Mg2+, Mn2+, Fe2+, and Co2+ had the highest Sp:Rp activity ratio of >900. Comparatively, the activity was much less affected using the thiophilic metals, including Pb2+, suggesting inner-sphere coordination. The pH-rate profiles showed that Pb2+ was different than the rest of the metal ions in having a smaller slope and a similar fitted apparent pKa and the pKa of metal-bound water. Combining previous reports and our current results, we propose that Pb2+ most likely plays the role of a general acid while the other metal ions are Lewis acid catalysts interacting with the scissile phosphate.
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Affiliation(s)
- Woohyun J Moon
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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4
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Huang PJJ, Liu J. In vitro selection and application of lanthanide-dependent DNAzymes. Methods Enzymol 2021; 651:373-396. [PMID: 33888210 DOI: 10.1016/bs.mie.2021.01.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Highly sensitive and selective detection of lanthanide ions is a major analytical challenge. In recent years, the use of DNA for this purpose has been pursued. For such highly charged cations, it is difficult to select their aptamers due to strong nonspecific binding. On the other hand, the use of catalytic DNA or DNAzymes has an advantage to overcome this problem, especially DNAzymes with RNA-cleaving activity. In this chapter, a few such DNAzymes are introduced and methods for in vitro selection of lanthanide-dependent RNA-cleaving DNAzymes are described in detail, including the selection protocols, the DNA sequences used, the characterization of selected DNAzymes and their conversion into biosensors. All of the experiments use only fluorophore-labeled DNA, and radioisotope labeling is completely avoided. The resulting DNAzymes can distinguish lanthanides from non-lanthanide metals, tell the difference between light and heavy lanthanides, and can be used together to discriminate individual lanthanides.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada.
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5
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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]
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6
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Huang PJ, Liu J. In vitro Selection of Chemically Modified DNAzymes. ChemistryOpen 2020; 9:1046-1059. [PMID: 33101831 PMCID: PMC7570446 DOI: 10.1002/open.202000134] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
DNAzymes are in vitro selected DNA oligonucleotides with catalytic activities. RNA cleavage is one of the most extensively studied DNAzyme reactions. To expand the chemical functionality of DNA, various chemical modifications have been made during and after selection. In this review, we summarize examples of RNA-cleaving DNAzymes and focus on those modifications introduced during in vitro selection. By incorporating various modified nucleotides via polymerase chain reaction (PCR) or primer extension, a few DNAzymes were obtained that can be specifically activated by metal ions such as Zn2+ and Hg2+. In addition, some modifications were introduced to mimic RNase A that can cleave RNA substrates in the absence of divalent metal ions. In addition, single modifications at the fixed regions of DNA libraries, especially at the cleavage junctions, have been tested, and examples of DNAzymes with phosphorothioate and histidine-glycine modified tertiary amine were successfully obtained specific for Cu2+, Cd2+, Zn2+, and Ni2+. Labeling fluorophore/quencher pair right next to the cleavage junction was also used to obtain signaling DNAzymes for detecting various metal ions and cells. Furthermore, we reviewed work on the cleavage of 2'-5' linked RNA and L-RNA substrates. Finally, applications of these modified DNAzymes as biosensors, RNases, and biochemical probes are briefly described with a few future research opportunities outlined at the end.
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Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of WaterlooWaterlooOntario, N2L 3G1Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of WaterlooWaterlooOntario, N2L 3G1Canada
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7
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Li Y, Liu J. Highly Specific Recognition of Guanosine Using Engineered Base-Excised Aptamers. Chemistry 2020; 26:13644-13651. [PMID: 32700427 DOI: 10.1002/chem.202001835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/20/2020] [Indexed: 12/18/2022]
Abstract
Purines and their derivatives are highly important molecules in biology for nucleic acid synthesis, energy storage, and signaling. Although many DNA aptamers have been obtained for binding adenine derivatives such as adenosine, adenosine monophosphate, and adenosine triphosphate, success for the specific binding of guanosine has been limited. Instead of performing new aptamer selections, we report herein a base-excision strategy to engineer existing aptamers to bind guanosine. Both a Na+ -binding aptamer and the classical adenosine aptamer have been manipulated as base-excising scaffolds. A total of seven guanosine aptamers were designed, of which the G16-deleted Na+ aptamer showed the highest bindng specificity and affinity for guanosine with an apparent dissociation constant of 0.78 mm. Single monophosphate difference in the target molecule was also recognizable. The generality of both the aptamer scaffold and excised site were systematically studied. Overall, this work provides a few guanosine binding aptamers by using a non-SELEX method. It also provides deeper insights into the engineering of aptamers for molecular recognition.
