51
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Shlaferman J, Paige A, Meserve K, Miech JA, Gerdon AE. Selected DNA Aptamers Influence Kinetics and Morphology in Calcium Phosphate Mineralization. ACS Biomater Sci Eng 2019; 5:3228-3236. [DOI: 10.1021/acsbiomaterials.9b00308] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jacob Shlaferman
- Department of Chemistry and Physics, Emmanuel College, 400 The Fenway, Boston, Massachusetts 02115, United States
| | - Alexander Paige
- Department of Chemistry and Physics, Emmanuel College, 400 The Fenway, Boston, Massachusetts 02115, United States
| | - Krista Meserve
- Department of Chemistry and Physics, Emmanuel College, 400 The Fenway, Boston, Massachusetts 02115, United States
| | - Jason A. Miech
- Department of Chemistry and Physics, Emmanuel College, 400 The Fenway, Boston, Massachusetts 02115, United States
| | - Aren E. Gerdon
- Department of Chemistry and Physics, Emmanuel College, 400 The Fenway, Boston, Massachusetts 02115, United States
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52
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Zong C, Zhang Z, Liu B, Liu J. Adsorption of Arsenite on Gold Nanoparticles Studied with DNA Oligonucleotide Probes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:7304-7311. [PMID: 31079464 DOI: 10.1021/acs.langmuir.9b01161] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Gold nanoparticles (AuNPs) have been extensively used for detecting arsenite, As(III). Many methods rely on a DNA aptamer that claimed to bind specifically to inorganic arsenic. In these cases, the focus was on arsenic binding to the aptamer, while the potential interactions between As(III) and the AuNP surface were ignored. Herein, a set of spectroscopic and isothermal titration calorimetry (ITC) experiments were conducted to measure the adsorption of As(III) by AuNPs and its competition with DNA adsorption. With 10 mM As(III), 18% of adsorbed DNA was displaced from AuNPs, while preadsorption of only 20 μM As(III) inhibited DNA adsorption by around 50%. The affinity of As(III) on AuNPs is comparable to Br- and guanosine. ITC and Raman spectroscopy both indicated that only As(III) can be adsorbed, while As(V) had no measurable interactions with the AuNPs. Based on this understanding, a random DNA sequence was used and a similar colorimetric response in the presence of As(III) was observed. This study confirmed the affinity between As(III) and the gold surface. The As(III)/gold interaction is strong enough to affect DNA adsorption, and care should be taken to interpret the observations based on the color change of AuNPs for the detection of As(III).
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Affiliation(s)
- Chenghua Zong
- Department of Chemistry and Materials Science, Jiangsu Key Laboratory of Green Synthesis for Functional Materials , Jiangsu Normal University , Xuzhou , Jiangsu 221116 , P. R. China
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Zijie Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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53
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Satyavolu NSR, Loh KY, Tan LH, Lu Y. Discovery of and Insights into DNA "Codes" for Tunable Morphologies of Metal Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900975. [PMID: 31074939 PMCID: PMC6663601 DOI: 10.1002/smll.201900975] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/14/2019] [Indexed: 05/28/2023]
Abstract
The discovery and elucidation of genetic codes has profoundly changed not only biology but also many fields of science and engineering. The fundamental building blocks of life comprises of four simple deoxyribonucleotides and yet their combinations serve as the carrier of genetic information that encodes for proteins that can carry out many biological functions due to their unique functionalities. Inspired by nature, the functionalities of DNA molecules have been used as a capping ligand for controlling morphology of nanomaterials, and such a control is sequence dependent, which translates into distinct physical and chemical properties of resulting nanoparticles. Herein, an overview on the use of DNA as engineered codes for controlling the morphology of metal nanoparticles, such as gold, silver, and Pd-Au bimetallic nanoparticles is provided. Fundamental insights into rules governing DNA controlled growth mechanisms are also summarized, based on understanding of the affinity of the DNA nucleobases to various metals, the effect of combination of nucleobases, functional modification of DNA, the secondary structures of DNA, and the properties of the seed employed. The resulting physical and chemical properties of these DNA encoded nanomaterials are also reviewed, while perspectives into the future directions of DNA-mediated nanoparticle synthesis are provided.
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Affiliation(s)
- Nitya Sai Reddy Satyavolu
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Kang Yong Loh
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Li Huey Tan
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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54
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Li X, Kong C, Chen Z. Colorimetric Sensor Arrays for Antioxidant Discrimination Based on the Inhibition of the Oxidation Reaction between 3,3',5,5'-Tetramethylbenzidine and Hydrogen Peroxides. ACS APPLIED MATERIALS & INTERFACES 2019; 11:9504-9509. [PMID: 30735025 DOI: 10.1021/acsami.8b18548] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The discrimination of antioxidants is of great significance because of their essential roles in various biological processes and many diseases. Compared with the traditional lock-key sensing mode for single target detection at a time, sensor arrays can discriminate various antioxidants simultaneously. Nanomaterial-based sensor arrays have shown great promise for antioxidant discrimination; however, as far as it is known, none of them have been reported for discriminating antioxidants based on the catalytic reaction of intrinsic peroxidase-like activity of two-dimensional nanomaterials. To fill the gap, we herein unveil a colorimetric (e.g., UV-vis absorption) approach for antioxidant discrimination based on the three nanomaterial [graphene oxide, molybdenum disulfide (MoS2), and tungsten disulfide (WS2)]-catalyzed 3,3',5,5'-tetramethylbenzidine (TMB)-hydrogen peroxide (H2O2) reaction system. In this sensor array, the antioxidants inhibit the reaction between TMB and H2O2, resulting in different colorimetric response patterns. The obtained patterns for five antioxidants, including ascorbic acid, cysteine, melatonin, uric acid, and glutathione (GSH), at the 60 nM level, were successfully discriminated using linear discriminant analysis both in buffer and serum samples.
