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Kavand A, Robin P, Mayoraz L, Mensi M, Gerber-Lemaire S. Achieving high hybridization density at DNA biosensor surfaces using branched spacer and click chemistry. RSC Adv 2023; 13:34003-34011. [PMID: 38020007 PMCID: PMC10660212 DOI: 10.1039/d3ra04928k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023] Open
Abstract
The COVID-19 pandemic has highlighted the necessity to develop fast, highly sensitive and selective virus detection methods. Surface-based DNA-biosensors are interesting candidates for this purpose. Functionalization of solid substrates with DNA must be precisely controlled to achieve the required accuracy and sensitivity. In particular, achieving high hybridization density at the sensing surface is a prerequisite to reach a low limit of detection. We herein describe a strategy based on peptides as anchoring units to immobilize DNA probes at the surface of borosilicate slides. While the coating pathway involves copper-catalyzed click chemistry, a copper-free variation is also reported. The resulting biochips display a high hybridization density (2.9 pmol per cm2) with their targeted gene sequences.
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Affiliation(s)
- Alireza Kavand
- Group for Functionalized Biomaterials, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne CH-1015 Lausanne Switzerland
| | - Perrine Robin
- Group for Functionalized Biomaterials, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne CH-1015 Lausanne Switzerland
| | - Lucas Mayoraz
- Group for Functionalized Biomaterials, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne CH-1015 Lausanne Switzerland
| | - Mounir Mensi
- ISIC-XRDSAP, EPFL Valais-Wallis Rue de l'Industrie 17 CH-1951 Sion Switzerland
| | - Sandrine Gerber-Lemaire
- Group for Functionalized Biomaterials, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne CH-1015 Lausanne Switzerland
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Okamura H, Yamano H, Tsuda T, Morihiro J, Hirayama K, Nagano H. Development of a clinical microarray system for genetic analysis screening. Pract Lab Med 2022; 33:e00306. [PMID: 36593945 PMCID: PMC9803787 DOI: 10.1016/j.plabm.2022.e00306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Objectives Research on the relationship between diseases and genes and the advancement of genetic analysis technologies have made genetic testing in medical care possible. There are various methods for genetic testing, including PCR-based methods and next-generation sequencing; however, screening tests in clinical laboratories are becoming more diverse; therefore, novel measurement systems and equipment are required to meet the needs of each situation. In this study, we aimed to develop a novel microarray-based genetic analysis system that uses a Peltier element to overcome the issues of conventional microarrays, such as the long measurement time and high cost. Methods We constructed a microarray system to detect the UDP-glucuronosyltransferase gene polymorphisms UGT1A1*6 and UGT1A1*28 in patients eligible for irinotecan hydrochloride treatment for use in clinical laboratories. To evaluate the performance of the system, the hybridization temperature and reaction time were determined, and the results were compared with those obtained using a conventional hybridization oven. Results The hybridization temperature reached its target in 1/27th of the time required by the conventional system. We assessed 111 human clinical samples and found that our results agreed with those obtained using existing methods. The total time for the newly developed device was reduced by 85 min compared to that for existing methods, as the automated DNA microarray eliminates the time that existing methods spend on manual operation. Conclusions The surface treatment technology used in our system enables high-density and strong DNA fixation, allowing the construction of a measurement system suitable for clinical applications.
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Affiliation(s)
- Hiroshi Okamura
- Toyo Kohan Co., Ltd., Shinagawa, Tokyo, Japan,Corresponding author. Toyo Kohan Co., Ltd., Japan.
| | | | | | | | | | - Hiroaki Nagano
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
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Ozkan-Ariksoysal D. Current Perspectives in Graphene Oxide-Based Electrochemical Biosensors for Cancer Diagnostics. BIOSENSORS 2022; 12:bios12080607. [PMID: 36005004 PMCID: PMC9405788 DOI: 10.3390/bios12080607] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/27/2022]
Abstract
Since the first commercial biosensor device for blood glucose measurement was introduced in the 1970s, many “biosensor types” have been developed, and this research area remains popular worldwide. In parallel with some global biosensor research reports published in the last decade, including a great deal of literature and industry statistics, it is predicted that biosensor design technologies, including handheld or wearable devices, will be preferred and highly valuable in many areas in the near future. Biosensors using nanoparticles still maintain their very important place in science and technology and are the subject of innovative research projects. Among the nanomaterials, carbon-based ones are considered to be one of the most valuable nanoparticles, especially in the field of electrochemical biosensors. In this context, graphene oxide, which has been used in recent years to increase the electrochemical analysis performance in biosensor designs, has been the subject of this review. In fact, graphene is already foreseen not only for biosensors but also as the nanomaterial of the future in many fields and is therefore drawing research attention. In this review, recent and prominent developments in biosensor technologies using graphene oxide (GO)-based nanomaterials in the field of cancer diagnosis are briefly summarized.