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Affiliation(s)
- Yuqing Li
- 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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8
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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.
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Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
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9
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Le Vay K, Salibi E, Song EY, Mutschler H. Nucleic Acid Catalysis under Potential Prebiotic Conditions. Chem Asian J 2020; 15:214-230. [PMID: 31714665 PMCID: PMC7003795 DOI: 10.1002/asia.201901205] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/05/2019] [Indexed: 01/25/2023]
Abstract
Catalysis by nucleic acids is indispensable for extant cellular life, and it is widely accepted that nucleic acid enzymes were crucial for the emergence of primitive life 3.5-4 billion years ago. However, geochemical conditions on early Earth must have differed greatly from the constant internal milieus of today's cells. In order to explore plausible scenarios for early molecular evolution, it is therefore essential to understand how different physicochemical parameters, such as temperature, pH, and ionic composition, influence nucleic acid catalysis and to explore to what extent nucleic acid enzymes can adapt to non-physiological conditions. In this article, we give an overview of the research on catalysis of nucleic acids, in particular catalytic RNAs (ribozymes) and DNAs (deoxyribozymes), under extreme and/or unusual conditions that may relate to prebiotic environments.
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Affiliation(s)
- Kristian Le Vay
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Elia Salibi
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Emilie Y. Song
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Hannes Mutschler
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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10
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Ma L, Kartik S, Liu B, Liu J. From general base to general acid catalysis in a sodium-specific DNAzyme by a guanine-to-adenine mutation. Nucleic Acids Res 2019; 47:8154-8162. [PMID: 31276580 PMCID: PMC6736077 DOI: 10.1093/nar/gkz578] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/20/2019] [Accepted: 06/26/2019] [Indexed: 02/07/2023] Open
Abstract
Recently, a few Na+-specific RNA-cleaving DNAzymes were reported, where nucleobases are likely to play critical roles in catalysis. The NaA43 and NaH1 DNAzymes share the same 16-nt Na+-binding motif, but differ in one or two nucleotides in a small catalytic loop. Nevertheless, they display an opposite pH-dependency, implicating distinct catalytic mechanisms. In this work, rational mutation studies locate a catalytic adenine residue, A22, in NaH1, while previous studies found a guanine (G23) to be important for the catalysis of NaA43. Mutation with pKa-perturbed analogs, such as 2-aminopurine (∼3.8), 2,6-diaminopurine (∼5.6) and hypoxanthine (∼8.7) affected the overall reaction rate. Therefore, we propose that the N1 position of G23 (pKa ∼6.6) in NaA43 functions as a general base, while that of A22 (pKa ∼6.3) in NaH1 as a general acid. Further experiments with base analogs and a phosphorothioate-modified substrate suggest that the exocyclic amine in A22 and both of the non-bridging oxygens at the scissile phosphate are important for catalysis for NaH1. This is an interesting example where single point mutations can change the mechanism of cleavage from general base to general acid, and it can also explain this Na+-dependent DNAzyme scaffold being sensitive to a broad range of metal ions and molecules.
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Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Sanjana Kartik
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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11
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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+.