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Affiliation(s)
- Xin Li
- Department of Chemistry , Capital Normal University , Beijing 100048 , China
| | - Caiyun Kong
- Department of Chemistry , Capital Normal University , Beijing 100048 , China
| | - Zhengbo Chen
- Department of Chemistry , Capital Normal University , Beijing 100048 , China
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55
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Chinnakkannu Vijayakumar S, Venkatakrishnan K, Tan B. 3D quantum theranosomes: a new direction for label-free theranostics. NANOSCALE HORIZONS 2019; 4:495-515. [PMID: 32254103 DOI: 10.1039/c8nh00287h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Quantum-scale materials offer great potential in the field of cancer theranostics. At present, quantum materials are severely limited due to 0D & 1D materials lacking biocompatibility, resulting in coated materials with labelled tags for fluorescence excitation. In addition, the application of magnetic quantum materials has not been reported to date for cancer theranostics. In this current research study, we introduce the concept of applying nickel-based magnetic 3D quantum theranosomes for label-free broadband fluorescence enhancement and cancer therapy. To begin with, we present two (primary and secondary) distinct quantum theranosomes for cancer detection and differentiation (HeLa & MDAMB-231) from mammalian fibroblast cells. The primary theranosomes exhibit a metal enhanced fluorescence (MEF) property through localized surface plasmon resonance to act as cancer detectors, whereas the secondary theranosomes act as cancer differentiators through the fluorescence quenching of HeLa cancer cells. Apart from the above, the synthesized magnetic quantum theranosomes introduced therapeutic functionality wherein the theranosomes mimicked a tumor microenvironment by selectively accelerating the proliferation of mammalian fibroblasts cells while at the same time inducing cancer therapy. These quantum theranosomes were synthesized using femtosecond pulse laser ablation and self-assembled to form an interconnected 3D structure. The 3D architecture and the physicochemical properties of the laser synthesized quantum theranosomes closely resembled a tumor microenvironment. Furthermore, we anticipate that our current recorded findings can shed further light upon these unique magnetic quantum theranosomes as potential contenders towards opening an entirely new direction in the field of cancer theranostics.
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Affiliation(s)
- Sivaprasad Chinnakkannu Vijayakumar
- Ultrashort Laser Manufacturing Research Facility, Department of Mechanical and Industrial Engineering, Ryerson University, 350 Victoria street, Toronto, Ontario M5B 2K3, Canada.
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56
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Ding W, Song C, Li T, Ma H, Yao Y, Yao C. TiO 2 nanowires as an effective sensing platform for rapid fluorescence detection of single-stranded DNA and double-stranded DNA. Talanta 2019; 199:442-448. [PMID: 30952281 DOI: 10.1016/j.talanta.2019.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 01/24/2019] [Accepted: 02/01/2019] [Indexed: 11/28/2022]
Abstract
Numerous nanomaterials have been utilized for novel biosensors with sensitivity and selectivity in the last decades due to their intrinsic unique properties. Herein, a facile fluorescence method for nucleic acid detection was developed by employing TiO2 nanowires (NWs) as the sensing platform. The quenching effect of TiO2 NWs to fluorophore-labelled single-stranded DNA (ssDNA) was found to be more significant than that to fluorophore-labelled double-stranded DNA (dsDNA) or triplex DNA probes. More importantly, the whole quenching process was also fast since it just took about ten minutes to reach the equilibrium. Based on the different affinities of TiO2 NWs to ssDNA, dsDNA and triplex DNA probes, the sequence-specific nucleic acids were detected with sensitivity and specificity. Further investigation has demonstrated that the quenching efficiency of TiO2 NWs to long ssDNA was apparently superior than that to short ssDNA. Moreover, the fluorescence from various ssDNA probes labelled with a wide spectrum of fluorescent dyes could also be quenched by TiO2 NWs. These inspiring results reveal that TiO2 NWs could be an excellent universal nanoquencher used in the next-generation biosensors.
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Affiliation(s)
- Wei Ding
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Chan Song
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Tianle Li
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Haoran Ma
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yuewei Yao
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Cheng Yao
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China.
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57
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Bandyopadhyay P, Jana R, Bhattacharyya K, Lebedev OI, Dutta U, Sarkar U, Datta A, Seikh MM. Interaction of a bioactive molecule with surfaces of nanoscale transition metal oxides: experimental and theoretical studies. NEW J CHEM 2019. [DOI: 10.1039/c9nj03124c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Schematic diagram of metal oxide–BTT interaction and the associated changes in experimental UV-Vis spectra. BTT adsorbed α-Fe2O3 is represented by red spectra, while green spectra represent BTT adsorbed NiO. Black spectra represent pure BTT spectra.
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Affiliation(s)
| | - Rajkumar Jana
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | | | | | - Uma Dutta
- Department of Chemistry
- Visva-Bharati
- Santiniketan-731235
- India
| | - Utpal Sarkar
- Department of Physics
- Assam University
- Silchar-788011
- India
| | - Ayan Datta
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Md Motin Seikh
- Department of Chemistry
- Visva-Bharati
- Santiniketan-731235
- India
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58
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Hlongwane GN, Dodoo-Arhin D, Wamwangi D, Daramola MO, Moothi K, Iyuke SE. DNA hybridisation sensors for product authentication and tracing: State of the art and challenges. SOUTH AFRICAN JOURNAL OF CHEMICAL ENGINEERING 2019. [DOI: 10.1016/j.sajce.2018.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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59
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Wang X, Liu B, Liu J. DNA-Functionalized Nanoceria for Probing Oxidation of Phosphorus Compounds. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15871-15877. [PMID: 30516388 DOI: 10.1021/acs.langmuir.8b03335] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Chemical reactions without an obvious optical signal change, such as fluorescence or color, are difficult to monitor. Often, more advanced analytical techniques such as high-performance liquid chromatography and mass spectroscopy are needed. It would be useful to convert such reactions to those with changes in optical signals. In this work, we demonstrate that fluorescently labeled DNA oligonucleotides adsorbed on nanomaterials can probe such reactions, and oxidation of phosphorus-containing species was used as an example. Various metal oxides were tested, and CeO2 nanoparticles were found to be the most efficient for this purpose. Among phosphate, phosphite, and hypophosphite, only phosphate produced a large signal, indicating its strongest adsorption on CeO2 to displace the DNA. This was further used to screen oxidation agents to convert lower oxidation-state compounds to phosphate, and bleach was found to be able to oxidize phosphite. Canonical discriminant analysis was performed to discriminate various phosphorus species using a sensor array containing different metal oxides. On the basis of this, glyphosate was studied for its adsorption and oxidation. Although this method is not specific enough for selective biosensors, it is useful as a tool to produce sensitive optical signals to follow important chemical transformations.
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Affiliation(s)
- Xiuzhong Wang
- College of Chemistry and Pharmaceutical Sciences , Qingdao Agricultural University , Qingdao 266109 , China
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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60
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Tong L, Wang X, Gao W, Liu Z, Chen Z, Cheng G, Cao W, Sui M, Tang B. CeO 2 Nanowire-BODIPY-Adenosine Triphosphate Fluorescent Sensing Platform for Highly Specific and Sensitive Detection of Arsenate. Anal Chem 2018; 90:14507-14513. [PMID: 30477304 DOI: 10.1021/acs.analchem.8b04354] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Effective and sensitive monitoring of arsenate in drinking water is significant for risk management of public health. Here, we demonstrated that a CeO2 nanowire acted as an efficient quencher for small fluorescent molecules with a phosphate group, BODIPY-adenosine triphosphate (BODIPY-ATP) and riboflavin-5'-phosphate (Rf-P), and developed a CeO2 nanowire-BODIPY-ATP platform for highly selective and sensitive detection of arsenate. The response strategy was based on the competitive coordination chemistry of CeO2 nanowire between arsenate and phosphate group of BODIPY-ATP. Arsenate displaced adsorbed BODIPY-ATP to enhance fluorescence, allowing detection of arsenate down to 7.8 nM, which is lower than the WHO-defined limit of 130 nM. An excellent linear range of 20-150 and 150-1000 nM was obtained. Importantly, this system was simple in design and convenient in operation. Also, the platform exhibited excellent selectivity for arsenate without the interference of phosphate ions. Finally, the proposed method had been successfully employed for determination of arsenate in real water samples.