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Affiliation(s)
- Dilsat Ozkan-Ariksoysal
- Department of Analytical Chemistry, Faculty of Pharmacy, Ege University, Izmir 35100, Turkey
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4
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Lateral field excited quartz crystal microbalances for biosensing applications. Biointerphases 2020; 15:030801. [PMID: 32486650 DOI: 10.1116/6.0000144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The most common bulk acoustic wave device used in biosensing applications is the quartz crystal microbalance (QCM), in which a resonant pure shear acoustic wave is excited via electrodes on both major faces of a thin AT-cut quartz plate. For biosensing, the QCM is used to detect the capture of a target by a target-capture film. The sensitivity of the QCM is typically based solely on the detection of mechanical property changes, as electrical property change detection is limited by the electrode on its sensing surface. A modification of the QCM called the lateral field excited (LFE) QCM (LFE-QCM) has been developed with a bare sensing surface as both electrodes are now on a single face of the quartz plate. Compared to the QCM, the LFE-QCM exhibits significantly higher sensitivity to both electrical and mechanical property changes. This paper presents theoretical and experimental aspects of LFE-QCMs. In particular, the presence and strength of the usual and newfound LFE-QCM modes depend on the electrical properties of the film and/or sensing environment. This work also presents examples of experimental setups for measuring the response of an LFE-QCM, followed by results of LFE-QCMs used to detect liquid electrical and mechanical properties, chemical targets, and biological targets. Finally, details are given about the attachment of various target-capture films to the LFE-QCM surface to capture biomarkers associated with diseases such as cancer.
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Cheng F, Ma X, Feng Q, Wang H, Yin M, He W. Preparation and characterization of DNA array slides via surface Michael addition. Biointerphases 2019; 14:061003. [PMID: 31752494 DOI: 10.1063/1.5124411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The reliability and stability of array slides are a big concern for array vendors and end users. Herein, we report on a new type of array slide with high reactivity toward DNA probes and low side reaction. A one-step surface reaction via the Michael addition involved in preparing array slides was developed and characterized by x-ray photoelectron spectroscopy, contact angle, and fluorescence labeling. The effects of array fabrication and storage conditions, i.e., spotting solution pH, high humidity, and long-term storage on the reactivity of the slides were examined. The fabricated DNA arrays could realize good hybridization efficiency (38.2% for slides with 0.88 pmol/cm2), low limit of detection (4 × 10-14M), as well as high mismatch selectivity.
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Affiliation(s)
- Fang Cheng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, Liaoning 116023, China
| | - Xiaochun Ma
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, Liaoning 116023, China
| | - Qiancheng Feng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, Liaoning 116023, China
| | - Hanqi Wang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, Liaoning 116023, China
| | - Meng Yin
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, Liaoning 116023, China
| | - Wei He
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, Liaoning 116023, China
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Henderson CA, Rail CA, Butt LE, Vincent HA, Callaghan AJ. Generation of small molecule-binding RNA arrays and their application to fluorogen-binding RNA aptamers. Methods 2019; 167:39-53. [PMID: 31055072 PMCID: PMC7068705 DOI: 10.1016/j.ymeth.2019.04.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/04/2019] [Accepted: 04/29/2019] [Indexed: 12/23/2022] Open
Abstract
The discovery and engineering of more and more functions of RNA has highlighted the utility of RNA-targeting small molecules. Recently, several fluorogen-binding RNA aptamers have been developed that have been applied to live cell imaging of RNA and metabolites as RNA tags or biosensors, respectively. Although the design and application of these fluorogen-binding RNA aptamer-based devices is straightforward in theory, in practice, careful optimisation is required. For this reason, high throughput in vitro screening techniques, capable of quantifying fluorogen-RNA aptamer interactions, would be beneficial. We recently developed a method for generating functional-RNA arrays and demonstrated that they could be used to detect fluorogen-RNA aptamer interactions. Specifically, we were able to visualise the interaction between malachite green and the malachite green-binding aptamer. Here we expand this study to demonstrate that functional-RNA arrays can be used to quantify fluorogen-aptamer interactions. As proof-of-concept, we provide detailed protocols for the production of malachite green-binding RNA aptamer and DFHBI-binding Spinach RNA aptamer arrays. Furthermore, we discuss the potential utility of the technology to fluorogen-binding RNA aptamers, including application as a molecular biosensor platform. We anticipate that functional-RNA array technology will be beneficial for a wide variety of biological disciplines.
