201
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Zhou H, Liu J, Xu JJ, Zhang SS, Chen HY. Optical nano-biosensing interface via nucleic acid amplification strategy: construction and application. Chem Soc Rev 2018; 47:1996-2019. [PMID: 29446429 DOI: 10.1039/c7cs00573c] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Modern optical detection technology plays a critical role in current clinical detection due to its high sensitivity and accuracy. However, higher requirements such as extremely high detection sensitivity have been put forward due to the clinical needs for the early finding and diagnosing of malignant tumors which are significant for tumor therapy. The technology of isothermal amplification with nucleic acids opens up avenues for meeting this requirement. Recent reports have shown that a nucleic acid amplification-assisted modern optical sensing interface has achieved satisfactory sensitivity and accuracy, high speed and specificity. Compared with isothermal amplification technology designed to work completely in a solution system, solid biosensing interfaces demonstrated better performances in stability and sensitivity due to their ease of separation from the reaction mixture and the better signal transduction on these optical nano-biosensing interfaces. Also the flexibility and designability during the construction of these nano-biosensing interfaces provided a promising research topic for the ultrasensitive detection of cancer diseases. In this review, we describe the construction of the burgeoning number of optical nano-biosensing interfaces assisted by a nucleic acid amplification strategy, and provide insightful views on: (1) approaches to the smart fabrication of an optical nano-biosensing interface, (2) biosensing mechanisms via the nucleic acid amplification method, (3) the newest strategies and future perspectives.
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Affiliation(s)
- Hong Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China.
| | - Jing Liu
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China.
| | - Jing-Juan Xu
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Shu-Sheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China.
| | - Hong-Yuan Chen
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
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202
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Shen ZF, Li F, Jiang YF, Chen C, Xu H, Li CC, Yang Z, Wu ZS. Palindromic Molecule Beacon-Based Cascade Amplification for Colorimetric Detection of Cancer Genes. Anal Chem 2018; 90:3335-3340. [DOI: 10.1021/acs.analchem.7b04895] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zhi-Fa Shen
- Henan Key Laboratory of Immunology and Targeted Drugs, Research Center for Molecular Oncology and Functional Nucleic Acids, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Feng Li
- Henan Key Laboratory of Immunology and Targeted Drugs, Research Center for Molecular Oncology and Functional Nucleic Acids, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Yi-Fan Jiang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Chang Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Huo Xu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Cong-Cong Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Zhe Yang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
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203
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Lian W, Liang J, Shen L, Jin Y, Liu H. Enzymatic logic calculation systems based on solid-state electrochemiluminescence and molecularly imprinted polymer film electrodes. Biosens Bioelectron 2018; 100:326-332. [DOI: 10.1016/j.bios.2017.09.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 12/22/2022]
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204
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Kim SU, Batule BS, Mun H, Shim WB, Kim MG. Ultrasensitive colorimetric detection of Salmonella enterica Typhimurium on lettuce leaves by HRPzyme-Integrated polymerase chain reaction. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.09.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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205
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Blanchard DJM, Manderville RA. An internal charge transfer-DNA platform for fluorescence sensing of divalent metal ions. Chem Commun (Camb) 2018; 52:9586-8. [PMID: 27399260 DOI: 10.1039/c6cc04613d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Replacement of guanine (G) nucleobases within G-quadruplex (GQ) folding oligonucleotides with push-pull fluorescent 8-arylvinyl-dG residues provides diagnostic emission signalling for divalent metal ion binding.
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Affiliation(s)
- Darian J M Blanchard
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, Ontario N1G 2w1, Canada.
| | - Richard A Manderville
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, Ontario N1G 2w1, Canada.
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206
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Buckhout-White S, Person C, Medintz IL, Goldman ER. Restriction Enzymes as a Target for DNA-Based Sensing and Structural Rearrangement. ACS OMEGA 2018; 3:495-502. [PMID: 31457907 PMCID: PMC6641459 DOI: 10.1021/acsomega.7b01333] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/10/2017] [Indexed: 05/04/2023]
Abstract
DNA nanostructures have been shown viable for the creation of complex logic-enabled sensing motifs. To date, most of these types of devices have been limited to the interaction with strictly DNA-type inputs. Restriction endonuclease represents a class of enzyme with endogenous specificity to DNA, and we hypothesize that these can be integrated with a DNA structure for use as inputs to trigger structural transformation and structural rearrangement. In this work, we reconfigured a three-arm DNA switch, which utilizes a cyclic Förster resonance energy transfer interaction between three dyes to produce complex output for the detection of three separate input regions to respond to restriction endonucleases, and investigated the efficacy of the enzyme targets. We demonstrate the ability to use three enzymes in one switch with no nonspecific interaction between cleavage sites. Further, we show that the enzymatic digestion can be harnessed to expose an active toehold into the DNA structure, allowing for single-pot addition of a small oligo in solution.
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Affiliation(s)
- Susan Buckhout-White
- Center for Bio/Molecular
Science and Engineering, Code 6900, U.S.
Naval Research Laboratory, Washington, DC 20375, United States
| | - Chanel Person
- Center for Bio/Molecular
Science and Engineering, Code 6900, U.S.
Naval Research Laboratory, Washington, DC 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular
Science and Engineering, Code 6900, U.S.
Naval Research Laboratory, Washington, DC 20375, United States
| | - Ellen R. Goldman
- Center for Bio/Molecular
Science and Engineering, Code 6900, U.S.
Naval Research Laboratory, Washington, DC 20375, United States
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207
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Huang JY, Lin HT, Chen TH, Chen CA, Chang HT, Chen CF. Signal Amplified Gold Nanoparticles for Cancer Diagnosis on Paper-Based Analytical Devices. ACS Sens 2018; 3:174-182. [PMID: 29282979 DOI: 10.1021/acssensors.7b00823] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this work, we report a highly sensitive colorimetric sensing strategy for cancer biomarker diagnosis using gold nanoparticles (AuNPs) labeled with biotinylated poly(adenine) ssDNA sequences and streptavidin-horseradish peroxidase for enzymatic signal enhancement. By adopting this DNA-AuNP nanoconjugate sensing strategy, we were able to eliminate the complicated and costly thiol-binding process typically used to modify AuNP surfaces with ssDNA. In addition, different antibodies can be introduced to the AuNP surfaced via electrostatic interactions to provide highly specific recognition sites for biomolecular sensing. Moreover, multiple, simultaneous tests can be rapidly performed with low sample consumption by incorporating these surface-modified AuNPs into a paper-based analytical device that can be read using just a smartphone. As a result of these innovations, we were able to achieve a detection limit of 10 pg/mL for a prostate specific antigen in a test that could be completed in as little as 15 min. These results suggest that the proposed paper platform possesses the capability for sensitive, high-throughput, and on-site prognosis in resource-limited settings.
