1
|
Dutta A, Tapio K, Suma A, Mostafa A, Kanehira Y, Carnevale V, Bussi G, Bald I. Molecular states and spin crossover of hemin studied by DNA origami enabled single-molecule surface-enhanced Raman scattering. NANOSCALE 2022; 14:16467-16478. [PMID: 36305892 PMCID: PMC9671141 DOI: 10.1039/d2nr03664a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
The study of biologically relevant molecules and their interaction with external stimuli on a single molecular scale is of high importance due to the availability of distributed rather than averaged information. Surface enhanced Raman scattering (SERS) provides direct chemical information, but is rather challenging on the single molecule (SM) level, where it is often assumed to require a direct contact of analyte molecules with the metal surface. Here, we detect and investigate the molecular states of single hemin by SM-SERS. A DNA aptamer based G-quadruplex mediated recognition of hemin directs its placement in the SERS hot-spot of a DNA Origami Nanofork Antenna (DONA). The configuration of the DONA structure allows the molecule to be trapped at the plasmonic hot-spot preferentially in no-contact configuration with the metal surface. Owing to high field enhancement at the plasmonic hot spot, the detection of a single folded G-quadruplex becomes possible. For the first time, we present a systematic study by SM-SERS where most hemin molecule adopt a high spin and oxidation state (III) that showed state crossover to low spin upon strong-field-ligand binding. The present study therefore, provides a platform for studying biologically relevant molecules and their properties at SM sensitivity along with demonstrating a conceptual advancement towards successful monitoring of single molecular chemical interaction using DNA aptamers.
Collapse
Affiliation(s)
- Anushree Dutta
- Institute of Chemistry, Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| | - Kosti Tapio
- Institute of Chemistry, Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| | - Antonio Suma
- Dipartimento di Fisica, Università degli Studi di Bari, and INFN, Sezione di Bari, via Amendola 173, 70126 Bari, Italy
| | - Amr Mostafa
- Institute of Chemistry, Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| | - Yuya Kanehira
- Institute of Chemistry, Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122, USA
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, Trieste 34136, Italy
| | - Ilko Bald
- Institute of Chemistry, Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| |
Collapse
|
2
|
Zhang Y, Ma X, Zhang J, Luo F, Wang W, Cui X. Design of a High-Sensitivity Dimeric G-Quadruplex/Hemin DNAzyme Biosensor for Norovirus Detection. Molecules 2021; 26:7352. [PMID: 34885931 PMCID: PMC8659037 DOI: 10.3390/molecules26237352] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes can bind with hemin to form peroxidase-like DNAzymes that are widely used in the design of biosensors. However, the catalytic activity of G-quadruplex/hemin DNAzyme is relatively low compared with natural peroxidase, which hampers its sensitivity and, thus, its application in the detection of nucleic acids. In this study, we developed a high-sensitivity biosensor targeting norovirus nucleic acids through rationally introducing a dimeric G-quadruplex structure into the DNAzyme. In this strategy, two separate molecular beacons each having a G-quadruplex-forming sequence embedded in the stem structure are brought together through hybridization with a target DNA strand, and thus forms a three-way junction architecture and allows a dimeric G-quadruplex to form, which, upon binding with hemin, has a synergistic enhancement of catalytic activities. This provides a high-sensitivity colorimetric readout by the catalyzing H2O2-mediated oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline -6-sulfonic acid) diammonium salt (ABTS). Up to 10 nM of target DNA can be detected through colorimetric observation with the naked eye using our strategy. Hence, our approach provides a non-amplifying, non-labeling, simple-operating, cost-effective colorimetric biosensing method for target nucleic acids, such as norovirus-conserved sequence detection, and highlights the further implication of higher-order multimerized G-quadruplex structures in the design of high-sensitivity biosensors.
Collapse
Affiliation(s)
- Yun Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; (Y.Z.); (X.M.); (J.Z.); (F.L.); (W.W.)
| | - Xinao Ma
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; (Y.Z.); (X.M.); (J.Z.); (F.L.); (W.W.)
| | - Jingtian Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; (Y.Z.); (X.M.); (J.Z.); (F.L.); (W.W.)
| | - Feixian Luo
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; (Y.Z.); (X.M.); (J.Z.); (F.L.); (W.W.)
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China
| | - Wenshu Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; (Y.Z.); (X.M.); (J.Z.); (F.L.); (W.W.)