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Affiliation(s)
- Charlotte A Henderson
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Callum A Rail
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Louise E Butt
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Helen A Vincent
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom.
| | - Anastasia J Callaghan
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom.
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Su Q, Vogt S, Nöll G. Langmuir Analysis of the Binding Affinity and Kinetics for Surface Tethered Duplex DNA and a Ligand-Apoprotein Complex. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14738-14748. [PMID: 30005576 DOI: 10.1021/acs.langmuir.7b04347] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this work, the hybridization and dehybridization of ssDNA with 20 bases at gold coated sensor surfaces modified with complementary 20 bases capture probe ssDNA was investigated at 18 °C by quartz crystal microbalance measurements with dissipation monitoring (QCM-D). A sequence of 20 base pairs with a melting temperature of about 64 °C was chosen, since in many biosensor studies the target molecules are DNA or RNA oligomers of similar length. It turned out that at the applied experimental conditions the DNA hybridization was irreversible, and therefore the hybridization and dehybridization process could not be described by the Langmuir model of adsorption. Nevertheless, quantitative dehybridization could be achieved by rinsing the sensor surface thoroughly with pure water. When in contrast the hybridization of a target with only 10 bases complementary to the outermost 10 bases of the 20 bases capture probe was studied, binding and unbinding were reversible, and the hybridization/dehybridization process could be satisfactorily described by the Langmuir model. For the 10 base pair sequence, the melting temperature was about 36 °C. Apparently, for Langmuir behavior, it is important that the experiments are applied at a temperature sufficiently close to the melting temperature of the sequence under investigation to ensure that at least traces of the target molecules are unhybridized (i.e., there needs to be an equilibrium between hybridized and dehybridized target molecules). To validate the reliability of our experimental approach we also studied the reconstitution and disassembly of the flavoprotein dodecin at flavin-terminated DNA monolayers, as according to previous studies it is assumed that the apododecin-flavin system can be well described by the Langmuir model. As a result, this assumption could be verified. Using three different approaches, KD values were obtained that differ not more than by a factor of 4.
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Affiliation(s)
- Qiang Su
- Organic Chemistry, Chem. Biol. Dept., Faculty IV , Siegen University , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany
| | - Stephan Vogt
- Organic Chemistry, Chem. Biol. Dept., Faculty IV , Siegen University , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany
| | - Gilbert Nöll
- Organic Chemistry, Chem. Biol. Dept., Faculty IV , Siegen University , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany
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Liu GC, Gao MJ, Chen W, Hu XY, Song LB, Liu B, Zhao YD. pH-modulated ion-current rectification in a cysteine-functionalized glass nanopipette. Electrochem commun 2018. [DOI: 10.1016/j.elecom.2018.09.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Akbari F, Foroutan M. Molecular investigation of evaporation of biodroplets containing single-strand DNA on graphene surface. Phys Chem Chem Phys 2018; 20:4936-4952. [PMID: 29387862 DOI: 10.1039/c7cp07932j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, the water droplet behaviour of four different types of single-strand DNA with homogeneous base sequence on a graphene substrate during evaporation of the droplet was investigated using molecular dynamics (MD) simulation. The simulation results indicated that the evaporation depended on the DNA sequence. The observed changes can be divided into four parts: (i) vaporization mode, (ii) evaporation flux, (iii) mechanism of single-strand placement on the surface, and (iv) consideration of remaining single strands after evaporation. Our simulation observations indicated different evaporation modes for thymine biodroplets as compared to those for other biodroplets. The evaporation of the thymine biodroplets occurred with an increase in the contact angle, while that of the other biodroplets occur in a constant contact angle mode. Moreover, thymine biodroplets generate the lowest contact line compared to other single strands, and it is always placed far away from the centre of the droplets during evaporation. Investigating variations in the evaporation flux shows that thymine has the highest evaporation flux and guanine has the lowest. Moreover, during initial evaporation, the flux of evaporation increases at the triple point of the biodroplets containing thymine single strands, while it decreases in the other biodroplets. The following observation was obtained from the study of the placement of single strands on the substrate: guanine and thymine interacted slower than other single strands during evaporation with graphene, adenine single strand had a higher folding during evaporation, and guanine single strand showed the lowest end-to-end distance. The investigation of single-strand DNA after evaporation shows that adenine produces the most stable structure at the end of evaporation. In addition, cytosine is the most stretched single-strand DNA due to its lack of internal π-π stacking and hydrogen bonding. Therefore, cytosine single strand is more accessible for use in microarrays to detect target single strands.