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Affiliation(s)
- Lili Tong
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences , Shandong Normal University , Jinan 250014 , People's Republic of China
| | - Xiuxiu Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences , Shandong Normal University , Jinan 250014 , People's Republic of China
| | - Wen Gao
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences , Shandong Normal University , Jinan 250014 , People's Republic of China
| | - Zhenhua Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences , Shandong Normal University , Jinan 250014 , People's Republic of China
| | - Zhenzhen Chen
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences , Shandong Normal University , Jinan 250014 , People's Republic of China
| | - Guiying Cheng
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences , Shandong Normal University , Jinan 250014 , People's Republic of China
| | - Wenhua Cao
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences , Shandong Normal University , Jinan 250014 , People's Republic of China
| | - Meiju Sui
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences , Shandong Normal University , Jinan 250014 , People's Republic of China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences , Shandong Normal University , Jinan 250014 , People's Republic of China
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61
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Affiliation(s)
- Teresa L. Mako
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Joan M. Racicot
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Mindy Levine
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
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62
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Meng Y, Liu P, Zhou W, Ding J, Liu J. Bioorthogonal DNA Adsorption on Polydopamine Nanoparticles Mediated by Metal Coordination for Highly Robust Sensing in Serum and Living Cells. ACS NANO 2018; 12:9070-9080. [PMID: 30130385 DOI: 10.1021/acsnano.8b03019] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
DNA-functionalized nanomaterials, such as various 2D materials, metal oxides, and gold nanoparticles, have been extensively explored as biosensors. However, their practical applications for selective sensing and imaging in biological samples remain challenging due to interference from the sample matrix. Bioorthogonal chemistry has allowed specific reactions in cells, and we want to employ this concept to design nanomaterials that can selectively adsorb DNA but not proteins or other abundant biomolecules. In this work, DNA oligonucleotides were found to be adsorbed on polydopamine nanoparticles (PDANs) via polyvalent metal-mediated coordination, and such adsorption bioorthogonally resisted DNA displacement by various biological ligands, showing better performance compared to graphene oxide and metal oxide nanoparticles for DNA detection. Using DNA/PDANs as biosensors, a detection limit of <1 nM target DNA was achieved in serum and other biological samples, and imaging of cancer-related microRNA in cells was demonstrated. The DNA binding mechanism on PDAN was further studied by ligand displacement experiments and X-ray photoelectron spectroscopy characterization, which demonstrated the critical role of polyvalent metal ions to bridge DNA with PDANs. This work provides fundamental insights into the biointerface science of PDANs with DNA, which can benefit applications in biosensor design, directed assembly of nanomaterials, bioimaging, and drug delivery.
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Affiliation(s)
- Yingcai Meng
- Xiangya School of Pharmaceutical Sciences , Central South University , Changsha , Hunan 410013 , China
| | - Peng Liu
- Xiangya School of Pharmaceutical Sciences , Central South University , Changsha , Hunan 410013 , China
| | - Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences , Central South University , Changsha , Hunan 410013 , China
| | - Jinsong Ding
- Xiangya School of Pharmaceutical Sciences , Central South University , Changsha , Hunan 410013 , China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario , Canada , N2L 3G1
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63
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Xu L, Zhang P, Liu Y, Fang X, Zhang Z, Liu Y, Peng L, Liu J. Continuously Tunable Nucleotide/Lanthanide Coordination Nanoparticles for DNA Adsorption and Sensing. ACS OMEGA 2018; 3:9043-9051. [PMID: 31459038 PMCID: PMC6644583 DOI: 10.1021/acsomega.8b01217] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 08/07/2018] [Indexed: 05/02/2023]
Abstract
Metal-organic coordination polymers (CPs) have attracted great research interest because they are easy to prepare, porous, flexible in composition, and designable in structure. Their applications in biosensor development, drug delivery, and catalysis have been explored. Lanthanides and nucleotides can form interesting CPs, although most previous works have focused on a single type of metal ligand. In this work, we explored mixed nucleotides and studied their DNA adsorption properties using fluorescently labeled oligonucleotides. Adenosine monophosphate (AMP) and guanosine monophosphate (GMP) formed negatively charged CP nanoparticles with most lanthanides, and thus a salt was required to adsorb negatively charged DNA. DNA adsorption was faster and reached a higher capacity with lighter lanthanides. Desorption of pre-adsorbed DNA by inorganic phosphates, urea, proteins, surfactants, and competing DNA was successively carried out. The results suggested the importance of the DNA phosphate backbone, although hydrogen bonding and DNA bases also contributed to adsorption. The AMP CPs adsorbed DNA more strongly than the GMP ones, and using mixtures of AMP and GMP, continuous tuning of DNA adsorption affinity was achieved. Such CPs were also used as a sensor for DNA detection based on the different affinities of single- and double-stranded DNA, and a detection limit of 0.9 nM target DNA was achieved. Instead of tuning DNA adsorption by varying the length and sequence of DNA, the composition of CPs can also be controlled to achieve this goal.