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Affiliation(s)
- Jia-Yu Huang
- Department of Chemistry, ‡Institute of Applied Mechanics, and §Center for Emerging Material and Advanced
Devices, National Taiwan University, Taipei 106, Taiwan
| | - Hong-Ting Lin
- Department of Chemistry, ‡Institute of Applied Mechanics, and §Center for Emerging Material and Advanced
Devices, National Taiwan University, Taipei 106, Taiwan
| | - Tzu-Heng Chen
- Department of Chemistry, ‡Institute of Applied Mechanics, and §Center for Emerging Material and Advanced
Devices, National Taiwan University, Taipei 106, Taiwan
| | - Chung-An Chen
- Department of Chemistry, ‡Institute of Applied Mechanics, and §Center for Emerging Material and Advanced
Devices, National Taiwan University, Taipei 106, Taiwan
| | - Huan-Tsung Chang
- Department of Chemistry, ‡Institute of Applied Mechanics, and §Center for Emerging Material and Advanced
Devices, National Taiwan University, Taipei 106, Taiwan
| | - Chien-Fu Chen
- Department of Chemistry, ‡Institute of Applied Mechanics, and §Center for Emerging Material and Advanced
Devices, National Taiwan University, Taipei 106, Taiwan
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208
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Harraz DM, Davis JT. A self-assembled peroxidase from 5'-GMP and heme. Chem Commun (Camb) 2018; 54:1587-1590. [PMID: 29368765 DOI: 10.1039/c7cc09900b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Guanosine 5'-monophosphate (5'-GMP) and Fe(iii)-heme form a supramolecular catalyst with peroxidase activity. Catalysis, which depends on self-assembly of 5'-GMP into a G-quadruplex that binds hemin, can be modulated by nucleotide concentration, temperature and the identity of the nucleotide's sugar.
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Affiliation(s)
- Deiaa M Harraz
- Department of Chemistry & Biochemistry, University of Maryland College Park, MD 20742, USA.
| | - Jeffery T Davis
- Department of Chemistry & Biochemistry, University of Maryland College Park, MD 20742, USA.
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209
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Rossetti M, Porchetta A. Allosterically regulated DNA-based switches: From design to bioanalytical applications. Anal Chim Acta 2018; 1012:30-41. [PMID: 29475471 DOI: 10.1016/j.aca.2017.12.046] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/10/2017] [Accepted: 12/28/2017] [Indexed: 02/07/2023]
Abstract
DNA-based switches are structure-switching biomolecules widely employed in different bioanalytical applications. Of particular interest are DNA-based switches whose activity is regulated through the use of allostery. Allostery is a naturally occurring mechanism in which ligand binding induces the modulation and fine control of a connected biomolecule function as a consequence of changes in concentration of the effector. Through this general mechanism, many different allosteric DNA-based switches able to respond in a highly controlled way at the presence of a specific molecular effector have been engineered. Here, we discuss how to design allosterically regulated DNA-based switches and their applications in the field of molecular sensing, diagnostic and drug release.
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Affiliation(s)
- Marianna Rossetti
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Porchetta
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy.
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210
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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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211
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Chemiluminescence assay for detection of 2-hydroxyfluorene using the G-quadruplex DNAzyme-H 2O 2-luminol system. Mikrochim Acta 2017; 185:54. [PMID: 29594378 DOI: 10.1007/s00604-017-2555-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/09/2017] [Indexed: 12/13/2022]
Abstract
A chemiluminescence (CL) based assay is described for the determination of the environmental pollutant 2-hydroxyfluorene (2-HOFlu) which is found to inhibit the CL of a system composed of the G-quadruplex/hemin complex (a DNAzyme), H2O2, and luminol. The G-rich aptamer PW17 is transformed to a potassium(I)-stabilized G-quadruplex-hemin complex which displays peroxidase-like activity to catalyze the oxidation of luminol by H2O2 which is accompanied by strong blue CL emission. On addition of 2-HOFlu, it will participate in the G-quadruplex DNAzyme-mediated oxidation by H2O2. As a result, CL intensity is decreased. The difference in CL intensity (ΔI) before and after addition of 2-HOFlu serves as the signal for its quantitation. In water of pH 9.0, a linear relationship is found for the 1 nM to 1 μM concentration range, with a 0.2 nM detection limit. The assay is highly selective over other fluorene derivatives. It was successfully applied to the determination of 2-HOFlu in spiked lake water samples. The method is rapid, cost-effective and convenient. Conceivably, it has a wide scope in that it may be applied to other target pollutants for which G-quadruplexes are available. Graphical abstract A chemiluminescence (CL) assay is described for the determination of the environmental pollutant 2-hydroxyfluorene (2-HOFlu) based on the inhibition of the CL system composed of the G-quadruplex/hemin complex (a DNAzyme), H2O2, and luminol.
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212
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Peng H, Newbigging AM, Wang Z, Tao J, Deng W, Le XC, Zhang H. DNAzyme-Mediated Assays for Amplified Detection of Nucleic Acids and Proteins. Anal Chem 2017; 90:190-207. [DOI: 10.1021/acs.analchem.7b04926] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hanyong Peng
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Ashley M. Newbigging
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Zhixin Wang
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Jeffrey Tao
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Wenchan Deng
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - X. Chris Le
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
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213
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Nosrati R, Golichenari B, Nezami A, Taghdisi SM, Karimi B, Ramezani M, Abnous K, Shaegh SAM. Helicobacter pylori point-of-care diagnosis: Nano-scale biosensors and microfluidic systems. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.10.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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214
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Guo Y, Chen J, Cheng M, Monchaud D, Zhou J, Ju H. A Thermophilic Tetramolecular G-Quadruplex/Hemin DNAzyme. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708964] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yuehua Guo
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P. R. China
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P. R. China
| | - Mingpan Cheng
- State Key Laboratory of Catalysis; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 160023 P. R. China
| | - David Monchaud
- Institut de Chimie Moléculaire; Université de Bourgogne (ICMUB); CNRS UMR6302; 21000 Dijon France
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P. R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P. R. China
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215
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Xu W, Huang Y, Zhao H, Li P, Liu G, Li J, Zhu C, Tian L. DNA Hydrogel with Tunable pH-Responsive Properties Produced by Rolling Circle Amplification. Chemistry 2017; 23:18276-18281. [PMID: 29071753 DOI: 10.1002/chem.201704390] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 11/10/2022]
Abstract
Recently, smart DNA hydrogels, which are generally formed by the self-assembly of oligonucleotides or through the cross-linking of oligonucleotide-polymer hybrids, have attracted tremendous attention. However, the difficulties of fabricating DNA hydrogels limit their practical applications. We report herein a novel method for producing pH-responsive hydrogels by rolling circle amplification (RCA). In this method, pH-sensitive cross-linking sites were introduced into the polymeric DNA chains during DNA synthesis. As the DNA sequence can be precisely defined by its template, the properties of such hydrogels can be finely tuned in a very facile way through template design. We have investigated the process of hydrogel formation and pH-responsiveness to provide rationales for functional hydrogel design based on the RCA reaction.