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Affiliation(s)
- Fahimeh Akbari
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran.
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10
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Knob R, Nelson DB, Robison RA, Woolley AT. Sequence-specific DNA solid-phase extraction in an on-chip monolith: Towards detection of antibiotic resistance genes. J Chromatogr A 2017; 1523:309-315. [PMID: 28734608 PMCID: PMC5675797 DOI: 10.1016/j.chroma.2017.07.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/05/2017] [Accepted: 07/09/2017] [Indexed: 12/13/2022]
Abstract
Antibiotic resistance of bacteria is a growing problem and presents a challenge for prompt treatment in patients with sepsis. Currently used methods rely on culturing or amplification; however, these steps are either time consuming or suffer from interference issues. A microfluidic device was made from black polypropylene, with a monolithic column modified with a capture oligonucleotide for sequence selective solid-phase extraction of a complementary target from a lysate sample. Porous properties of the monolith allow flow and hybridization of a target complementary to the probe immobilized on the column surface. Good flow-through properties enable extraction of a 100μL sample and elution of target DNA in 12min total time. Using a fluorescently labeled target oligonucleotide related to Verona Integron-Mediated Metallo-β-lactamase it was possible to extract and detect a 1pM sample with 83% recovery. Temperature-mediated elution by heating above the duplex melting point provides a clean extract without any agents that interfere with base pairing, allowing various labeling methods or further downstream processing of the eluent. Further integration of this extraction module with a system for isolation and lysis of bacteria from blood, as well as combining with single-molecule detection should allow rapid determination of antibiotic resistance.
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Affiliation(s)
- Radim Knob
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Daniel B Nelson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Richard A Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Adam T Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA.
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A Quasi-direct LC-MS/MS-based Targeted Proteomics Approach for miRNA Quantification via a Covalently Immobilized DNA-peptide Probe. Sci Rep 2017; 7:5669. [PMID: 28720752 PMCID: PMC5515972 DOI: 10.1038/s41598-017-05495-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/30/2017] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) play a vital role in regulating gene expression and are associated with a variety of cancers, including breast cancer. Their distorted and unique expression is a potential marker in clinical diagnoses and prognoses. Thus, accurate determination of miRNA expression levels is a prerequisite for their applications. However, the assays currently available for miRNA detection typically require pre-enrichment, amplification and labeling steps, and most of the assays are only semi-quantitative. Therefore, we developed a quasi-direct liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted proteomics approach to quantify target miRNA by innovatively converting the miRNA signal into the mass response of a reporter peptide via a covalently immobilized DNA-peptide probe. Specifically, the probe containing the targeted proteomics-selected substrate/reporter peptide, GDRAVQLGVDPFR/AVQLGVDPFR, and the DNA sequence complementary to the target miRNA (i.e., miR-21) was first immobilized on APMTS modified silica nanoparticles using PDITC. After the immobilized probe was recognized and hybridized with the target miRNA, the excess probe was degraded using MBN and followed by a trypsin digestion of the hybrids. The reporter peptide was released and quantified using LC-MS/MS. The obtained LOQ was 5 pM. Finally, the developed assay was used for the quantitative analysis of miR-21 in breast cells and tissue samples.