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Affiliation(s)
- Li Xu
- School of Chemistry
and Chemical Engineering, Guangdong Pharmaceutical
University, Zhongshan 528458, P. R. China
- Department
of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Peipei Zhang
- School of Chemistry
and Chemical Engineering, Guangdong Pharmaceutical
University, Zhongshan 528458, P. R. China
| | - Yan Liu
- School of Chemistry
and Chemical Engineering, Guangdong Pharmaceutical
University, Zhongshan 528458, P. R. China
| | - Xiaoqiang Fang
- School of Chemistry
and Chemical Engineering, Guangdong Pharmaceutical
University, Zhongshan 528458, P. R. China
| | - Zijie Zhang
- Department
of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Yibo Liu
- Department
of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Lulu Peng
- School of Chemistry
and Chemical Engineering, Guangdong Pharmaceutical
University, Zhongshan 528458, P. R. China
| | - Juewen Liu
- Department
of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
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64
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Qin L, Wang X, Liu Y, Wei H. 2D-Metal-Organic-Framework-Nanozyme Sensor Arrays for Probing Phosphates and Their Enzymatic Hydrolysis. Anal Chem 2018; 90:9983-9989. [PMID: 30044077 DOI: 10.1021/acs.analchem.8b02428] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The detection of phosphates and their enzymatic hydrolysis is of great importance because of their essential roles in various biological processes and numerous diseases. Compared with individual sensors for detecting one given phosphate at a time, sensor arrays are able to discriminate multiple phosphates simultaneously. Although nanomaterial-based sensor arrays have shown great promise for the discrimination of phosphates, very few of them have been explored for probing phosphates involved enzymatic hydrolysis. To fill this gap, herein we fabricated two-dimensional-metal-organic-framework (2D-MOF)-nanozyme-based sensor arrays by modulating their peroxidase-mimicking activity with various phosphates, including AMP, ADP, ATP, pyrophosphate (PPi), and phosphate (Pi). The sensor arrays were used to successfully discriminate the five phosphates not only in aqueous solutions but also in biological samples. The practical application of the sensor arrays was then validated with blind samples, where 30 unknown samples containing phosphates were accurately identified. Moreover, the sensor arrays were successfully applied to probing hydrolytic processes involving ATP and PPi that are catalyzed by apyrase and PPase, respectively. This work demonstrates a nanozyme-based sensor array as a convenient and reliable analytical platform for probing phosphates and their related enzymatic processes, which could be applied to other analytes and enzymatic reactions.
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Affiliation(s)
- Li Qin
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures , Nanjing University , Nanjing , Jiangsu 210093 , China
| | - Xiaoyu Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures , Nanjing University , Nanjing , Jiangsu 210093 , China
| | - Yufeng Liu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures , Nanjing University , Nanjing , Jiangsu 210093 , China
| | - Hui Wei
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures , Nanjing University , Nanjing , Jiangsu 210093 , China.,State Key Laboratory of Analytical Chemistry for Life Science and State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences , Nanjing University , Nanjing , Jiangsu 210023 , China
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65
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Chen L, Liu B, Xu Z, Liu J. NiO Nanoparticles for Exceptionally Stable DNA Adsorption and Its Extraction from Biological Fluids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:9314-9321. [PMID: 30001142 DOI: 10.1021/acs.langmuir.8b01743] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Selective extraction of a small amount of nucleic acids from complex biological samples containing a high concentration of proteins is critical for bioanalytical chemistry. A number of previously published studies have focused on long, double-stranded DNA such as plasmid DNA. On the other hand, we are interested in short oligonucleotides. Nucleic acids have a negatively charged phosphate backbone that interacts with metal oxides strongly, and this may be used to distinguish them from proteins. In this work, a few metal oxide nanoparticles were screened, including NiO, CoO, ZnO, TiO2, CeO2, and Fe3O4 for DNA recovery. NiO had the highest DNA adsorption efficiency from mixtures containing bovine serum albumin or human blood serum. The adsorption of DNA by NiO was further characterized as a function of the pH, salt concentration, DNA length, and DNA sequence. The adsorption mechanism was studied by adding competing chemicals or denaturing agents. A striking observation was the extremely high adsorption affinity of NiO, much higher than that of the other tested oxides. Polyphosphate was the most effective agent for displacing adsorbed DNA, whereas simple inorganic phosphate was less effective. NiO was able to concentrate DNA from a serum mixture by 33- to 55-fold, depending on the serum concentration. NiO is thus a promising candidate for extracting DNA from biological samples.
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Affiliation(s)
- Lei Chen
- Research Center for Analytical Sciences , Northeastern University , Shenyang 110004 , China
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Zhangrun Xu
- Research Center for Analytical Sciences , Northeastern University , Shenyang 110004 , China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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66
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Das S, Mukhopadhyay S, Chatterjee S, Devi PS, Suresh Kumar G. Fluorescent ZnO-Au Nanocomposite as a Probe for Elucidating Specificity in DNA Interaction. ACS OMEGA 2018; 3:7494-7507. [PMID: 30087915 PMCID: PMC6068853 DOI: 10.1021/acsomega.7b02096] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 05/08/2018] [Indexed: 05/10/2023]
Abstract
In this work, we report the interaction of a fluorescent ZnO-Au nanocomposite with deoxyribonucleic acid (DNA), leading to AT-specific DNA interaction, which is hitherto not known. For this study, three natural double-stranded (ds) DNAs having different AT:GC compositions were chosen and a ZnO-Au nanocomposite has been synthesized by anchoring a glutathione-protected gold nanocluster on the surface of egg-shell-membrane (ESM)-based ZnO nanoparticles. The ESM-based bare ZnO nanoparticles did not show any selective interaction toward DNA, whereas intrinsic fluorescence of the ZnO-Au nanocomposite shows an appreciable blue shift (Δλmax = 18 nm) in the luminescence wavelength of 520 nm in the presence of ds calf thymus (CT) DNA over other studied DNAs. In addition, the interaction of the nanocomposite through fluorescence studies with single-stranded (ss) CT DNA, synthetic polynucleotides, and nucleobases/nucleotides (adenine, thymine, deoxythymidine monophosphate, deoxyadenosine monophosphate) was also undertaken to delineate the specificity in interaction. A minor blue shift (Δλmax = 5 nm) in the emission wavelength at 520 nm was observed for single-stranded CT DNA, suggesting the proficiency of the nanocomposite for discriminating ss and ds CT DNA. More importantly, fluorescence signals from the nano-bio-interaction could be measured directly without any modification of the target, which is the foremost advantage emanated from this study compared with other previous reports. The AT base-pair-induced enhancement was also found to be highest for the melting temperature of CT DNA (ΔTmCT = 6.7 °C). Furthermore, spectropolarimetric experiments followed by calorimetric analysis provided evidence for specificity in AT-rich DNA interaction. This study would lead to establish the fluorescent ZnO-Au nanocomposite as a probe for nanomaterial-based DNA-binding study, featuring its specific interaction toward AT-rich DNA.