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China
| | - Xiaojie Cui
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; (Y.Z.); (X.M.); (J.Z.); (F.L.); (W.W.)
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China
| |
Collapse
|
3
|
Chang T, He S, Amini R, Li Y. Functional Nucleic Acids Under Unusual Conditions. Chembiochem 2021; 22:2368-2383. [PMID: 33930229 DOI: 10.1002/cbic.202100087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/24/2021] [Indexed: 02/06/2023]
Abstract
Functional nucleic acids (FNAs), including naturally occurring ribozymes and riboswitches as well as artificially created DNAzymes and aptamers, have been popular molecular toolboxes for diverse applications. Given the high chemical stability of nucleic acids and their ability to fold into diverse sequence-dependent structures, FNAs are suggested to be highly functional under unusual reaction conditions. This review will examine the progress of research on FNAs under conditions of low pH, high temperature, freezing conditions, and the inclusion of organic solvents and denaturants that are known to disrupt nucleic acid structures. The FNA species to be discussed include ribozymes, riboswitches, G-quadruplex-based peroxidase mimicking DNAzymes, RNA-cleaving DNAzymes, and aptamers. Research within this space has not only revealed the hidden talents of FNAs but has also laid important groundwork for pursuing these intriguing functional macromolecules for unique applications.
Collapse
Affiliation(s)
- Tianjun Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.,Department of Biology, Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, Henan, P. R. China
| | - Sisi He
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.,School of Science, Harbin Institute of Technology (Shenzhen), University Town, Shenzhen, 518055, Guangdong, P. R. China
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| |
Collapse
|
4
|
Highly-sensitive and fast detection of human telomeric G-Quadruplex DNA based on a hemin-conjugated fluorescent metal-organic framework platform. Biosens Bioelectron 2021; 178:112999. [PMID: 33493897 DOI: 10.1016/j.bios.2021.112999] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/06/2021] [Accepted: 01/10/2021] [Indexed: 02/02/2023]
Abstract
The formation of G-quadruplex (G4) structures in Human telomeric DNA (H-Telo) has been demonstrated to inhibit the activity of telomerase enzyme that is associated with the proliferation of many cancer cells. Accordingly, G-quadruplex structures have become one of the well-established targets in anticancer therapeutic strategies. And, the development of simple and selective detection platforms for G4 structures has become a significant focus of research in recent years. In this study, a simple "off-on" fluorometric method was developed for the selective detection of picomolar quantities of H-Telo G4 DNA based on a fluorescent cerium-based metal organic framework (Ce-MOF) conjugated with hemin to form the sensing probe, Hemin@Ce-MOF. The solvothermal synthesis of the Ce-MOF took advantage of 5-aminoisophtlalic acid (5AIPA) as the organic bridging ligand, (Ce2(5AIPA)3(DMF)2). Characterization of Ce-MOF and Hemin@Ce-MOF was performed by XRD, XPS, TEM, SEM, BET and FTIR techniques. The detection and quantification of the H-Telo was carried out through the adsorption/incorporation of hemin molecules on the pores and surface of Ce-MOF resulting in the fluorescent quenching of the system followed by the restoration of the fluorescence upon addition of H-Telo probably due to a competition between H-Telo and Ce-MOF to bind to hemin. The impact of the key variables including MOF quantity, hemin concentration and detection time was investigated and optimized. Under the optimized conditions, the developed probe provides a limit of detection (LOD) of 665 pM, linear dynamic range (LDR) of 1.6-39.7 nM and excellent selectivity towards H-Telo. Taken together, these results present a simple, novel and superior platform for the selective detection of H-Telo G4 DNA.