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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
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12
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He Y, Lopez A, Zhang Z, Chen D, Yang R, Liu J. Nucleotide and DNA coordinated lanthanides: From fundamentals to applications. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.02.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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13
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Nie F, Ga L, Ai J. One-Pot Synthesis of Nucleoside-Templated Fluorescent Silver Nanoparticles and Gold Nanoparticles. ACS OMEGA 2019; 4:7643-7649. [PMID: 31459856 PMCID: PMC6649123 DOI: 10.1021/acsomega.9b00701] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/12/2019] [Indexed: 06/10/2023]
Abstract
In this study, a simple one-pot method was proposed to synthesize water-soluble nucleoside-templated fluorescent silver nanoparticles (Ag NPs) and gold nanoparticles (Au NPs). The nucleoside-templated fluorescent Ag NPs and Au NPs were further characterized by transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and fluorescence spectroscopy (FLS). The effects of the molar ratio of reactants, reaction environment, and nucleotides on the synthesis of Ag NPs and Au NPs were also discussed. The results showed that nucleoside and ascorbic acid acted as a stabilizer and reductant, respectively, in the synthesis of Ag NPs and Au NPs, while citrate buffer acted as both a pH regulator and reductant. The synthesized nucleoside-templated fluorescent Ag NPs and Au NPs have good fluorescence stability and easy water solubility. In this study, a simple one-pot method was proposed to synthesize water-soluble nucleoside-templated fluorescent silver nanoparticles (Ag NPs) and gold nanoparticles (Au NPs).
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Affiliation(s)
- Furong Nie
- College
of Chemistry and Enviromental Science and Inner Mongolia Key Laboratory for
Physics and Chemistry of Functional Materials, Inner Mongolia Normal University, 81 Zhaowudalu, Hohhot 010022, China
| | - Lu Ga
- College
of Pharmacy, Inner Mongolia Medical University, Jinchuankaifaqu, Hohhot 010110, People’s Republic of China
| | - Jun Ai
- College
of Chemistry and Enviromental Science and Inner Mongolia Key Laboratory for
Physics and Chemistry of Functional Materials, Inner Mongolia Normal University, 81 Zhaowudalu, Hohhot 010022, China
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14
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He Y, Zhou Y, Chen D, Liu J. Global Folding of a Na
+
‐Specific DNAzyme Studied by FRET. Chembiochem 2018; 20:385-393. [DOI: 10.1002/cbic.201800548] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Yanping He
- State Key Laboratory of Precision Measurement Technology and InstrumentsUniversity of Tianjin Tianjin 300072 P.R. China
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of Waterloo Waterloo Ontario N2L 3G1 Canada
| | - Yibo Zhou
- School of Chemistry and Biological EngineeringChangsha University of Science and Technology Changsha 410114 P.R. China
| | - Da Chen
- State Key Laboratory of Precision Measurement Technology and InstrumentsUniversity of Tianjin Tianjin 300072 P.R. China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of Waterloo Waterloo Ontario N2L 3G1 Canada
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15
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Jimmy Huang PJ, Moon WJ, Liu J. Instantaneous Iodine-Assisted DNAzyme Cleavage of Phosphorothioate RNA. Biochemistry 2018; 58:422-429. [PMID: 30272443 DOI: 10.1021/acs.biochem.8b00900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Metal ions play a critical role in the RNA-cleavage reaction by interacting with the scissile phosphate and stabilizing the highly negatively charged transition state. Many metal-dependent DNAzymes have been selected for RNA cleavage. Herein, we report that the Ce13d DNAzyme can use nonmetallic iodine (I2) to cleave a phosphorothioate (PS)-modified substrate. The cleavage yield exceeded 60% for both the Rp and Sp stereoisomers in 10 s, while the yield without the enzyme strand was only ∼10%. The Ce13d cleavage with I2 also required Na+, consistent with the property of Ce13d and confirming the similar role of I2 as a metal ion. Ce13d had the highest yield among eight tested DNAzymes, with the second highest DNAzyme showing only 20% cleavage. The incomplete cleavage was due to competition from desulfurization and isomerization reactions. This DNAzyme was engineered for fluorescence-based I2 detection. With EDTA for masking metal ions, I2 was selectively detected down to 4.7 nM. Oxidation of I- with Fe3+ produced I2 in situ, allowing detection of Fe3+ down to 78 nM. By harnessing nonelectrostatic interactions, such as the I2/sulfur interaction observed here, more nonmetal species might be discovered to assist DNAzyme-based RNA cleavage.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Woohyun J Moon
- 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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16
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Ma L, Liu J. An in Vitro-Selected DNAzyme Mutant Highly Specific for Na + under Slightly Acidic Conditions. Chembiochem 2018; 20:537-542. [PMID: 29989277 DOI: 10.1002/cbic.201800322] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Indexed: 12/19/2022]
Abstract