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Affiliation(s)
- Sumita Das
- Sensor
and Actuator Division, CSIR-Central Glass
and Ceramic Research Institute, Kolkata 700032, India
| | - Soumita Mukhopadhyay
- Sensor
and Actuator Division, CSIR-Central Glass
and Ceramic Research Institute, Kolkata 700032, India
| | - Sabyasachi Chatterjee
- Biophysical
Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Parukuttyamma Sujatha Devi
- Sensor
and Actuator Division, CSIR-Central Glass
and Ceramic Research Institute, Kolkata 700032, India
- E-mail: , . Phone: +91-33-2483
8082. Fax: 91-33-2473 0957
| | - Gopinatha Suresh Kumar
- Biophysical
Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
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67
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Wang X, Lopez A, Liu J. Adsorption of Phosphate and Polyphosphate on Nanoceria Probed by DNA Oligonucleotides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:7899-7905. [PMID: 29886738 DOI: 10.1021/acs.langmuir.8b01482] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Phosphate-containing molecules exist in many forms in biology and the environment, and their interaction with metal oxides is an important aspect of their chemistry and biochemistry. In this work, phosphates with different degrees of polymerization (e.g., orthophosphate, pyrophosphate (PPi), sodium triphosphate (STPP), sodium trimetaphosphate (STMP), and polyphosphate with 25 phosphate units) and phosphates with one or two capping groups were studied. CeO2 nanoparticles (nanoceria) were used as a model metal oxide. DNA is also a polyphosphate, and a fluorescently labeled DNA oligonucleotide was mixed with nanoceria. These phosphate species were individually added to displace the adsorbed DNA. Longer phosphate chains were more efficient when each molecule was used at the same molar concentration, whereas PPi and STPP were most efficient at the same total phosphorus atom concentration. By capping the phosphate with organic groups, the affinity was significantly decreased. Isothermal titration calorimetry (ITC) was also performed to quantitatively measure thermodynamic parameters. Although STMP was very slow at displacing DNA, it was still adsorbed very strongly by nanoceria from ITC, indicating kinetic effects likely due to its ring structure. This observation allowed us to use the DNA as a probe to study the hydrolysis of STMP to form STPP. In summary, this study provides a systematic understanding of phosphate species interacting with metal oxides, and interestingly, it demonstrates an analytical application as well.
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Affiliation(s)
- Xiuzhong Wang
- College of Chemistry and Pharmaceutical Sciences , Qingdao Agricultural University , Qingdao 266109 , China
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Anand Lopez
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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68
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Wang M, Yang L, Hu B, Liu J, He L, Jia Q, Song Y, Zhang Z. Bimetallic NiFe oxide structures derived from hollow NiFe Prussian blue nanobox for label-free electrochemical biosensing adenosine triphosphate. Biosens Bioelectron 2018; 113:16-24. [PMID: 29709777 DOI: 10.1016/j.bios.2018.04.050] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 12/20/2022]
Abstract
We designed and constructed a novel aptasensor based on the porous nanostructured bimetallic NiFe-oxides embedded with the mesoporous carbon (represented by NiOxFeOy@mC) for sensitively detecting adenosine triphosphate (ATP), of which the porous NiOxFeOy@mC was derived from the hollow NiFe Prussian blue analogue (hollow NiFe PBA) by calcinating under high temperature. Owning to the excellent electrochemical activity originated from the metal oxides and mesoporous carbon and the strong binding interaction between the aptamer strands and the nanostructure hybrid, the formed porous NiOxFeOy@mC composite calcinated at 900 °C exhibited superior sensitivity toward ATP determination in comparison with other porous nanocubes obtained at 500 and 700 °C. The proposed aptasensor not only revealed a wide linear range from 5.0 fg·mL-1 to 5.0 ng mL-1 with a extremely low detection limit of 0.98 fg·mL-1 (1.62 fM) (S/N = 3), but also displayed high selectivity towards other interferences, good stability and reproducibility, and acceptable applicability. Therefore, this proposed approach provides a promising platform for ultra-sensitive detection of ATP, further having the potential applications on diagnosis of ATP-related diseases.
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Affiliation(s)
- Minghua Wang
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450001, China; Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Materials and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450001, China
| | - Longyu Yang
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450001, China
| | - Bin Hu
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450001, China
| | - Jiameng Liu
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450001, China
| | - Linghao He
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450001, China; Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Materials and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450001, China
| | - Qiaojuan Jia
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450001, China
| | - Yingpan Song
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450001, China
| | - Zhihong Zhang
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450001, China; Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Materials and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450001, China.
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69
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Wang L, Huang Z, Liu Y, Wu J, Liu J. Fluorescent DNA Probing Nanoscale MnO 2: Adsorption, Dissolution by Thiol, and Nanozyme Activity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:3094-3101. [PMID: 29457975 DOI: 10.1021/acs.langmuir.7b03797] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Manganese dioxide (MnO2) is an interesting material due to its excellent biocompatibility and magnetic properties. Adsorption of DNA to MnO2 is potentially of interest for drug delivery and sensing applications. However, little fundamental understanding is known about their interactions. In this work, carboxyfluorescein (FAM)-labeled DNA oligonucleotides were used to explore the effect of salt concentration, pH, and DNA sequence and length for adsorption by MnO2, and comparisons were made with graphene oxide (GO). The DNA desorbs from MnO2 by free inorganic phosphate, while it desorbs from GO by adenosine and urea. Therefore, DNA is mainly adsorbed on MnO2 through its phosphate backbone, and DNA has a stronger affinity on MnO2 than on GO based on a salt-shock assay. At the same time, DNA was used to study the effect of thiol containing compounds on the dissolution of MnO2. Adsorbed DNA was released from MnO2 after its dissolution by thiol, but not from other metal oxides with lower solubility such as CeO2, TiO2, and Fe3O4. DNA-functionalized MnO2 was then used for detecting glutathione (GSH) with a detection limit of 383 nM. Finally, DNA was found to inhibit the peroxidase-like activity of MnO2. This study has offered many fundamental insights into the interaction between MnO2 and two important biomolecules: DNA and thiol-containing compounds.
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Affiliation(s)
- Liu Wang
- College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou 310058 , China
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo N2L 3G1 , Ontario , Canada
| | - Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo N2L 3G1 , Ontario , Canada
| | - Yibo Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo N2L 3G1 , Ontario , Canada
| | - Jian Wu
- College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou 310058 , China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo N2L 3G1 , Ontario , Canada
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70
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Bülbül G, Hayat A, Mustafa F, Andreescu S. DNA assay based on Nanoceria as Fluorescence Quenchers (NanoCeracQ DNA assay). Sci Rep 2018; 8:2426. [PMID: 29402996 PMCID: PMC5799284 DOI: 10.1038/s41598-018-20659-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 01/22/2018] [Indexed: 01/05/2023] Open
Abstract
Functional nanomaterials with fluorescent or quenching abilities are important for the development of molecular probes for detection and studies of nucleic acids. Here, we describe a new class of molecular nanoprobes, the NanoCeracQ that uses nanoceria particles as a nanoquencher of fluorescent oligonucleotides for rapid and sensitive detection of DNA sequences and hybridization events. We show that nanoceria forms stable and reversible bionanoconjugates with oligonucleotides and can specifically recognize and detect DNA sequences in a single step. In absence of the target DNA, the nanoprobe produced minimal background fluorescence due to the high quenching efficiency of nanoceria. Competitive binding of the target induced a concentration dependent increase in the fluorescence signal due to hybridization and release of the fluorescent tag from the nanoparticle surface. The nanoprobe enabled sensitive detection of the complementary strand with a detection limit of 0.12 nM, using a single step procedure. The results show that biofunctionalized nanoceria can be used as a universal nanoquencher and nanosensing platform for fluorescent DNA detection and studies of nucleic acid interactions. This approach can find broad applications in molecular diagnostics, sensor development, gene expression profiling, imaging and forensic analysis.