Collapse
|
5
|
Cao Y, Yang L, Ding P, Li W, Pei R. Ligand Selectivity by Inserting GCGC‐Tetrads into G‐Quadruplex Structures. Chemistry 2020; 26:14730-14737. [DOI: 10.1002/chem.202003004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/22/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| | - Luyan Yang
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| | - Pi Ding
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| | - Wenjing Li
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| |
Collapse
|
6
|
Huangxian Ju. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
7
|
Huangxian Ju. Angew Chem Int Ed Engl 2020; 59:14190. [DOI: 10.1002/anie.202002723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
8
|
Cao Y, Li W, Gao T, Ding P, Pei R. One Terminal Guanosine Flip of Intramolecular Parallel G-Quadruplex: Catalytic Enhancement of G-Quadruplex/Hemin DNAzymes. Chemistry 2020; 26:8631-8638. [PMID: 32428287 DOI: 10.1002/chem.202001462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/13/2020] [Indexed: 11/09/2022]
Abstract
Numerous studies have shown compelling evidence that incorporation of an inversion of polarity site (IPS) in G-rich sequences can affect the topological and structural characteristics of G-quadruplexes (G4s). Herein, the influence of IPS on the formation of a previously studied intramolecular parallel G4 of d(G3 TG3 TG3 TG3 ) (TTT) and its stacked higher-order structures is explored. Insertion of 3'-3' or 5'-5' IPS did not change the parallel folding pattern of TTT. However, both the species and position of the IPS in TTT have a significant impact on the G4 stability and end-stacking through the alteration of G4-G4 interfaces properties. The data demonstrate that one base flip in each terminal G-tetrad can stabilize parallel G4s and facilitate intermolecular packing of monomeric G4s. Such modifications can also enhance the fluorescence and enzymatic performances by promoting interactions between parallel G4s with N-methyl mesoporphyrin IX (NMM) and hemin, respectively.
Collapse
Affiliation(s)
- Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionic, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
| | - Wenjing Li
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionic, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
| | - Tian Gao
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionic, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
| | - Pi Ding
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionic, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionic, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
| |
Collapse
|
9
|
Wang Z, Li Y, Wang H, Wan K, Liu Q, Shi X, Ding B. Enzyme Mimic Based on a Self‐Assembled Chitosan/DNA Hybrid Exhibits Superior Activity and Tolerance. Chemistry 2019; 25:12576-12582. [DOI: 10.1002/chem.201902509] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/15/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Zhen‐Gang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
- State Key Laboratory of Organic-Inorganic CompositesBeijing University of Chemical Technology Beijing 100029 China
| | - Yunzhe Li
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
| | - Hui Wang
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
| | - Kaiwei Wan
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
| | - Xinghua Shi
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| |
Collapse
|
10
|
Xia LY, Li MJ, Wang HJ, Yuan R, Chai YQ. A novel "signal on" photoelectrochemical strategy based on dual functional hemin for microRNA assay. Chem Commun (Camb) 2019; 55:9721-9724. [PMID: 31355383 DOI: 10.1039/c9cc04899e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, a novel "signal on" photoelectrochemistry (PEC) biosensor was constructed with dual-functional hemin as a signal quencher and electronic mediator for ultrasensitive target microRNA-141 assay with the assistance of T7 exonuclease (Exo)-initiated target amplification technology.
Collapse
Affiliation(s)
- Ling-Ying Xia
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Meng-Jie Li
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Hai-Jun Wang
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Ruo Yuan
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Ya-Qin Chai
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| |
Collapse
|
11
|
Feng G, Luo X, Lu X, Xie S, Deng L, Kang W, He F, Zhang J, Lei C, Lin B, Huang Y, Nie Z, Yao S. Engineering of Nucleic Acids and Synthetic Cofactors as Holo Sensors for Probing Signaling Molecules in the Cellular Membrane Microenvironment. Angew Chem Int Ed Engl 2019; 58:6590-6594. [DOI: 10.1002/anie.201901320] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Guangfu Feng
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Xingyu Luo
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Xu Lu
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Shiyi Xie
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Lu Deng
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Wenyuan Kang
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Fang He
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Jiaheng Zhang
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Bin Lin
- Pharmaceutical Engineering & Key Laboratory of Structure-Based Drug Design & DiscoveryMinistry of EducationShenyang Pharmaceutical University Shenyang 110016 P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| |
Collapse
|
12
|
Feng G, Luo X, Lu X, Xie S, Deng L, Kang W, He F, Zhang J, Lei C, Lin B, Huang Y, Nie Z, Yao S. Engineering of Nucleic Acids and Synthetic Cofactors as Holo Sensors for Probing Signaling Molecules in the Cellular Membrane Microenvironment. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901320] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Guangfu Feng
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Xingyu Luo
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Xu Lu
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Shiyi Xie
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Lu Deng
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Wenyuan Kang
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Fang He