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Affiliation(s)
- Wanlin Xu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong, 518055, P.R. China.,School of Materials Science and Engineering, Zhengzhou University, 100 Kexue Road, Zhengzhou, Henan, 450001, P.R. China
| | - Yishun Huang
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong, 518055, P.R. China
| | - Haoran Zhao
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong, 518055, P.R. China
| | - Pan Li
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong, 518055, P.R. China
| | - Guoyuan Liu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong, 518055, P.R. China
| | - Jing Li
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong, 518055, P.R. China
| | - Chengshen Zhu
- School of Materials Science and Engineering, Zhengzhou University, 100 Kexue Road, Zhengzhou, Henan, 450001, P.R. China
| | - Leilei Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong, 518055, P.R. China
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216
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Guo Y, Chen J, Cheng M, Monchaud D, Zhou J, Ju H. A Thermophilic Tetramolecular G-Quadruplex/Hemin DNAzyme. Angew Chem Int Ed Engl 2017; 56:16636-16640. [DOI: 10.1002/anie.201708964] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/24/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Yuehua Guo
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P. R. China
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P. R. China
| | - Mingpan Cheng
- State Key Laboratory of Catalysis; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 160023 P. R. China
| | - David Monchaud
- Institut de Chimie Moléculaire; Université de Bourgogne (ICMUB); CNRS UMR6302; 21000 Dijon France
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P. R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P. R. China
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217
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Hu Y, Cecconello A, Idili A, Ricci F, Willner I. Triplex DNA Nanostructures: From Basic Properties to Applications. Angew Chem Int Ed Engl 2017; 56:15210-15233. [PMID: 28444822 DOI: 10.1002/anie.201701868] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Indexed: 12/16/2022]
Abstract
Triplex nucleic acids have recently attracted interest as part of the rich "toolbox" of structures used to develop DNA-based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex-DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH-responsive systems and materials are described. Examples include semiconductor-loaded DNA-stabilized microcapsules, DNA-functionalized dye-loaded metal-organic frameworks (MOFs), and the pH-induced release of the loads. Furthermore, the design of stimuli-responsive DNA-based hydrogels undergoing reversible pH-induced hydrogel-to-solution transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape-memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.
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Affiliation(s)
- Yuwei Hu
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Alessandro Cecconello
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Andrea Idili
- Department of Chemistry, University of Rome, Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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218
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Hu Y, Cecconello A, Idili A, Ricci F, Willner I. Triplex-DNA-Nanostrukturen: von grundlegenden Eigenschaften zu Anwendungen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701868] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Yuwei Hu
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | | | - Andrea Idili
- Department of Chemistry; Universität Rom; Tor Vergata, via della Ricerca Scientifica 00133 Rom Italien
| | - Francesco Ricci
- Department of Chemistry; Universität Rom; Tor Vergata, via della Ricerca Scientifica 00133 Rom Italien
| | - Itamar Willner
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
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219
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Li J, Green AA, Yan H, Fan C. Engineering nucleic acid structures for programmable molecular circuitry and intracellular biocomputation. Nat Chem 2017; 9:1056-1067. [PMID: 29064489 PMCID: PMC11421837 DOI: 10.1038/nchem.2852] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/11/2017] [Indexed: 12/12/2022]
Abstract
Nucleic acids have attracted widespread attention due to the simplicity with which they can be designed to form discrete structures and programmed to perform specific functions at the nanoscale. The advantages of DNA/RNA nanotechnology offer numerous opportunities for in-cell and in-vivo applications, and the technology holds great promise to advance the growing field of synthetic biology. Many elegant examples have revealed the potential in integrating nucleic acid nanostructures in cells and in vivo where they can perform important physiological functions. In this Review, we summarize the current abilities of DNA/RNA nanotechnology to realize applications in live cells and then discuss the key problems that must be solved to fully exploit the useful properties of nanostructures. Finally, we provide viewpoints on how to integrate the tools provided by DNA/RNA nanotechnology and related new technologies to construct nucleic acid nanostructure-based molecular circuitry for synthetic biology.
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Affiliation(s)
- Jiang Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Alexander A Green
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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220
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Wei J, Gong X, Wang Q, Pan M, Liu X, Liu J, Xia F, Wang F. Construction of an autonomously concatenated hybridization chain reaction for signal amplification and intracellular imaging. Chem Sci 2017; 9:52-61. [PMID: 29629073 PMCID: PMC5869291 DOI: 10.1039/c7sc03939e] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/22/2017] [Indexed: 12/16/2022] Open
Abstract
The concatenated hybridization chain reaction (C-HCR) was constructed as a versatile and robust tool for signal amplification and intracellular imaging, which was attributed to the synergistic amplification effect between HCR-1 and HCR-2.
Biomolecular self-assembly has spurred substantial research efforts for the development of low-cost point-of-care diagnostics. Herein, we introduce an isothermal enzyme-free concatenated hybridization chain reaction (C-HCR), in which the output of the upstream hybridization chain reaction (HCR-1) layer acts as an intermediate input to activate the downstream hybridization chain reaction (HCR-2) layer. The initiator motivates HCR-1 through the autonomous cross-opening of two functional DNA hairpins, yielding polymeric dsDNA nanowires composed of numerous tandem triggers T as output of the primary sensing event. The reconstituted amplicon T then initiates HCR-2 and transduces the analyte recognition into an amplified readout, originating from the synergistic effect between HCR-1 and HCR-2 layers. Native gel electrophoresis, atom force microscopy (AFM) and fluorescence spectra revealed that C-HCR mediated the formation of frond-like branched dsDNA nanowires and the generation of an amplified FRET signal. As a versatile and robust amplification strategy, the unpreceded C-HCR can discriminate DNA analyte from its mutants with high accuracy and specificity. By incorporating an auxiliary sensing module, the integrated C-HCR amplifier was further adapted for highly sensitive and selective detection of microRNA (miRNA), as a result of the hierarchical and sequential hybridization chain reactions, in human serum and even living cells through an easy-to-integrate “plug-and-play” procedure. In addition, the C-HCR amplifier was successfully implemented for intracellular miRNA imaging by acquiring an accurate and precise signal localization inside living cells, which was especially suitable for the ex situ and in situ amplified detection of trace amounts of analyte. The C-HCR amplification provides a comprehensive and smart toolbox for highly sensitive detection of various biomarkers and thus should hold great promise in clinical diagnosis and assessment. The infinite layer of multilayered C-HCR is anticipated to further strengthen the amplification capacity and reliability (anti-invasion performance) of intracellular imaging approach, which is of great significance for its bioanalytical applications.
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Affiliation(s)
- Jie Wei
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Xue Gong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Qing Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Min Pan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Jing Liu
- Department of Gastroenterology , Zhongnan Hospital of Wuhan University , Hubei Clinical Center & Key Lab of Intestinal & Colorectal Diseases , Wuhan , P. R. China
| | - Fan Xia
- Department of Urology , Union Hospital , Tongji Medical College , Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica , School of Chemistry and Chemical Engineering , Department of Epidemiology and Biostatistics , School of Public Health , Huazhong University of Science and Technology (HUST) , Wuhan 430074 , P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
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221
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Ribes À, Santiago‐Felipe S, Bernardos A, Marcos MD, Pardo T, Sancenón F, Martínez‐Máñez R, Aznar E. Two New Fluorogenic Aptasensors Based on Capped Mesoporous Silica Nanoparticles to Detect Ochratoxin A. ChemistryOpen 2017; 6:653-659. [PMID: 29046860 PMCID: PMC5641899 DOI: 10.1002/open.201700106] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Indexed: 01/05/2023] Open
Abstract
Aptamers have been used as recognition elements for several molecules due to their great affinity and selectivity. Additionally, mesoporous nanomaterials have demonstrated great potential in sensing applications. Based on these concepts, we report herein the use of two aptamer-capped mesoporous silica materials for the selective detection of ochratoxin A (OTA). A specific aptamer for OTA was used to block the pores of rhodamine B-loaded mesoporous silica nanoparticles. Two solids were prepared in which the aptamer capped the porous scaffolds by using a covalent or electrostatic approach. Whereas the prepared materials remained capped in water, dye delivery was selectively observed in the presence of OTA. The protocol showed excellent analytical performance in terms of sensitivity (limit of detection: 0.5-0.05 nm), reproducibility, and selectivity. Moreover, the aptasensors were tested for OTA detection in commercial foodstuff matrices, which demonstrated their potential applicability in real samples.