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Affiliation(s)
- Gonca Bülbül
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, 13699, United States
| | - Akhtar Hayat
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, 13699, United States
| | - Fatima Mustafa
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, 13699, United States
| | - Silvana Andreescu
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, 13699, United States.
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71
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Huang H, Qin J, Wang G, Guo Z, Yu X, Zhao Y, Wei J. Synthesis of spiny metal–phenolic coordination crystals as a sensing platform for sequence-specific detection of nucleic acids. CrystEngComm 2018. [DOI: 10.1039/c8ce01555d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Metal–phenolic coordination crystals with a spiny surface and tunable compositions are synthesized, and can be used as DNA sensors.
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Affiliation(s)
- Hengbo Huang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University Xi'an
- P. R. China
| | - Jing Qin
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University Xi'an
- P. R. China
| | - Gen Wang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University Xi'an
- P. R. China
| | - Zehua Guo
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University Xi'an
- P. R. China
| | - Xu Yu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University Xi'an
- P. R. China
| | - Yongxi Zhao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University Xi'an
- P. R. China
| | - Jing Wei
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University Xi'an
- P. R. China
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72
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Das S, Chatterjee S, Pramanik S, Devi PS, Kumar GS. A new insight into the interaction of ZnO with calf thymus DNA through surface defects. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 178:339-347. [DOI: 10.1016/j.jphotobiol.2017.10.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 10/17/2017] [Accepted: 10/30/2017] [Indexed: 01/14/2023]
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73
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Zhou Y, Huang Z, Yang R, Liu J. Selection and Screening of DNA Aptamers for Inorganic Nanomaterials. Chemistry 2017; 24:2525-2532. [PMID: 29205597 DOI: 10.1002/chem.201704600] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Indexed: 11/10/2022]
Abstract
Searching for DNA sequences that can strongly and selectively bind to inorganic surfaces is a long-standing topic in bionanotechnology, analytical chemistry and biointerface research. This can be achieved either by aptamer selection starting with a very large library of ≈1014 random DNA sequences, or by careful screening of a much smaller library (usually from a few to a few hundred) with rationally designed sequences. Unlike typical molecular targets, inorganic surfaces often have quite strong DNA adsorption affinities due to polyvalent binding and even chemical interactions. This leads to a very high background binding making aptamer selection difficult. Screening, on the other hand, can be designed to compare relative binding affinities of different DNA sequences and could be more appropriate for inorganic surfaces. The resulting sequences have been used for DNA-directed assembly, sorting of carbon nanotubes, and DNA-controlled growth of inorganic nanomaterials. It was recently discovered that poly-cytosine (C) DNA can strongly bind to a diverse range of nanomaterials including nanocarbons (graphene oxide and carbon nanotubes), various metal oxides and transition-metal dichalcogenides. In this Concept article, we articulate the need for screening and potential artifacts associated with traditional aptamer selection methods for inorganic surfaces. Representative examples of application are discussed, and a few future research opportunities are proposed towards the end of this article.
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Affiliation(s)
- Yibo Zhou
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, 410114, P. R. China
| | - Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Ronghua Yang
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, 410114, P. R. China
| | - Juewen Liu
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, 410114, P. R. China.,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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74
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Wang L, Zhang Z, Liu B, Liu Y, Lopez A, Wu J, Liu J. Interfacing DNA Oligonucleotides with Calcium Phosphate and Other Metal Phosphates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 34:14975-14982. [PMID: 29228772 DOI: 10.1021/acs.langmuir.7b03204] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Calcium phosphate (CaP) has long been used for DNA delivery, although its fundamental interaction with DNA, especially with single-stranded DNA oligonucleotides, remains to be fully understood. Using fluorescently labeled oligonucleotides, we herein studied DNA adsorption isotherm and the effect of DNA length and sequence. Longer DNAs are adsorbed more strongly, and at neutral pH, poly-C DNAs are adsorbed more than the other three DNA homopolymers. However, at near pH 11, the pH of CaP synthesis, T30 DNA is adsorbed more strongly than C30 or A30. This can explain why T30 and G30 can fully inhibit the growth of CaP, while A30 and C30 only retarded its growth kinetics. DNA adsorption also reduces aggregation of CaP. DNA desorption experiments were carried out using concentrated urea, thymidine, or inorganic phosphate as competitors, and desorption was observed only in the presence of phosphate, suggesting that DNA uses its phosphate backbone to interact with the CaP surface. Desorption was also promoted by raising the NaCl concentration suggesting the electrostatic nature of interaction. Finally, ten different metal phosphate materials were synthesized by co-precipitating each metal ion (Ce3+, Fe3+, Ca2+, Ni2+, Zn2+, Mn2+, Ba2+, Cu2+, Sr2+, Co2+), and DNA adsorption by these phosphate precipitants was found to be related to their surface charge and metal chemistry. This work has revealed fundamental surface science of DNA adsorption by CaP and other metal phosphate salts, and this knowledge might be useful for gene delivery, biomineralization, and DNA-directed assembly of metal phosphate materials.
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Affiliation(s)
- Liu Wang
- College of Biosystems Engineering and Food Science, Zhejiang University , Hangzhou 310058, China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, N2L 3G1 Ontario, Canada
| | - Zijie Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, N2L 3G1 Ontario, Canada
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, N2L 3G1 Ontario, Canada
| | - Yibo Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, N2L 3G1 Ontario, Canada
| | - Anand Lopez
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, N2L 3G1 Ontario, Canada
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University , Hangzhou 310058, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, N2L 3G1 Ontario, Canada
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75
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Ma L, Sun N, Zhang J, Tu C, Cao X, Duan D, Diao A, Man S. Polyethylenimine-coated Fe 3O 4 nanoparticles effectively quench fluorescent DNA, which can be developed as a novel platform for protein detection. NANOSCALE 2017; 9:17699-17703. [PMID: 29130087 DOI: 10.1039/c7nr07085c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report a novel assembly of polyethyleneimine (PEI)-coated Fe3O4 nanoparticles (NPs) with single-stranded DNA (ssDNA), and the fluorescence of the dye labeled in the DNA is remarkably quenched. In the presence of a target protein, the protein-DNA aptamer mutual interaction releases the ssDNA from this assembly and hence restores the fluorescence. This feature could be adopted to develop an aptasensor for protein detection. As a proof-of-concept, for the first time, we have used this proposed sensing strategy to detect thrombin selectively and sensitively. Furthermore, simultaneous multiple detection of thrombin and lysozyme in a complex protein mixture has been proven to be possible.