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Liu SG, Luo D, Li N, Zhang W, Lei JL, Li NB, Luo HQ. Water-Soluble Nonconjugated Polymer Nanoparticles with Strong Fluorescence Emission for Selective and Sensitive Detection of Nitro-Explosive Picric Acid in Aqueous Medium. ACS APPLIED MATERIALS & INTERFACES 2016; 8:21700-9. [PMID: 27471907 DOI: 10.1021/acsami.6b07407] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Water-soluble nonconjugated polymer nanoparticles (PNPs) with strong fluorescence emission were prepared from hyperbranched poly(ethylenimine) (PEI) and d-glucose via Schiff base reaction and self-assembly in aqueous phase. Preparation of the PEI-d-glucose (PEI-G) PNPs was facile (one-pot reaction) and environmentally friendly under mild conditions. Also, PEI-G PNPs showed a high fluorescence quantum yield in aqueous solution, and the fluorescence properties (such as concentration- and solvent-dependent fluorescence) and origin of intrinsic fluorescence were investigated and discussed. PEI-G PNPs were then used to develop a fluorescent probe for fast, selective, and sensitive detection of nitro-explosive picric acid (PA) in aqueous medium, because the fluorescence can be easily quenched by PA whereas other nitro-explosives and structurally similar compounds only caused negligible quenching. A wide linear range (0.05-70 μM) and a low detection limit (26 nM) were obtained. The fluorescence quenching mechanism was carefully explored, and it was due to a combined effect of electron transfer, resonance energy transfer, and inner filter effect between PA and PEI-G PNPs, which resulted in good selectivity and sensitivity for PA. Finally, the developed sensor was successfully applied to detection of PA in environmental water samples.
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Affiliation(s)
- Shi Gang Liu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, People's Republic of China
| | - Dan Luo
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, People's Republic of China
| | - Na Li
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, People's Republic of China
| | - Wei Zhang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714, People's Republic of China
| | - Jing Lei Lei
- School of Chemistry and Chemical Engineering, Chongqing University , Chongqing 400044, People's Republic of China
| | - Nian Bing Li
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, People's Republic of China
| | - Hong Qun Luo
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, People's Republic of China
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13
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Liu SG, Li N, Ling Y, Kang BH, Geng S, Li NB, Luo HQ. pH-Mediated Fluorescent Polymer Particles and Gel from Hyperbranched Polyethylenimine and the Mechanism of Intrinsic Fluorescence. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:1881-9. [PMID: 26829461 DOI: 10.1021/acs.langmuir.6b00201] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We report that fluorescence properties and morphology of hyperbranched polyethylenimine (hPEI) cross-linked with formaldehyde are highly dependent on the pH values of the cross-linking reaction. Under acidic and neutral conditions, water-soluble fluorescent copolymer particles (CPs) were produced. However, under basic conditions, white gels with weak fluorescence emission would be obtained. The water-soluble hPEI-formaldehyde (hPEI-F) CPs show strong intrinsic fluorescence without the conjugation to any classical fluorescent agents. By the combination of spectroscopy and microscopy techniques, the mechanism of fluorescence emission was discussed. We propose that the intrinsic fluorescence originates from the formation of a Schiff base in the cross-linking process between hPEI and formaldehyde. Schiff base bonds are the fluorescence-emitting moieties, and the compact structure of hPEI-F CPs plays an important role in their strong fluorescence emission. The exploration on fluorescence mechanism may provide a new strategy to prepare fluorescent polymer particles. In addition, the investigation shows that the hPEI-F CPs hold potential as a fluorescent probe for the detection of copper ions in aqueous media.
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Affiliation(s)
- Shi Gang Liu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, P. R. China
| | - Na Li
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, P. R. China
| | - Yu Ling
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, P. R. China
| | - Bei Hua Kang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, P. R. China
| | - Shuo Geng
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, P. R. China
| | - Nian Bing Li
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, P. R. China
| | - Hong Qun Luo
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, P. R. China
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14
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Zheng Y, Hu T, Chen C, Yang F, Yang X. An anti-fouling aptasensor for detection of thrombin by dual polarization interferometry. Chem Commun (Camb) 2016; 51:5645-8. [PMID: 25714792 DOI: 10.1039/c4cc10337h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An anti-fouling surface was designed to effectively resist nonspecific protein adsorption using dual polarization interferometry, based on which the aptasensor for detection of thrombin was fabricated according to the specific interaction between thrombin and its 15-mer aptamer.
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Affiliation(s)
- Yu Zheng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
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15
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Surface Modification Chemistries of Materials Used in Diagnostic Platforms with Biomolecules. J CHEM-NY 2016. [DOI: 10.1155/2016/9241378] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biomolecules including DNA, protein, and enzymes are of prime importance in biomedical field. There are several reports on the technologies for the detection of these biomolecules on various diagnostic platforms. It is important to note that the performance of the biosensor is highly dependent on the substrate material used and its meticulous modification for particular applications. Therefore, it is critical to understand the principles of a biosensor to identify the correct substrate material and its surface modification chemistry. The imperative surface modification for the attachment of biomolecules without losing their bioactivity is a key to sensitive detection. Therefore, finding of a modification method which gives minimum damage to the surface as well as biomolecule is highly inevitable. Different surface modification technologies are invented according to the type of a substrate used. Surface modification techniques of the materials used as platforms in the fabrication of biosensors are reviewed in this paper.