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Affiliation(s)
- Àngela Ribes
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de ValènciaUniversitat de ValènciaCamino de Vera s/n46022ValenciaSpain
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER-BBN)50018ZaragozaSpain
- Unidad Mixta de Investigación en Nanomedicina y SensoresUniversitat Politècnica de València, Instituto de Investigación Sanitaria La Fe46022ValenciaSpain
| | - Sara Santiago‐Felipe
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de ValènciaUniversitat de ValènciaCamino de Vera s/n46022ValenciaSpain
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER-BBN)50018ZaragozaSpain
- Unidad Mixta de Investigación en Nanomedicina y SensoresUniversitat Politècnica de València, Instituto de Investigación Sanitaria La Fe46022ValenciaSpain
| | - Andrea Bernardos
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de ValènciaUniversitat de ValènciaCamino de Vera s/n46022ValenciaSpain
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER-BBN)50018ZaragozaSpain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y NanomedicinaUniversitat Politècnica de València, Centro de Investigación Príncipe Felipe46022ValenciaSpain
| | - M. Dolores Marcos
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de ValènciaUniversitat de ValènciaCamino de Vera s/n46022ValenciaSpain
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER-BBN)50018ZaragozaSpain
- Unidad Mixta de Investigación en Nanomedicina y SensoresUniversitat Politècnica de València, Instituto de Investigación Sanitaria La Fe46022ValenciaSpain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y NanomedicinaUniversitat Politècnica de València, Centro de Investigación Príncipe Felipe46022ValenciaSpain
| | - Teresa Pardo
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de ValènciaUniversitat de ValènciaCamino de Vera s/n46022ValenciaSpain
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER-BBN)50018ZaragozaSpain
- Unidad Mixta de Investigación en Nanomedicina y SensoresUniversitat Politècnica de València, Instituto de Investigación Sanitaria La Fe46022ValenciaSpain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y NanomedicinaUniversitat Politècnica de València, Centro de Investigación Príncipe Felipe46022ValenciaSpain
| | - Félix Sancenón
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de ValènciaUniversitat de ValènciaCamino de Vera s/n46022ValenciaSpain
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER-BBN)50018ZaragozaSpain
- Unidad Mixta de Investigación en Nanomedicina y SensoresUniversitat Politècnica de València, Instituto de Investigación Sanitaria La Fe46022ValenciaSpain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y NanomedicinaUniversitat Politècnica de València, Centro de Investigación Príncipe Felipe46022ValenciaSpain
| | - Ramón Martínez‐Máñez
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de ValènciaUniversitat de ValènciaCamino de Vera s/n46022ValenciaSpain
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER-BBN)50018ZaragozaSpain
- Unidad Mixta de Investigación en Nanomedicina y SensoresUniversitat Politècnica de València, Instituto de Investigación Sanitaria La Fe46022ValenciaSpain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y NanomedicinaUniversitat Politècnica de València, Centro de Investigación Príncipe Felipe46022ValenciaSpain
| | - Elena Aznar
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de ValènciaUniversitat de ValènciaCamino de Vera s/n46022ValenciaSpain
- CIBER de BioingenieríaBiomateriales y Nanomedicina (CIBER-BBN)50018ZaragozaSpain
- Unidad Mixta de Investigación en Nanomedicina y SensoresUniversitat Politècnica de València, Instituto de Investigación Sanitaria La Fe46022ValenciaSpain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y NanomedicinaUniversitat Politècnica de València, Centro de Investigación Príncipe Felipe46022ValenciaSpain
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222
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Yin HS, Li BC, Zhou YL, Wang HY, Wang MH, Ai SY. Signal-on fluorescence biosensor for microRNA-21 detection based on DNA strand displacement reaction and Mg 2+ -dependent DNAzyme cleavage. Biosens Bioelectron 2017; 96:106-112. [DOI: 10.1016/j.bios.2017.04.049] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/28/2017] [Accepted: 04/28/2017] [Indexed: 01/09/2023]
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223
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Bhattacharyya T, Kumar YP, Dash J. Supramolecular Hydrogel Inspired from DNA Structures Mimics Peroxidase Activity. ACS Biomater Sci Eng 2017; 3:2358-2365. [DOI: 10.1021/acsbiomaterials.7b00563] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tanima Bhattacharyya
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Y. Pavan Kumar
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Jyotirmayee Dash
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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224
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Wang L, Zhou H, Liu B, Zhao C, Fan J, Wang W, Tong C. Fluorescence Assay for Ribonuclease H Based on Nonlabeled Substrate and DNAzyme Assisted Cascade Amplification. Anal Chem 2017; 89:11014-11020. [DOI: 10.1021/acs.analchem.7b02899] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Lanbo Wang
- College
of Biology, Hunan Province Key Laboratory of Plant Functional Genomics
and Developmental Regulation, State Key Laboratory of Chem/Biosensing
and Chemometrics, Hunan University, Changsha, Hunan 410082, China
| | - Hongyan Zhou
- College
of Biology, Hunan Province Key Laboratory of Plant Functional Genomics
and Developmental Regulation, State Key Laboratory of Chem/Biosensing
and Chemometrics, Hunan University, Changsha, Hunan 410082, China
| | - Bin Liu
- College
of Biology, Hunan Province Key Laboratory of Plant Functional Genomics
and Developmental Regulation, State Key Laboratory of Chem/Biosensing
and Chemometrics, Hunan University, Changsha, Hunan 410082, China
| | - Chuan Zhao
- College
of Biology, Hunan Province Key Laboratory of Plant Functional Genomics
and Developmental Regulation, State Key Laboratory of Chem/Biosensing
and Chemometrics, Hunan University, Changsha, Hunan 410082, China
| | - Jialong Fan
- College
of Biology, Hunan Province Key Laboratory of Plant Functional Genomics
and Developmental Regulation, State Key Laboratory of Chem/Biosensing
and Chemometrics, Hunan University, Changsha, Hunan 410082, China
| | - Wei Wang
- TCM
and Ethnomedicine Innovation and Development Laboratory, Sino-Luxemburg
TCM Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan 410208, China
| | - Chunyi Tong
- College
of Biology, Hunan Province Key Laboratory of Plant Functional Genomics
and Developmental Regulation, State Key Laboratory of Chem/Biosensing
and Chemometrics, Hunan University, Changsha, Hunan 410082, China
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225
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Shi L, Peng P, Du Y, Li T. Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device. Nucleic Acids Res 2017; 45:4306-4314. [PMID: 28369541 PMCID: PMC5416763 DOI: 10.1093/nar/gkx202] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/18/2017] [Indexed: 01/24/2023] Open
Abstract
Four-stranded DNAs including G-quadruplexes and i-motifs are formed from four stretches of identical bases (G or C). A challenge remains in controlling the intermolecular folding of different G-rich or C-rich strands due to the self-association of each component. Here, we introduce a well-designed bimolecular i-motif that does not allow the dimerization of the same strand, and illustrate its usefulness in a pH-switched ATP-sensing DNA molecular device. We analyze two groups of i-motif DNAs containing two stretches of different C-residues (Cn-1TmCn and CnTmCn-1; n = 3−6, m = 1, 3) and show that their bimolecular folding patterns (L- and H-form) noticeably differs in the thermal stability. The L-form structures generally display a relatively low stability, with a bigger difference from that of conventional i-motifs formed by CnTmCn. It inspires us to at utmost improving the structural stability by extending the core of L-form bimolecular i-motifs with a few flanking noncanonical base pairs, and therefore to avoid the dimeric association of each component. This meaningful bimolecular i-motif is then incorporated into a three-way junction (3WJ) and a four-way junction (4WJ) functionalized with two components of a ATP-binding split DNA aptamer, allowing the pH-triggered directional assembly of 3WJ and 4WJ into the desired (3+4)WJ structure that is verified by gel electrophoresis. It therefore enables the ATP-induced association of the split aptamer within the (3+4)WJ structure, as monitored by fluorescence quenching. In this way, the designed DNA system behaves as a pH-switched reversible molecular device, showing a high sensitivity and selectivity for fluorescent ATP analysis. The i-motif folding topology-programmed DNA nanoassembly may find more applications in the context of larger 2D/3D DNA nanostructures like lattices and polyhedra.