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Affiliation(s)
- Long Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China.
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76
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Wang M, Hu B, Ji H, Song Y, Liu J, Peng D, He L, Zhang Z. Aptasensor Based on Hierarchical Core-Shell Nanocomposites of Zirconium Hexacyanoferrate Nanoparticles and Mesoporous mFe 3O 4@mC: Electrochemical Quantitation of Epithelial Tumor Marker Mucin-1. ACS OMEGA 2017; 2:6809-6818. [PMID: 30023533 PMCID: PMC6044583 DOI: 10.1021/acsomega.7b01065] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/19/2017] [Indexed: 06/08/2023]
Abstract
A novel nanostructured hierarchical core-shell nanocomposite of zirconium hexacyanoferrate (ZrHCF) and a mesoporous nanomaterial composed of Fe3O4 and carbon nanospheres (denoted as ZrHCF@mFe3O4@mC) was prepared and used as a novel platform for an aptasensor to detect the epithelial tumor marker mucin-1 (MUC1) sensitively and selectively. The prepared ZrHCF@mFe3O4@mC nanocomposite exhibited good chemical functionality, water stability, and high specific surface area. Therefore, large amounts of aptamer molecules resulted in high sensitivity of the developed electrochemical aptasensor toward traces of MUC1. The constructed sensor also showed a good linear relationship with the logarithm of MUC1 concentration in the broad range of 0.01 ng·mL-1 to 1.0 μg·mL-1, with a low detection limit of 0.90 pg·mL-1. The fabricated ZrHCF@mFe3O4@mC-based aptasensor exhibited not only high selectivity because of the formation of aptamer-MUC1 complex but also good stability, acceptable reproducibility, and applicability. The proposed novel strategy based on a newly prepared hierarchical core-shell nanocomposite demonstrated outstanding biosensing performance and presents potential applications in biomedical fields.
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77
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Hizir MS, Robertson NM, Balcioglu M, Alp E, Rana M, Yigit MV. Universal sensor array for highly selective system identification using two-dimensional nanoparticles. Chem Sci 2017; 8:5735-5745. [PMID: 28989614 PMCID: PMC5621473 DOI: 10.1039/c7sc01522d] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/13/2017] [Indexed: 12/13/2022] Open
Abstract
A typical lock-and-key sensing strategy, relying only on the most dominant interactions between the probe and target, could be too limiting. In reality, the information received upon sensing is much richer. Non-specific events due to various intermolecular forces contribute to the overall received information with different degrees, and when analyzed, could provide a much more powerful detection opportunity. Here, we have assembled a highly selective universal sensor array using water-soluble two-dimensional nanoparticles (nGO, MoS2 and WS2) and fluorescent DNA molecules. The array is composed of 12 fluorescently silent non-specific nanoreceptors (2D-nps) and used for the identification of three radically different systems; five proteins, three types of live breast cancer cells and a structure-switching event of a macromolecule. The data matrices for each system were processed using Partial Least Squares (PLS) discriminant analysis. In all of the systems, the sensor array was able to identify each object or event as separate clusters with 95% confidence and without any overlap. Out of 15 unknown entities with unknown protein concentrations tested, 14 of them were predicted successfully with correct concentration. 8 breast cancer cell samples out of 9 unknown entities from three cell types were predicted correctly. During the assembly of each nanoprobe, the intrinsic non-covalent interactions between unmodified 2D nanoparticles and ssDNAs were exploited. The unmodified 2D materials offer remarkable simplicity in the layout and the use of ssDNAs as probes provides limitless possibilities because the natural interaction of a ssDNA and 2D surface can be fine-tuned with the nucleobase composition, oligonucleotide length and type of 2D nanomaterial. Therefore, the approach described here can be advanced and fine-tuned indefinitely for meeting a particular sensing criterion. Though we have only studied three distinct elements, this approach is universal enough to be applied to a wide-range of systems.
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Affiliation(s)
- Mustafa Salih Hizir
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002
| | - Neil M Robertson
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002
| | - Mustafa Balcioglu
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002
| | - Esma Alp
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002
| | - Muhit Rana
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002
| | - Mehmet V Yigit
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002
- The RNA Institute , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA
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78
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Wang M, Hu B, Yang C, Zhang Z, He L, Fang S, Qu X, Zhang Q. Electrochemical biosensing based on protein-directed carbon nanospheres embedded with SnO x and TiO 2 nanocrystals for sensitive detection of tobramycin. Biosens Bioelectron 2017; 99:176-185. [PMID: 28756323 DOI: 10.1016/j.bios.2017.07.059] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 07/23/2017] [Accepted: 07/24/2017] [Indexed: 01/03/2023]
Abstract
A series of nanocomposites comprised of homogeneous mesoporous carbon nanospheres embedded with SnOx (x = 0, 1, or 2) and TiO2 nanocrystals using bovine serum albumin (BSA) as template followed by calcinated at different temperatures (300, 500, 700, and 900°C) were prepared, and were denoted as SnOx@TiO2@mC. Then a novel electrochemical biosensing strategy for detecting tobramycin (TOB) based on the nanocomposites was constructed. The as-prepared SnOx@TiO2@mC nanocomposites not only possess high specific surface area and good electrochemical activity but also exhibit strong bioaffinity with the aptamer strands, therefore, they were applied as the scaffold for anchoring TOB-targeted aptamer and further used to sensitively detect trace TOB in aqueous solutions. By comparing the electrochemical biosensing responses toward TOB detection based on the four SnOx@TiO2@mC nanocomposites, the biosensing system constructed with SnOx@TiO2@mC900 (derived at 900°C) demonstrated the highest determination efficiency, high selectivity, and good stability. In particular, the new proposed aptasensing method based on SnOx@TiO2@mC nanocomposite exhibits considerable potential for the quantitative detection of TOB in the biomedical field.
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Affiliation(s)
- Minghua Wang
- School of Materials Science and Engineering, Hebei University of Technology, Tianjin 300130, China; Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Materials and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Bin Hu
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Materials and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Chuang Yang
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Materials and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Zhihong Zhang
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Materials and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China.
| | - Linghao He
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Materials and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Shaoming Fang
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Materials and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Xiongwei Qu
- School of Materials Science and Engineering, Hebei University of Technology, Tianjin 300130, China
| | - Qingxin Zhang
- School of Materials Science and Engineering, Hebei University of Technology, Tianjin 300130, China.