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Jiaheng Zhang
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Bin Lin
- Pharmaceutical Engineering & Key Laboratory of Structure-Based Drug Design & DiscoveryMinistry of EducationShenyang Pharmaceutical University Shenyang 110016 P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan University Changsha 410082 P. R. China
| |
Collapse
|
13
|
Ida J, Chan SK, Glökler J, Lim YY, Choong YS, Lim TS. G-Quadruplexes as An Alternative Recognition Element in Disease-Related Target Sensing. Molecules 2019; 24:E1079. [PMID: 30893817 PMCID: PMC6471233 DOI: 10.3390/molecules24061079] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/14/2019] [Accepted: 03/16/2019] [Indexed: 12/05/2022] Open
Abstract
G-quadruplexes are made up of guanine-rich RNA and DNA sequences capable of forming noncanonical nucleic acid secondary structures. The base-specific sterical configuration of G-quadruplexes allows the stacked G-tetrads to bind certain planar molecules like hemin (iron (III)-protoporphyrin IX) to regulate enzymatic-like functions such as peroxidase-mimicking activity, hence the use of the term DNAzyme/RNAzyme. This ability has been widely touted as a suitable substitute to conventional enzymatic reporter systems in diagnostics. This review will provide a brief overview of the G-quadruplex architecture as well as the many forms of reporter systems ranging from absorbance to luminescence readouts in various platforms. Furthermore, some challenges and improvements that have been introduced to improve the application of G-quadruplex in diagnostics will be highlighted. As the field of diagnostics has evolved to apply different detection systems, the need for alternative reporter systems such as G-quadruplexes is also paramount.
Collapse
Affiliation(s)
- Jeunice Ida
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Soo Khim Chan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Jörn Glökler
- Division of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany.
| | - Yee Ying Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang 11800, Malaysia.
| |
Collapse
|
14
|
Zhang Z, Li Y, Zhang X, Liu J. Molecularly imprinted nanozymes with faster catalytic activity and better specificity. NANOSCALE 2019; 11:4854-4863. [PMID: 30820498 DOI: 10.1039/c8nr09816f] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanozymes are nanomaterials mimicking the activity of natural enzymes, while most nanozymes lack substrate specificity. Molecular imprinting on nanozymes provides a simple solution to this problem, and the catalytic activity is also enhanced. To understand enhanced activity, a surface science approach is taken by dissecting the nanozyme reaction into adsorption of substrates, reaction, and product release. Each step is individually studied using reaction kinetics measurement, dynamic light scattering, UV-vis spectrometry. Enrichment of local substrate concentration due to imprinting is around 8-fold, and increased substrate concentration could contribute to increased activity. Diffusion of the substrate across the imprinted gel layer is studied by a pre-incubation experiment, also highlighting the difference between imprinted and non-imprinted gel layers. The activation energy is measured and a substrate-imprinted sample had the lowest activation energy of 13.8 kJ mol-1. Product release is also improved after imprinting as indicated by isothermal titration calorimetry using samples respectively imprinted with the substrate and the product. This study has rationalized improved activity and specificity of molecularly imprinted nanozymes and may guide further rational design of such materials.
Collapse
Affiliation(s)
- Zijie Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1 Canada.
| | | | | | | |
Collapse
|
15
|
Zhang L, Zhou J, Ma F, Wang Q, Xu H, Ju H, Lei J. Single‐Sided Competitive Axial Coordination of G‐Quadruplex/Hemin as Molecular Switch for Imaging Intracellular Nitric Oxide. Chemistry 2018; 25:490-494. [DOI: 10.1002/chem.201804897] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/03/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Lei Zhang
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P.R. China
- School of Chemistry and Molecular Engineering, Institute of, Advanced SynthesisJiangsu National Synergetic Innovation Center for, Advanced MaterialsNanjing Tech University Nanjing 211816 P.R. China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P.R. China
| | - Fengjiao Ma
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P.R. China
| | - Quanbo Wang
- Laboratory of Immunology for Environment and HealthShandong Analysis and Test CenterShandong Academy of Sciences Jinan 250014 P.R. China
| | - Hui Xu
- School of Chemistry and Molecular Engineering, Institute of, Advanced SynthesisJiangsu National Synergetic Innovation Center for, Advanced MaterialsNanjing Tech University Nanjing 211816 P.R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P.R. China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P.R. China
| |
Collapse
|
16
|
Cheng Y, Cheng M, Hao J, Jia G, Li C. Fluorescence Spectroscopic Insight into the Supramolecular Interactions in DNA-Based Enantioselective Sulfoxidation. Chembiochem 2018; 19:2233-2240. [PMID: 30070000 DOI: 10.1002/cbic.201800393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Indexed: 12/31/2022]
Abstract
Interactions of copper(II)-bipyridine cofactors and thioanisole substrate with human telomeric G-quadruplex DNA were studied by UV/Vis absorption, circular dichroism, and fluorescence quenching titration. Three copper(II)-bipyridine complexes are equivalently anchored to the G-quadruplex scaffold at all five fluorescently labeled sites. Thioanisole interacts with the DNA architecture at both the second loop and 3' terminus in the absence or presence of copper(II)-bipyridine complexes. These nonspecificities in the weak interactions of CuII complexes and thioanisole with G-quadruplex might explain why DNA only affords a modest enantioselectivity in the oxidation of thioanisole. These findings provide insights toward the construction of highly enantioselective DNA-based catalysts.