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Affiliation(s)
- Lili Shi
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Pai Peng
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Yi Du
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
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226
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Yu Y, Su G, Zhu H, Zhu Q, Chen Y, Xu B, Li Y, Zhang W. Proximity hybridization-mediated isothermal exponential amplification for ultrasensitive electrochemical protein detection. Int J Nanomedicine 2017; 12:5903-5914. [PMID: 28860756 PMCID: PMC5566414 DOI: 10.2147/ijn.s142015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In this study, we fabricated a novel electrochemical biosensing platform on the basis of target-triggered proximity hybridization-mediated isothermal exponential amplification reaction (EXPAR) for ultrasensitive protein analysis. Through rational design, the aptamers for protein recognition were integrated within two DNA probes. Via proximity hybridization principle, the affinity protein-binding event was converted into DNA assembly process. The recognition of protein by aptamers can trigger the strand displacement through the increase of the local concentrations of the involved probes. As a consequence, the output DNA was displaced, which can hybridize with the duplex probes immobilized on the electrode surface subsequently, leading to the initiation of the EXPAR as well as the cleavage of duplex probes. Each cleavage will release the gold nanoparticles (AuNPs) binding sequence. With the modification of G-quadruplex sequence, electrochemical signals were yielded by the AuNPs through oxidizing 3,3',5,5'-tetramethylbenzidine in the presence of H2O2. The study we proposed exhibited high sensitivity toward platelet-derived growth factor BB (PDGF-BB) with the detection limit of 52 fM. And, this method also showed great selectivity among the PDGF isoforms and performed well in spiked human serum samples.
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Affiliation(s)
- Yanyan Yu
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Gaoxing Su
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Hongyan Zhu
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Qing Zhu
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Yong Chen
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Bohui Xu
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Yuqin Li
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Wei Zhang
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
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227
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Wang J, Qin H, Wang F, Ren J, Qu X. Metal-Ion-Activated DNAzymes Used for Regulation of Telomerase Activity in Living Cells. Chemistry 2017. [DOI: 10.1002/chem.201702236] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jiasi Wang
- Laboratory of Chemical Biology; and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
- University of Chinese Academy of Sciences; Beijing 100039 P. R. China
| | - Hongshuang Qin
- Laboratory of Chemical Biology; and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
| | - Faming Wang
- Laboratory of Chemical Biology; and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
- University of Chinese Academy of Sciences; Beijing 100039 P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology; and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology; and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
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228
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Maiti S, Prins LJ. A modular self-assembled sensing system for heavy metal ions with tunable sensitivity and selectivity. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.05.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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229
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Wang S, Yue L, Shpilt Z, Cecconello A, Kahn JS, Lehn JM, Willner I. Controlling the Catalytic Functions of DNAzymes within Constitutional Dynamic Networks of DNA Nanostructures. J Am Chem Soc 2017. [DOI: 10.1021/jacs.7b04531] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Shan Wang
- Institute
of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Liang Yue
- Institute
of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zohar Shpilt
- Institute
of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alessandro Cecconello
- Institute
of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jason S. Kahn
- Institute
of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jean-Marie Lehn
- Institut
de Science et d’Ingénierie Supramoléculaires
(ISIS), University of Strasbourg, 8 Rue Gaspard Monge, Strasbourg 67000, France
| | - Itamar Willner
- Institute
of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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230
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Smith AL, Kolpashchikov DM. Divide and Control: Comparison of Split and Switch Hybridization Sensors. ChemistrySelect 2017; 2:5427-5431. [PMID: 29372178 PMCID: PMC5777618 DOI: 10.1002/slct.201701179] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hybridization probes have been intensively used for nucleic acid analysis in medicine, forensics and fundamental research. Instantaneous hybridization probes (IHPs) enable signalling immediately after binding to a targeted DNA or RNA sequences without the need to isolate the probe-target complex (e. g. by gel electrophoresis). The two most common strategies for IHP design are conformational switches and split approach. A conformational switch changes its conformation and produces signal upon hybridization to a target. Split approach uses two (or more) strands that independently or semi independently bind the target and produce an output signal only if all components associate. Here, we compared the performance of split vs switch designs for deoxyribozyme (Dz) hybridization probes under optimal conditions for each of them. The split design was represented by binary Dz (BiDz) probes; while catalytic molecular beacon (CMB) probes represented the switch design. It was found that BiDz were significantly more selective than CMBs in recognition of single base substitution. CMBs produced high background signal when operated at 55°C. An important advantage of BiDz over CMB is more straightforward design and simplicity of assay optimization.