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Bilgic T, Klok HA. Oligonucleotide Immobilization and Hybridization on Aldehyde-Functionalized Poly(2-hydroxyethyl methacrylate) Brushes. Biomacromolecules 2015; 16:3657-65. [PMID: 26441148 DOI: 10.1021/acs.biomac.5b01116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
DNA biosensing requires high oligonucleotide binding capacity interface chemistries that can be tuned to maximize probe presentation as well as hybridization efficiency. This contribution investigates the feasibility of aldehyde-functionalized poly(2-hydroxyethyl methacrylate) (PHEMA) brush-based interfaces for oligonucleotide binding and hybridization. These polymer brushes, which allow covalent immobilization of oligonucleotides, are prepared by surface-initiated atom transfer radical polymerization (SI-ATRP) of HEMA followed by a postpolymerization oxidation step to generate side chain aldehyde groups. A series of polymer brushes covering a range of film thicknesses and grafting densities was investigated with regard to their oligonucleotide binding capacity as well as their ability to support oligonucleotide hybridization. Densely grafted brushes were found to have probe oligonucleotide binding capacities of up to ∼30 pmol/cm(2). Increasing the thickness of these densely grafted brush films, however, resulted in a decrease in the oligonucleotide binding capacity. Less densely grafted brushes possess binding capacities of ∼10 pmol/cm(2), which did not significantly depend on film thickness. The oligonucleotide hybridization efficiencies, however, were highest (93%) on those brushes that present the lowest surface concentration of the probe oligonucleotide. These results highlight the importance of optimizing the probe oligonucleotide surface concentration and binding interface chemistry. The versatility and tunability of the PHEMA-based brushes presented herein makes these films a very attractive platform for the immobilization and hybridization of oligonucleotides.
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Affiliation(s)
- Tugba Bilgic
- Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
| | - Harm-Anton Klok
- Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
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Jee SH, Kim JW, Lee JH, Yoon YS. Improvement in the amine glass platform by bubbling method for a DNA microarray. Int J Nanomedicine 2015; 10:273-80. [PMID: 26468293 PMCID: PMC4601307 DOI: 10.2147/ijn.s88320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A glass platform with high sensitivity for sexually transmitted diseases microarray is described here. An amino-silane-based self-assembled monolayer was coated on the surface of a glass platform using a novel bubbling method. The optimized surface of the glass platform had highly uniform surface modifications using this method, as well as improved hybridization properties with capture probes in the DNA microarray. On the basis of these results, the improved glass platform serves as a highly reliable and optimal material for the DNA microarray. Moreover, in this study, we demonstrated that our glass platform, manufactured by utilizing the bubbling method, had higher uniformity, shorter processing time, lower background signal, and higher spot signal than the platforms manufactured by the general dipping method. The DNA microarray manufactured with a glass platform prepared using bubbling method can be used as a clinical diagnostic tool.