Collapse
Affiliation(s)
- Yu Cheng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P.R. China.,Department of Chemical Physics, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, P.R. China
| | - Mingpan Cheng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P.R. China.,Department of Chemical Physics, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, P.R. China
| | - Jingya Hao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P.R. China.,Department of Chemical Physics, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, P.R. China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P.R. China
| | - Can Li
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P.R. China
| |
Collapse
|
17
|
Li W, Chen S, Xu D, Wen Q, Yang T, Liu J. A DNA as a Substrate and an Enzyme: Direct Profiling of Methyltransferase Activity by Cytosine Methylation of a DNAzyme. Chemistry 2018; 24:14500-14505. [DOI: 10.1002/chem.201802822] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Wang Li
- Hunan Key Laboratory of Processed Food for Special Medical Purpose; College of Food Science and Engineering; Central South University of Forestry and Technology; Changsha 410004 P. R. China
- Department of Chemistry, Water Institute and Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Siyi Chen
- Hunan Key Laboratory of Processed Food for Special Medical Purpose; College of Food Science and Engineering; Central South University of Forestry and Technology; Changsha 410004 P. R. China
| | - Dong Xu
- Hunan Key Laboratory of Processed Food for Special Medical Purpose; College of Food Science and Engineering; Central South University of Forestry and Technology; Changsha 410004 P. R. China
| | - Qian Wen
- Hunan Key Laboratory of Processed Food for Special Medical Purpose; College of Food Science and Engineering; Central South University of Forestry and Technology; Changsha 410004 P. R. China
| | - Tao Yang
- Hunan Key Laboratory of Processed Food for Special Medical Purpose; College of Food Science and Engineering; Central South University of Forestry and Technology; Changsha 410004 P. R. China
| | - Juewen Liu
- Department of Chemistry, Water Institute and Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| |
Collapse
|
18
|
Zhang H, Li X, He F, Zhao M, Ling L. Turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA based upon Y-shaped DNA structure. Sci Rep 2018; 8:12021. [PMID: 30104740 PMCID: PMC6089895 DOI: 10.1038/s41598-018-30529-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/31/2018] [Indexed: 12/19/2022] Open
Abstract
A novel turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA (ssDNA) was established by combining Y-shaped DNA duplex and G-quadruplex-hemin DNAzyme. A G-rich single-stranded DNA (Oligo-1) displays peroxidase mimicking catalytic activity due to the specific binding with hemin in the presence of K+, which was able to catalyze the oxidation of colorless 2,2'-azinobis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS2-) by H2O2 to generate green ABTS•- radical for colorimetric assay. Oligonucleotide 2 (Oligo-2) was partly complementary with Oligo-1 and the target DNA. Upon addition of target DNA, Oligo-1, Oligo-2 and target DNA can hybridize with each other to form Y-shaped DNA duplex. The DNAzyme sequence of Oligo-1 was partly caged into Y-shaped DNA duplex, resulting in the inactivation of the DNAzyme and a sharp decrease of the absorbance of the oxidation product of ABTS2-. Under the optimum condition, the absorbance decreased linearly with the concentration of target DNA over the range of 1.0-250 nM and the detection limit was 0.95 nM (3σ/slope) Moreover, satisfied result was obtained for the discrimination of single-base or two-base mismatched DNA.
Collapse
Affiliation(s)
- Hong Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, P. R. China
| | - Xintong Li
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, P. R. China
| | - Fan He
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, P. R. China
| | - Mingqin Zhao
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, P. R. China.
| | - Liansheng Ling
- School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China.
| |
Collapse
|