Sodium is one of the most common metal ions in biology; however, DNA-based sodium probes have only been reported recently. A Na+ -specific RNA-cleaving DNAzyme named NaA43 is active with Na+ alone. In this work, we were using Co(NH3 )6 3+ as the intended metal cofactor for in vitro selection, but obtained a mutant of the NaA43 DNAzyme. The mutant was named NaH1, and differs from NaA43 by only two nucleotides. NaA43 has an optimal pH of 7.0, whereas the optimal pH for NaH1 is 6.0. This difference might be due to our selection having been performed at pH 6.0. NaH1 also displays an excellent selectivity for sodium relative to other competing monovalent ions, as well as a fast catalytic rate of (0.11±0.01) min-1 with 50 mm Na+ . At low Na+ concentrations, the selected DNAzyme exhibited a higher cleavage rate than NaA43 and thus a tighter apparent Kd of (12.0±1.6) mm Na+ . Furthermore, the NaH1 DNAzyme was engineered into a fluorescent Na+ biosensor by attaching a fluorophore/quencher pair to the DNAzyme with a detection limit of 223 μm Na+ . Preliminary work on detection of Na+ in serum was demonstrated as well. This study provides a useful mutant that works in a slightly acidic environment, which might be useful for sensing Na+ in acidic in vivo environments.
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Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
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17
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Affiliation(s)
- Tianmeng Yu
- Department of Chemistry and Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
| | - 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
| | - Juewen Liu
- Department of Chemistry and Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
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18
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Zhou W, Ding J, Liu J. Splitting a DNAzyme enables a Na +-dependent FRET signal from the embedded aptamer. Org Biomol Chem 2018; 15:6959-6966. [PMID: 28792040 DOI: 10.1039/c7ob01709j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Recently, a few Na+-specific RNA-cleaving DNAzymes have been reported, and a Na+ aptamer was identified from the NaA43 and Ce13d DNAzymes. These DNAzymes and the embedded aptamer have been used for Na+ detection. In this work, we studied the Na+-dependent folding of the Ce13d DNAzyme using fluorescence resonance energy transfer (FRET). When a FRET donor and an acceptor were respectively labeled at the ends of the DNAzyme, Na+ failed to induce an obvious end-to-end distance change, suggesting a rigid global structure. To relax this rigidity, the Ce13d DNAzyme was systematically split at various sites on both the enzyme and the substrate strands. The Na+ binding activity of the split structures was characterized by 2-aminopurine fluorescence, enzymatic activity, Tb3+-sensitized luminescence, and DMS footprinting. Among the various constructs, the only one that retained Na+ binding was the split at the cleavage site, and this construct was further labeled with two dyes near the split site. This FRET result showed Na+-dependent folding with a Kd of 26 mM Na+. This study provides important structural information related to Na+ binding to this new aptamer, which might also be useful for future work in biosensor design.
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Affiliation(s)
- Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
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19
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Zhang Z, Morishita K, Lin WTD, Huang PJJ, Liu J. Nucleotide coordination with 14 lanthanides studied by isothermal titration calorimetry. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.06.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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20
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Abstract
Nucleic acid enzymes require metal ions for activity, and many recently discovered enzymes can use multiple metals, either binding to the scissile phosphate or also playing an allosteric role.
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Affiliation(s)
- Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences
- Central South University
- Changsha
- China
| | - Juewen Liu
- Department of Chemistry
- Water Institute, and Waterloo Institute for Nanotechnology
- University of Waterloo
- Waterloo
- Canada
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21
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Ma H, Li W, Zhou W, Liu J. Site-Selective Labeling of Chromium(III) as a Quencher on DNA for Molecular Beacons. Chempluschem 2017; 82:1224-1230. [DOI: 10.1002/cplu.201700361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Huan Ma
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Wang Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
- Department of Chemistry; Water Institute and Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo ON N2L 3G1 Canada
| | - Wenhu Zhou
- Department of Chemistry; Water Institute and Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo ON N2L 3G1 Canada
- Xiangya School of Pharmaceutical Sciences; Central South University; Changsha Hunan 410013 P. R. China
| | - Juewen Liu
- Department of Chemistry; Water Institute and Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo ON N2L 3G1 Canada
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22
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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.