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79
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Qiu H, Pu F, Ran X, Ren J, Qu X. A DNA-Based Label-Free Artificial Tongue for Pattern Recognition of Metal Ions. Chemistry 2017; 23:9258-9261. [DOI: 10.1002/chem.201702342] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Hao Qiu
- 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), Fax:(+86) 0431-85262625
- University of Science and Technology of China, Hefei; Anhui 230026 P. R. China
| | - Fang Pu
- 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), Fax:(+86) 0431-85262625
| | - Xiang Ran
- 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), Fax:(+86) 0431-85262625
- University of Science and Technology of China, Hefei; Anhui 230026 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), Fax:(+86) 0431-85262625
| | - 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), Fax:(+86) 0431-85262625
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80
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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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81
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Lu C, Huang Z, Liu B, Liu Y, Ying Y, Liu J. Poly-cytosine DNA as a High-Affinity Ligand for Inorganic Nanomaterials. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702998] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Chang Lu
- College of Biosystems Engineering and Food Science; Zhejiang University; Hangzhou 310058 China
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Zhicheng Huang
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Biwu Liu
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Yibo Liu
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Yibin Ying
- College of Biosystems Engineering and Food Science; Zhejiang University; Hangzhou 310058 China
| | - Juewen Liu
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
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82
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Lu C, Huang Z, Liu B, Liu Y, Ying Y, Liu J. Poly-cytosine DNA as a High-Affinity Ligand for Inorganic Nanomaterials. Angew Chem Int Ed Engl 2017; 56:6208-6212. [DOI: 10.1002/anie.201702998] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Chang Lu
- College of Biosystems Engineering and Food Science; Zhejiang University; Hangzhou 310058 China
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Zhicheng Huang
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Biwu Liu
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Yibo Liu
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
| | - Yibin Ying
- College of Biosystems Engineering and Food Science; Zhejiang University; Hangzhou 310058 China
| | - Juewen Liu
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo Ontario N2L 3G1 Canada
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83
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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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84
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Lu C, Liu Y, Ying Y, Liu J. Comparison of MoS 2, WS 2, and Graphene Oxide for DNA Adsorption and Sensing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:630-637. [PMID: 28025885 DOI: 10.1021/acs.langmuir.6b04502] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Interfacing DNA with two-dimensional (2D) materials has been intensely researched for various analytical and biomedical applications. Most of these studies have been performed on graphene oxide (GO) and two metal dichalcogenides, molybdenum disulfide (MoS2) and tungsten disulfide (WS2); all of them can all adsorb single-stranded DNA. However, they use different surface forces for adsorption based on their chemical structures. In this work, fluorescently labeled DNA oligonucleotides were used and their adsorption capacities and kinetics were studied as a function of ionic strength, DNA length, and sequence. Desorption of DNA from these surfaces was also measured. DNA is more easily desorbed from GO by various denaturing agents, whereas surfactants yield more desorption from MoS2 and WS2. Our results are consistent with the fact that DNA can be adsorbed by GO via π-π stacking and hydrogen bonding, and MoS2 and WS2 mainly use van der Waals force for adsorption. Finally, fluorescent DNA probes were adsorbed by these 2D materials for detecting complementary DNA. For this assay, GO gave the highest sensitivity, whereas they all showed a similar detection limit. This study has enhanced our fundamental understanding of DNA adsorption by two important types of 2D materials and is useful for further rational optimization of their analytical and biomedical applications.
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Affiliation(s)
- Chang Lu
- College of Biosystems Engineering and Food Science, Zhejiang University , Hangzhou 310058, China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo N2L 3G1, Ontario, Canada
| | - Yibo Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo N2L 3G1, Ontario, Canada
| | - Yibin Ying
- College of Biosystems Engineering and Food Science, Zhejiang University , Hangzhou 310058, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo N2L 3G1, Ontario, Canada
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85
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Lopez A, Zhang Y, Liu J. Tuning DNA adsorption affinity and density on metal oxide and phosphate for improved arsenate detection. J Colloid Interface Sci 2017; 493:249-256. [PMID: 28110059 DOI: 10.1016/j.jcis.2017.01.037] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 11/20/2022]
Abstract
Arsenic (As) contamination in groundwater presents a major health and environmental concern in developing countries. Typically, As is found in two oxidation states. Most chemical tests for inorganic arsenic are focused on As(III), and few have been developed for As(V). We are interested in developing biosensors for As(V) based on its similarity with phosphate. Building upon previous work involving DNA-capped Fe3O4 nanoparticles for As(V) detection, we investigated two other nanomaterials: CeO2 and CePO4 in terms of DNA adsorption and As(V) induced DNA desorption. Fluorescently labeled DNA is physically adsorbed to the surface sites on the nanoparticle surface via its phosphate backbone. In the cases of CeO2 and Fe3O4, the fluorescence was quenched due to electron transfer, whereas for the insulating CePO4, no quenching was observed. Arsenate, being similar to phosphate, can also bind to the surface of the nanoparticles and displace the DNA, increasing the fluorescence signal. The length and sequence of DNA were systematically studied. Using this method, CeO2 performed significantly better than Fe3O4, lowering the detection limit by almost 10-fold. In addition, for CeO2 and CePO4, using shorter DNA was more effective for As(V) detection than using the longer DNA since they both adsorb DNA more tightly than Fe3O4 does. Overall, CeO2 has the best performance since it has an intermediate adsorption affinity of DNA, while CePO4 adsorbs DNA too strongly.
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Affiliation(s)
- Anand Lopez
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yifei Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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86
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Tan L, Chen Z, Zhao Y, Wei X, Li Y, Zhang C, Wei X, Hu X. Dual channel sensor for detection and discrimination of heavy metal ions based on colorimetric and fluorescence response of the AuNPs-DNA conjugates. Biosens Bioelectron 2016; 85:414-421. [DOI: 10.1016/j.bios.2016.05.038] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 04/27/2016] [Accepted: 05/11/2016] [Indexed: 11/25/2022]
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87
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Carnerero JM, Jimenez‐Ruiz A, Castillo PM, Prado‐Gotor R. Covalent and Non‐Covalent DNA–Gold‐Nanoparticle Interactions: New Avenues of Research. Chemphyschem 2016; 18:17-33. [DOI: 10.1002/cphc.201601077] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Jose M. Carnerero
- Physical Chemistry. Faculty of Chemistry University of Seville C/Profesor Garcia Gonzalez, s/n 41012 Seville Spain
| | - Aila Jimenez‐Ruiz
- Physical Chemistry. Faculty of Chemistry University of Seville C/Profesor Garcia Gonzalez, s/n 41012 Seville Spain
| | - Paula M. Castillo
- Physical Chemistry. Faculty of Chemistry University of Seville C/Profesor Garcia Gonzalez, s/n 41012 Seville Spain
| | - Rafael Prado‐Gotor
- Physical Chemistry. Faculty of Chemistry University of Seville C/Profesor Garcia Gonzalez, s/n 41012 Seville Spain
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