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Affiliation(s)
- Alexandra L Smith
- Chemistry Department, University of Central Florida, 4000 N. Central Florida Ave, Orlando, FL 32826
| | - Dmitry M Kolpashchikov
- Chemistry Department, Burnett School of Biomedical Sciences, National Center for Forensic Science, University of Central Florida, 4000 N. Central Florida Ave, Orlando, FL 32826
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231
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Zhang L, Ma F, Lei J, Liu J, Ju H. Target-triggered cascade assembly of a catalytic network as an artificial enzyme for highly efficient sensing. Chem Sci 2017; 8:4833-4839. [PMID: 28959405 PMCID: PMC5602372 DOI: 10.1039/c7sc01453h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 04/25/2017] [Indexed: 11/21/2022] Open
Abstract
Determining the catalytic activity of artificial enzymes is an ongoing challenge. In this work, we design a porphyrin-based enzymatic network through the target-triggered cascade assembly of catalytic nanoparticles. The nanoparticles are synthesized via the covalent binding of hemin to amino-coated gold nanoparticles and then the axial coordination of the Fe center with a dual-functional imidazole or pyridine derivative. The network, which is specifically formed by coordination polymerization triggered by Hg2+ as the target, shows high catalytic activity due to the triple amplification of enzymatic activity during the cascade assembly. The catalytic dynamics are comparable to those of natural horseradish peroxidase. The catalytic characteristics can be ultrasensitively regulated by the target, leading to a selective methodology for the analysis of sub-attomolar Hg2+. It has also been used for "signal-on" imaging of reactive oxygen species in living cells. This work provides a new avenue for the design of enzyme mimics, and a powerful biocatalyst with signal switching for the development of biosensing protocols.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China . ; ; Tel: +86 25 89681922
| | - Fengjiao Ma
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China . ; ; Tel: +86 25 89681922
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China . ; ; Tel: +86 25 89681922
| | - Jintong Liu
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China . ; ; Tel: +86 25 89681922
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China . ; ; Tel: +86 25 89681922
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232
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Jafari M, Rezaei M, Kalantari H, Tabarzad M, Daraei B. DNAzyme-aptamer or aptamer-DNAzyme paradigm: Biochemical approach for aflatoxin analysis. Biotechnol Appl Biochem 2017; 65:274-280. [PMID: 28326608 DOI: 10.1002/bab.1563] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/15/2017] [Indexed: 12/22/2022]
Abstract
DNAzyme and aptamer conjugations have already been used for sensitive and accurate detection of several molecules. In this study, we tested the relationship between conjugation orientation of DNAzyme and aflatoxin B1 aptamer and their subsequent peroxidase activity. Circular dichroism (CD) spectroscopy and biochemical analysis were used here to differentiate between these two conjugation patterns. Results showed that DNAzyme-aptamer has more catalytic activity and efficiency than aptamer-DNAzyme. Thereby, DNAzyme-aptamer with its superior efficiency can be used for design and development of more sensitive aflatoxin B1 DNA based biosensors.
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Affiliation(s)
- Marzieh Jafari
- Department of Pharmacology and Toxicology, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohsen Rezaei
- Department of Pharmacology and Toxicology, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Toxicology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Heibatullah Kalantari
- Department of Pharmacology and Toxicology, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Tabarzad
- Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahram Daraei
- Department of Toxicology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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233
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Li X, Zhang H, Tang Y, Wu P, Xu S, Zhang X. A Both-End Blocked Peroxidase-Mimicking DNAzyme for Low-Background Chemiluminescent Sensing of miRNA. ACS Sens 2017; 2:810-816. [PMID: 28723123 DOI: 10.1021/acssensors.7b00178] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
G-quadruplex DNAzymes that exhibited peroxidase-like activity have been shown to be appealing reporters for amplified readout of biosensing events simply by their formation or dissociation in the presence of analytes. For low background signaling, the efficient preblock of DNAzymes is critically important. Herein, we report a both-end blocked DNAzyme beacon strategy for chemiluminescent biosensing. The catalytic activity of peroxidase-mimicking DNAzyme can be inactivated fully by fixing both ends of the DNAzyme sequence, and easily recovered via a strand displace reaction between the miRNA and the block DNA. The efficient block and recovery of DNAzymes provide the both-end blocked beacon the highest signal-to-background ratio (over 25) among the reported DNAzymes for amplification-free detection of miRNA. As a result, the beacon allowed detection of subpicomolar miRNA without any labeling and amplification procedures, which is about 40-fold more sensitive than the traditional hairpin fluorescence beacon. Also, it exhibited excellent discrimination ability that can distinguish single-base mismatch miRNA. The simplicity, high sensitivity, and selectivity provided by the beacon make it a promising alternative tool for nucleic acid detection.
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Affiliation(s)
- Xianming Li
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Houchun Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Yurong Tang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Peng Wu
- Analytical & Testing Center, Sichuan University, Chengdu 610064, China
| | - Shuxia Xu
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Xinfeng Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
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234
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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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235
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Ribes À, Aznar E, Bernardos A, Marcos MD, Amorós P, Martínez-Máñez R, Sancenón F. Fluorogenic Sensing of Carcinogenic Bisphenol A using Aptamer-Capped Mesoporous Silica Nanoparticles. Chemistry 2017; 23:8581-8584. [PMID: 28498545 DOI: 10.1002/chem.201701024] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Indexed: 12/21/2022]
Abstract
Mesoporous silica nanoparticles loaded with rhodamine B and capped with a bisphenol A aptamer were used for the selective and sensitive detection of this lethal chemical. The pores of the nanoparticles are selectively opened in the presence of bisphenol A (through its selective coordination with the aptamer) with subsequent rhodamine B delivery. With this capped material a limit of detection as low as 3.5 μm of bisphenol A was measured.
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Affiliation(s)
- Àngela Ribes
- Instituto Interuniversitario de Investigación de Reconocimiento MolecularyDesarrollo Tecnológico (IDM)., Universitat Politècnica de València, Universitat de València, Camí de Vera s/N, 46022, Valencia, Spain.,CIBER de Bioingeniería, BiomaterialesyNanomedicina (CIBER-BBN)
| | - Elena Aznar
- Instituto Interuniversitario de Investigación de Reconocimiento MolecularyDesarrollo Tecnológico (IDM)., Universitat Politècnica de València, Universitat de València, Camí de Vera s/N, 46022, Valencia, Spain.,CIBER de Bioingeniería, BiomaterialesyNanomedicina (CIBER-BBN)
| | - Andrea Bernardos
- Instituto Interuniversitario de Investigación de Reconocimiento MolecularyDesarrollo Tecnológico (IDM)., Universitat Politècnica de València, Universitat de València, Camí de Vera s/N, 46022, Valencia, Spain.,CIBER de Bioingeniería, BiomaterialesyNanomedicina (CIBER-BBN)
| | - M Dolores Marcos
- Instituto Interuniversitario de Investigación de Reconocimiento MolecularyDesarrollo Tecnológico (IDM)., Universitat Politècnica de València, Universitat de València, Camí de Vera s/N, 46022, Valencia, Spain.,CIBER de Bioingeniería, BiomaterialesyNanomedicina (CIBER-BBN).,Departamento de química, Universitat Politècnica de València, Camí de Vera s/N, 46022, Valencia, Spain
| | - Pedro Amorós
- Institut de Ciència dels Materials (ICMUV), Universitat de València, P.O. Box 22085, 46071, Valencia, Spain
| | - Ramón Martínez-Máñez
- Instituto Interuniversitario de Investigación de Reconocimiento MolecularyDesarrollo Tecnológico (IDM)., Universitat Politècnica de València, Universitat de València, Camí de Vera s/N, 46022, Valencia, Spain.,CIBER de Bioingeniería, BiomaterialesyNanomedicina (CIBER-BBN).,Departamento de química, Universitat Politècnica de València, Camí de Vera s/N, 46022, Valencia, Spain
| | - Félix Sancenón
- Instituto Interuniversitario de Investigación de Reconocimiento MolecularyDesarrollo Tecnológico (IDM)., Universitat Politècnica de València, Universitat de València, Camí de Vera s/N, 46022, Valencia, Spain.,CIBER de Bioingeniería, BiomaterialesyNanomedicina (CIBER-BBN).,Departamento de química, Universitat Politècnica de València, Camí de Vera s/N, 46022, Valencia, Spain
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236
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Yang Y, Wang KZ, Yan D. Smart Luminescent Coordination Polymers toward Multimode Logic Gates: Time-Resolved, Tribochromic and Excitation-Dependent Fluorescence/Phosphorescence Emission. ACS APPLIED MATERIALS & INTERFACES 2017; 9:17399-17407. [PMID: 28441860 DOI: 10.1021/acsami.7b00594] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this work, we propose that lanthanide cations (such as Eu3+ and Tb3+)-doped long-afterglow coordination polymers (CPs) can be an effective tool for designing multimode optical logic gates based on their tunable fluorescence/phosphorescence transformation and state-dependent emission. First, multicolor and white-light luminescence across the blue/green/yellow/red visible regions can be obtained by balancing the co-doping ratio of Eu3+/Tb3+ cations and suitable excitations. Additionally, a new tribochromic Eu-Cd-CP was developed based on the mechanism of a change in structural symmetry. Benefitting from long-afterglow, tribochromism, and excitation-dependent emission on the same luminescent CP, a new three-input and three-output logic gate was obtained. Therefore, this work not only provides detailed insights into the interesting fields of tribochromism and tunable photoemission, but also confirms that long-afterglow CPs can serve as a new platform for the construction of smart luminescent systems and multimode optical logic gates.