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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
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Folding of the silver aptamer in a DNAzyme probed by 2-aminopurine fluorescence. Biochimie 2017; 145:145-150. [PMID: 28711684 DOI: 10.1016/j.biochi.2017.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 07/04/2017] [Indexed: 12/28/2022]
Abstract
The RNA-cleaving Ag10c DNAzyme was recently isolated via in vitro selection and it can bind two Ag+ ions for activity. The Ag10c contains a well-defined Ag+ binding aptamer as indicated by DMS footprinting. Since aptamer binding is often accompanied with conformational changes, we herein used 2-aminopurine (2AP) to probe its folding in the presence of Ag+. The Ag10c was respectively labeled with 2AP at three different positions, both in the substrate strand and in the enzyme strand, one at a time. Ag+-induced folding was observed at the substrate cleavage junction and the A9 position of the enzyme strand, consistent with aptamer binding. The measured Kd at the A9 position was 18 μM Ag+ with a Hill coefficient of 2.17, similar to those obtained from the previous cleavage activity based assays. However, labeling a 2AP at the A2 position inhibited the activity and folding. Compared to other metal ions, Ag+ has a unique sigmoidal folding profile indicative of multiple silver binding cooperatively. This suggests that Ag+ can induce a local folding in the enzyme loop and this folding is important for activity. This study provides important biophysical insights into this new DNAzyme, suggesting the possibility of designing folding-based biosensors for Ag+.
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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25
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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.
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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
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26
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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
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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.
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Affiliation(s)
- Wenhu Zhou
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China.,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jinsong Ding
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Juewen Liu
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China .,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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28
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Zhou W, Yu T, Vazin M, Ding J, Liu J. Cr3+ Binding to DNA Backbone Phosphate and Bases: Slow Ligand Exchange Rates and Metal Hydrolysis. Inorg Chem 2016; 55:8193-200. [DOI: 10.1021/acs.inorgchem.6b01357] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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
| | - Tianmeng Yu
- Department of Chemistry,
Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Mahsa Vazin
- Department of Chemistry,
Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jinsong Ding
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Juewen Liu
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department of Chemistry,
Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Zhou W, Ding J, Liu J. A Selective Na(+) Aptamer Dissected by Sensitized Tb(3+) Luminescence. Chembiochem 2016; 17:1563-70. [PMID: 27238890 DOI: 10.1002/cbic.201600174] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Indexed: 02/04/2023]
Abstract
A previous study of two RNA-cleaving DNAzymes, NaA43 and Ce13d, revealed the possibility of a common Na(+) aptamer motif. Because Na(+) binding to DNA is a fundamental biochemical problem, the interaction between Ce13d and Na(+) was studied in detail by using sensitized Tb(3+) luminescence spectroscopy. Na(+) displaces Tb(3+) from the DNAzyme, and thus quenches the emission from Tb(3+) . The overall requirement for Na(+) binding includes the hairpin and the highly conserved 16-nucleotide loop in the enzyme strand, along with a few unpaired nucleotides in the substrate. Mutation studies indicate good correlation between Na(+) binding and cleavage activity, thus suggesting a critical role of Na(+) binding for the enzyme activity. Ce13d displayed a Kd of ∼20 mm with Na(+) (other monovalent cations: 40-60 mm). The Kd values for other metal ions are mainly due to non-specific competition. With a single nucleotide mutation, the specific Na(+) binding was lost. Another mutant improved Kd to 8 mm with Na(+) . This study has demonstrated a Na(+) aptamer with important biological implications and analytical applications. It has also defined the structural requirements for Na(+) binding and produced an improved mutant.
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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
| | - 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.
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Zhou W, Vazin M, Yu T, Ding J, Liu J. In Vitro Selection of Chromium-Dependent DNAzymes for Sensing Chromium(III) and Chromium(VI). Chemistry 2016; 22:9835-40. [DOI: 10.1002/chem.201601426] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Wenhu Zhou
- School of Pharmaceutical Sciences; Central South University, Changsha; Hunan 410013 P.R. China
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Mahsa Vazin
- 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
| | - Jinsong Ding
- School of Pharmaceutical Sciences; Central South University, Changsha; Hunan 410013 P.R. China
| | - Juewen Liu
- School of Pharmaceutical Sciences; Central South University, Changsha; Hunan 410013 P.R. China
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
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Huang PJJ, Vazin M, Liu J. In Vitro Selection of a DNAzyme Cooperatively Binding Two Lanthanide Ions for RNA Cleavage. Biochemistry 2016; 55:2518-25. [PMID: 27054549 DOI: 10.1021/acs.biochem.6b00132] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Trivalent lanthanide ions (Ln(3+)) were recently employed to select RNA-cleaving DNAzymes, and three new DNAzymes have been reported so far. In this work, dysprosium (Dy(3+)) was used with a library containing 50 random nucleotides. After six rounds of in vitro selection, a new DNAzyme named Dy10a was obtained and characterized. Dy10a has a bulged hairpin structure cleaving a RNA/DNA chimeric substrate. Dy10a is highly active in the presence of the five Ln(3+) ions in the middle of the lanthanide series (Sm(3+), Eu(3+), Gd(3+), Tb(3+), and Dy(3+)), while its activity descends on the two sides. The cleavage rate reaches 0.6 min(-1) at pH 6 with just 200 nM Sm(3+), which is the fastest among all known Ln(3+)-dependent enzymes. Dy10a binds two Ln(3+) ions cooperatively. When a phosphorothioate (PS) modification is introduced at the cleavage junction, the activity decreases by >2500-fold for both the Rp and Sp diastereomers, and thiophilic Cd(2+) cannot rescue the activity. The pH-rate profile has a slope of 0.37 between pH 4.2 and 5.2, and the slope was even lower at higher pH. On the basis of these data, a model of metal binding is proposed. Finally, a catalytic beacon sensor that can detect Ho(3+) down to 1.7 nM is constructed.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
| | - Mahsa Vazin
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
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Zhou W, Ding J, Liu J. An Efficient Lanthanide-Dependent DNAzyme Cleaving 2'-5'-Linked RNA. Chembiochem 2016; 17:890-4. [PMID: 26957420 DOI: 10.1002/cbic.201500690] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Indexed: 12/29/2022]
Abstract
RNA can form two types of linkage. In addition to the predominant 3'-5' linkage, 2'-5'-linked RNA is also important in biology, medicine, and prebiotic studies. Here, in vitro selection was used to isolate a DNAzyme that specifically cleaves 2'-5' RNA by using Ce(3+) as the metal cofactor, but leaves the 3'-5' counterpart intact. This Ce5 DNAzyme requires trivalent light lanthanide ions and shows a rate of 0.16 min(-1) in the presence of 10 μm Ce(3+) ; the activity decreases with heavier lanthanide ions. This is the fastest DNAzyme reported for this reaction, and it might enable applications in chemical biology. As a proof-of-concept, using this DNAzyme, the reactions between phosphorothioate-modified RNA and strongly thiophilic metals (Hg(2+) and Tl(3+) ) were studied as a function of pH.
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Affiliation(s)
- Wenhu Zhou
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, China.,Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Jinsong Ding
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, China
| | - Juewen Liu
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, China. .,Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.
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Affiliation(s)
- Runjhun Saran
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario Canada, N2L 3G1
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario Canada, N2L 3G1
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Huang PJJ, Liu J. An Ultrasensitive Light-up Cu(2+) Biosensor Using a New DNAzyme Cleaving a Phosphorothioate-Modified Substrate. Anal Chem 2016; 88:3341-7. [PMID: 26857405 DOI: 10.1021/acs.analchem.5b04904] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cu(2+) is a very important metal ion in biology, environmental science, and industry. Developing biosensors for Cu(2+) is a key topic in analytical chemistry. DNAzyme-based sensors are highly attractive for their excellent sensitivity, stability, and programmability. In the past decade, a few Cu(2+) biosensors were reported using DNAzymes with DNA cleavage or DNA ligation activity. However, they require unstable ascorbate or imidazole activation. So far, no RNA-cleaving DNAzymes specific for Cu(2+) are known. In this work, a phosphorothioate (PS) RNA-containing library was used for in vitro selection, and a few new Cu(2+)-specific RNA-cleaving DNAzymes were isolated. Among them, a DNAzyme named PSCu10 was studied further. It has only eight nucleotides in the enzyme loop with a cleavage rate of 0.1 min(-1) in the presence of 1 μM Cu(2+) at pH 6.0 (its optimal pH). Between the two diastereomers of the PS RNA chiral center, the R(p) isomer is 37 times more active than the S(p) one. Among the other divalent metal ions, only Hg(2+) can cleave the substrate due to its extremely high thiophilicity. A catalytic beacon sensor was designed with a detection limit of 1.6 nM Cu(2+) and extremely high selectivity. PSCu10 is specific for Cu(2+), and it has no cleavage in the presence of ascorbate, which reduces Cu(2+) to Cu(+).