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Affiliation(s)
- Yongsheng Yang
- Beijing Key Laboratory of Energy Conversion and Storage Materials College of Chemistry, Beijing Normal University , Beijing 100875, P. R. China
| | - Ke-Zhi Wang
- Beijing Key Laboratory of Energy Conversion and Storage Materials College of Chemistry, Beijing Normal University , Beijing 100875, P. R. China
| | - Dongpeng Yan
- Beijing Key Laboratory of Energy Conversion and Storage Materials College of Chemistry, Beijing Normal University , Beijing 100875, P. R. China
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing 100029, P. R. China
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237
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Fozooni T, Ravan H, Sasan H. Signal Amplification Technologies for the Detection of Nucleic Acids: from Cell-Free Analysis to Live-Cell Imaging. Appl Biochem Biotechnol 2017; 183:1224-1253. [DOI: 10.1007/s12010-017-2494-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 04/24/2017] [Indexed: 12/15/2022]
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238
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Zhang X, Soh S. Performing Logical Operations with Stimuli-Responsive Building Blocks. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1606483. [PMID: 28247973 DOI: 10.1002/adma.201606483] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/23/2017] [Indexed: 06/06/2023]
Abstract
Chemical logic gates can be fabricated by synthesizing molecules that have the ability to detect external stimuli (e.g., temperature or pH) and provide logical outputs. It is, however, challenging to fabricate a system that consists of many logic gates using this method: complex molecules can be difficult to synthesize and these logic gates typically cannot be integrated together. Here, we fabricated different types of logic gates by assembling a combination of different types of stimuli-responsive hydrogels that change their size under the influence of one type of stimulus. Importantly, the preparation of these stimuli-responsive hydrogels is widely reported and technically simple. Through designing the geometry of the systems, we fabricated the YES, NOT, OR, AND, NOR, and NAND gates. Although the hydrogels respond to different types of stimuli, their outputs are the same: a change in size of the hydrogel. Hence, we show that the logic gates can be integrated easily (e.g., by connecting an AND gate to an OR gate). In addition, we fabricated a standalone system with the size of a normal drug tablet (i.e., a "smart tablet") that can analyze (or diagnose) different stimuli and control the release of a chemical (or drug) via the logic gates.
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Affiliation(s)
- Xuan Zhang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Siowling Soh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
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239
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Dolot R, Sobczak M, Mikołajczyk B, Nawrot B. Synthesis, crystallization and preliminary crystallographic analysis of a 52-nucleotide DNA/2'-OMe-RNA oligomer mimicking 10-23 DNAzyme in the complex with a substrate. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:292-301. [PMID: 28323518 DOI: 10.1080/15257770.2016.1276291] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
A 52-nucleotide DNA/2'-OMe-RNA oligomer mimicking 10-23 DNAzyme in the complex with its substrate was synthesized, purified and crystallized by the hanging-drop method using 0.8 M sodium potassium tartrate as a precipitant. A data set to 1.21 Å resolution was collected from a monocrystal at 100 K using synchrotron radiation on a beamline BL14.1 at BESSY. The crystal belonged to the P21 group with unit-cell a = 49.42, b = 24.69, c = 50.23, β = 118.48.
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Affiliation(s)
- Rafał Dolot
- a Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences , Department of Bioorganic Chemistry , Łódź , Poland
| | - Milena Sobczak
- a Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences , Department of Bioorganic Chemistry , Łódź , Poland
| | - Barbara Mikołajczyk
- a Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences , Department of Bioorganic Chemistry , Łódź , Poland
| | - Barbara Nawrot
- a Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences , Department of Bioorganic Chemistry , Łódź , Poland
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240
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Li Y, Zou X, Ma F, Tang B, Zhang CY. Development of fluorescent methods for DNA methyltransferase assay. Methods Appl Fluoresc 2017; 5:012002. [DOI: 10.1088/2050-6120/aa6127] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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241
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Lashgari N, Badiei A, Mohammadi Ziarani G, Faridbod F. Isatin functionalized nanoporous SBA-15 as a selective fluorescent probe for the detection of Hg(II) in water. Anal Bioanal Chem 2017; 409:3175-3185. [PMID: 28271223 DOI: 10.1007/s00216-017-0258-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/15/2017] [Accepted: 02/13/2017] [Indexed: 01/21/2023]
Abstract
A highly ordered mesoporous silica material functionalized with isatin (SBA-Pr-IS) was designed and synthesized. Characterization techniques including XRD, TGA, BET, SEM, and FT-IR were employed to characterize the pore structure, textural properties, microscopic morphology, and molecular composition of grafted organic moieties of SBA-Pr-IS. The successful attachment of the organic moiety (0.34 mmol g-1) without the SBA-15 structure collapsing after the modification steps was confirmed. Fluorescence characterization of SBA-Pr-IS was examined upon addition of a wide variety of cations in aqueous medium and it showed high sensitivity toward Hg2+ ions. During testing in an ion competition experiment, it was observed that the fluorescence changes of the probe were remarkably specific for Hg2+ ions. Furthermore, a good linearity between the fluorescence intensity of this material and the concentration of Hg2+ ions was constructed with a suitable detection limit of 3.7 × 10-6 M. Finally, the applicability of the proposed method was successfully evaluated for the determination of Hg2+ ions in real samples. Therefore, SBA-Pr-IS can be used as an efficient fluorescence probe for Hg2+ ions. Graphical Abstract A novel organic-inorganic hybrid material was designed and synthesized by functionalization of SBA-15 mesoporous silica material with isatin. The evaluation of the sensing ability of SBA-Pr-IS using fluorescence spectroscopy revealed that the SBA-Pr-IS was a selective fluorescent probe for Hg2+ ion in water in the presence of a wide range of metal cations.