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
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Zhou W, Zhang Y, Huang PJJ, Ding J, Liu J. A DNAzyme requiring two different metal ions at two distinct sites. Nucleic Acids Res 2015; 44:354-63. [PMID: 26657636 PMCID: PMC4705669 DOI: 10.1093/nar/gkv1346] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 11/18/2015] [Indexed: 12/21/2022] Open
Abstract
Most previously reported RNA-cleaving DNAzymes require only a single divalent metal ion for catalysis. We recently reported a general trivalent lanthanide-dependent DNAzyme named Ce13d. This work shows that Ce13d requires both Na+ and a trivalent lanthanide (e.g. Ce3+), simultaneously. This discovery is facilitated by the sequence similarity between Ce13d and a recently reported Na+-specific DNAzyme, NaA43. The Ce13d cleavage rate linearly depends on the concentration of both metal ions. Sensitized Tb3+ luminescence and DMS footprinting experiments indicate that the guanines in the enzyme loop are important for Na+-binding. The Na+ dissociation constants of Ce13d measured from the cleavage activity assay, Tb3+ luminescence and DMS footprinting are 24.6, 16.3 and 47 mM, respectively. Mutation studies indicate that the role of Ce3+ might be replaced by G23 in NaA43. Ce3+ functions by stabilizing the transition state phosphorane, thus promoting cleavage. G23 competes favorably with low concentration Ce3+ (below 1 μM). The G23-to-hypoxanthine mutation suggests the N1 position of the guanine as a hydrogen bond donor. Together, Ce13d has two distinct metal binding sites, each fulfilling a different role. DNAzymes can be quite sophisticated in utilizing metal ions for catalysis and molecular recognition, similar to protein metalloenzymes.
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Affiliation(s)
- Wenhu Zhou
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yupei Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jinsong Ding
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Juewen Liu
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Identification of the Same Na(+)-Specific DNAzyme Motif from Two In Vitro Selections Under Different Conditions. J Mol Evol 2015; 81:225-34. [PMID: 26577294 DOI: 10.1007/s00239-015-9715-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/03/2015] [Indexed: 12/27/2022]
Abstract
We report an investigation of the functional relationship between two independently selected RNA-cleaving DNAzymes, NaA43, and Ce13, through in vitro selection. The NaA43 DNAzyme was obtained through a combination of gel-based and column-based in vitro selection in the presence of Na(+) and reported to be highly selective for Na(+) over other metal ions. The Ce13 DNAzyme was isolated via a gel-based method in the presence of Ce(4+) and found to be active with trivalent lanthanides, Y(3+) and Pb(2+). Despite completely different activities reported for the two DNAzymes, they share a high level of sequence similarity (~60% sequence identity). In this work, we systematically analyzed the activity of both DNAzymes to elucidate their potential functional relationship. We found that Na(+) is an obligate cofactor of the Ce13 DNAzyme and lanthanides cannot initiate the cleavage reaction in the absence of Na(+). Hence, we conclude that the Ce13 DNAzyme is a variant of the NaA43 DNAzyme that catalyzes reaction in the presence Na(+) and also utilizes lanthanides in a potentially allosteric manner. These results have identified a new DNAzyme motif that is not only remarkably Na(+)-specific, but also allows for design of novel allosteric DNAzymes for different biotechnological applications.
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