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Affiliation(s)
- Negar Lashgari
- School of Chemistry, College of Science, University of Tehran, 16th Azar St., Enghelab Sq., 1417466191, Tehran, Iran
| | - Alireza Badiei
- School of Chemistry, College of Science, University of Tehran, 16th Azar St., Enghelab Sq., 1417466191, Tehran, Iran. .,Nanobiomedicine Center of Excellence, Nanoscience and Nanotechnology Research Center, University of Tehran, 16th Azar St., Enghelab Sq., 1417466191, Tehran, Iran.
| | | | - Farnoush Faridbod
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, 16th Azar St., Enghelab Sq., 1417466191, Tehran, Iran
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242
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Chen J, Guo Y, Zhou J, Ju H. The Effect of Adenine Repeats on G-quadruplex/hemin Peroxidase Mimicking DNAzyme Activity. Chemistry 2017; 23:4210-4215. [PMID: 28121370 DOI: 10.1002/chem.201700040] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 01/19/2023]
Abstract
The catalytic activity of G-quadruplex/hemin is much lower than that of proteinous enzymes, so it is very important to increase its activity. Very recently, flanking sequences, which can be regarded as an external part of G-quadruplexes, were found to enhance the activity of G-quadruplex/hemin DNAzyme. However, little is known about the effect of internal parts, such as loop sequences and linkers, on the activity. In the present study, adenine repeats were incorporated into several designed G-quadruplex structures either in the loops, bulges, or linkers, and the constructed G-quadruplex/hemin DNAzyme exhibit about fivefold improvement in peroxidase-mimicking activity in some cases. The enhancement effect may result from the formation of compound I, protoporphyrin⋅FeIV =O.+ , accelerated by dA repeats, which was demonstrated by H2 O2 decay kinetics and pH dependency analysis. The novel enhancement methods described here may help in the development of high-activity DNAzymes, illustrated by a dimer G-quadruplex with flanking adenine at one end, a relatively long adenine run in one loop, and another adenine run in the linker.
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Affiliation(s)
- Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yuehua Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
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243
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Yu T, Liu B, Liu J. Adsorption of Selenite and Selenate by Metal Oxides Studied with Fluorescent DNA Probes for Analytical Application. JOURNAL OF ANALYSIS AND TESTING 2017. [DOI: 10.1007/s41664-017-0001-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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244
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Wu N, Willner I. Programmed dissociation of dimer and trimer origami structures by aptamer-ligand complexes. NANOSCALE 2017; 9:1416-1422. [PMID: 28084482 DOI: 10.1039/c6nr08209b] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Dimer- and trimer-origami frames are bridged by duplexes that include caged, sequence-specific, anti-ATP and/or anti-cocaine aptamer sequences. The programmed dissociation of the origami dimers or trimers in the presence of ATP and/or cocaine ligands is demonstrated. The processes are followed by AFM imaging and by electrophoretic experiments.
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Affiliation(s)
- Na Wu
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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245
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Song X, Eshra A, Dwyer C, Reif J. Renewable DNA seesaw logic circuits enabled by photoregulation of toehold-mediated strand displacement. RSC Adv 2017. [DOI: 10.1039/c7ra02607b] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We propose a scalable design and verifications for photoregulated renewable DNA seesaw logic circuits, which can be repeatedly reset to reliably process new inputs. Synchronized control of complex DNA reaction networks could be achieved efficiently.
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Affiliation(s)
- Xin Song
- Department of Electrical and Computer Engineering
- Duke University
- Durham
- USA
| | - Abeer Eshra
- Department of Computer Science
- Duke University
- Durham
- USA
- Department of Computer Science and Engineering
| | - Chris Dwyer
- Department of Electrical and Computer Engineering
- Duke University
- Durham
- USA
- Department of Computer Science
| | - John Reif
- Department of Electrical and Computer Engineering
- Duke University
- Durham
- USA
- Department of Computer Science
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246
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Yan Y, Yue S, Zhao T, Luo B, Bi S. Exonuclease-assisted target recycling amplification for label-free chemiluminescence assay and molecular logic operations. Chem Commun (Camb) 2017; 53:12201-12204. [DOI: 10.1039/c7cc06835b] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A versatile exonuclease-assisted target recycling amplification strategy is demonstrated to achieve label-free chemiluminescence detection of DNA and construction of a series of two-input molecular logic gates.
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Affiliation(s)
- Yongcun Yan
- Collaborative Innovation Center for Marine Biomass Fiber
- Materials and Textiles of Shandong Province
- College of Chemistry and Chemical Engineering
- Laboratory of Fiber Materials and Modern Textiles
- the Growing Base for State Key Laboratory
| | - Shuzhen Yue
- Collaborative Innovation Center for Marine Biomass Fiber
- Materials and Textiles of Shandong Province
- College of Chemistry and Chemical Engineering
- Laboratory of Fiber Materials and Modern Textiles
- the Growing Base for State Key Laboratory
| | - Tingting Zhao
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Baoyu Luo
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Sai Bi
- Collaborative Innovation Center for Marine Biomass Fiber
- Materials and Textiles of Shandong Province
- College of Chemistry and Chemical Engineering
- Laboratory of Fiber Materials and Modern Textiles
- the Growing Base for State Key Laboratory
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247
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Computational Biosensors: Molecules, Algorithms, and Detection Platforms. MODELING, METHODOLOGIES AND TOOLS FOR MOLECULAR AND NANO-SCALE COMMUNICATIONS 2017. [PMCID: PMC7123247 DOI: 10.1007/978-3-319-50688-3_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Advanced nucleic acid-based sensor-applications require computationally intelligent biosensors that are able to concurrently perform complex detection and classification of samples within an in vitro platform. Realization of these cutting-edge computational biosensor systems necessitates innovation and integration of three key technologies: molecular probes with computational capabilities, algorithmic methods to enable in vitro computational post processing and classification, and immobilization and detection approaches that enable the realization of deployable computational biosensor platforms. We provide an overview of current technologies, including our contributions towards the development of computational biosensor systems.
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248
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Bi S, Yue S, Zhang S. Hybridization chain reaction: a versatile molecular tool for biosensing, bioimaging, and biomedicine. Chem Soc Rev 2017; 46:4281-4298. [DOI: 10.1039/c7cs00055c] [Citation(s) in RCA: 393] [Impact Index Per Article: 56.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review provides a comprehensive overview of the fundamental principles, analysis techniques, and application fields of hybridization chain reaction and its development status.
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Affiliation(s)
- Sai Bi
- Collaborative Innovation Center for Marine Biomass Fiber
- Materials and Textiles of Shandong Province
- College of Chemistry and Chemical Engineering
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- Laboratory of Fiber Materials and Modern Textiles
| | - Shuzhen Yue
- Collaborative Innovation Center for Marine Biomass Fiber
- Materials and Textiles of Shandong Province
- College of Chemistry and Chemical Engineering
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- Laboratory of Fiber Materials and Modern Textiles
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Makers
- College of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005
- P. R. China
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249
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Alizadeh N, Salimi A, Hallaj R. Hemin/G-Quadruplex Horseradish Peroxidase-Mimicking DNAzyme: Principle and Biosensing Application. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 170:85-106. [DOI: 10.1007/10_2017_37] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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250
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George AK, Singh H. Enzyme-Free Scalable DNA Digital Design Techniques: A Review. IEEE Trans Nanobioscience 2016; 15:928-938. [DOI: 10.1109/tnb.2016.2623218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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