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Affiliation(s)
- Seung Hyun Jee
- Department of Chemical and Biological Engineering, Gachon University, Seongnam, Gyeonggi, Republic of Korea
| | - Jong Won Kim
- Genomics Clinical Research Institute, LabGenomics Co., Ltd., Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Ji Hyeong Lee
- Genomics Clinical Research Institute, LabGenomics Co., Ltd., Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Young Soo Yoon
- Department of Chemical and Biological Engineering, Gachon University, Seongnam, Gyeonggi, Republic of Korea
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18
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Mahapatro A. Bio-functional nano-coatings on metallic biomaterials. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2015; 55:227-51. [DOI: 10.1016/j.msec.2015.05.018] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 03/20/2015] [Accepted: 05/07/2015] [Indexed: 11/28/2022]
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Loukanov A, Filipov C, Lecheva M, Saim Emin. Immobilization and stretching of 5′-pyrene-terminated DNA on carbon film deposited on electron microscope grid. Microsc Res Tech 2015; 78:994-1000. [DOI: 10.1002/jemt.22564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 01/11/2023]
Affiliation(s)
- Alexandre Loukanov
- Graduate School of Science and Engineering, Saitama University; Shimo-Ohkubo 255, Sakura-Ku Saitama 338-8570 Japan
- Laboratory of Engineering NanoBiotechnology; Department of Engineering Geoecology; University of Mining and Geology “St. Ivan Rilski”; Sofia Bulgaria
| | - Chavdar Filipov
- Department of Infectious Pathology; Hygiene, Technology and Control of Food Stuffs of Animal Origin, Faculty of Veterinary Medicine, University of Forestry; Sofia Bulgaria
| | - Marta Lecheva
- Laboratory of Engineering NanoBiotechnology; Department of Engineering Geoecology; University of Mining and Geology “St. Ivan Rilski”; Sofia Bulgaria
| | - Saim Emin
- Materials Research Laboratory, University of Nova Gorica; Nova Gorica SI-5000 Slovenia
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Roy S, Soh JH, Ying JY. A microarray platform for detecting disease-specific circulating miRNA in human serum. Biosens Bioelectron 2015; 75:238-46. [PMID: 26319167 DOI: 10.1016/j.bios.2015.08.039] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 08/17/2015] [Accepted: 08/18/2015] [Indexed: 12/26/2022]
Abstract
Circulating microRNAs (miRNAs) are emerging as potential blood-based biomarkers for cancer and other critical diseases. To profile the expression levels of these tiny molecules, especially in a point-of-care setting, it is imperative to quantify them directly in complex biological fluids. Herein, we report the development of a microarray platform with carboxyl-polyethylene glycol (PEG) as a functional layer and aminated hairpin nucleic acid molecules as target-specific capture probes (CPs). Due to the anti-fouling effect conferred by the carboxyl-PEG layer, we could directly detect as little as 10fM of miRNA targets in 20µl of unprocessed human serum. In contrast to the conventional miRNA microarrays, our platform does not require RNA extraction, labeling and target amplification, thus significantly reducing both the sample preparation steps as well as the total assay duration. The use of specially designed hairpin CPs entails reliable discrimination of miRNA sequences with high sequence homology. A nanoparticle-based detection technique, with the help of differential interference contrast (DIC) microscopy, offers excellent resolution down to a single molecule. With the capability of detecting disease-specific miRNA targets directly in human serum, our microarray platform has potential applications in rapid, minimally invasive clinical diagnostic assays.
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Affiliation(s)
- Somenath Roy
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore
| | - Jun Hui Soh
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore
| | - Jackie Y Ying
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore.
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21
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Aptamer Microarrays—Current Status and Future Prospects. MICROARRAYS 2015; 4:115-32. [PMID: 27600216 PMCID: PMC4996391 DOI: 10.3390/microarrays4020115] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/09/2015] [Accepted: 03/18/2015] [Indexed: 12/16/2022]
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Mavrogiannopoulou E, Petrou PS, Koukouvinos G, Yannoukakos D, Siafaka-Kapadai A, Fornal K, Awsiuk K, Budkowski A, Kakabakos SE. Improved DNA microarray detection sensitivity through immobilization of preformed in solution streptavidin/biotinylated oligonucleotide conjugates. Colloids Surf B Biointerfaces 2015; 128:464-472. [PMID: 25805150 DOI: 10.1016/j.colsurfb.2015.02.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 11/18/2022]
Abstract
A novel immobilization approach involving binding of preformed streptavidin/biotinylated oligonucleotide conjugates onto surfaces coated with biotinylated bovine serum albumin is presented. Microarrays prepared according to the proposed method were compared, in terms of detection sensitivity and specificity, with other immobilization schemes employing coupling of biotinylated oligonucleotides onto directly adsorbed surface streptavidin, or sequential coupling of streptavidin and biotinylated oligonucleotides onto a layer of adsorbed biotinylated bovine serum albumin. A comparison was performed employing biotinylated oligonucleotides corresponding to wild- and mutant-type sequences of seven single point mutations of the BRCA1 gene. With respect to the other immobilization protocols, the proposed oligonucleotide immobilization approach offered the highest hybridization signals (at least 5 times higher) and permitted more elaborative washings, thus providing considerably higher discrimination between complimentary and non-complementary DNA sequences for all mutations tested. In addition, the hybridization kinetics were significantly enhanced compared to two other immobilization protocols, permitting PCR sample analysis in less than 40 min. Thus, the proposed oligonucleotide immobilization approach offered improved detection sensitivity and discrimination ability along with considerably reduced analysis time, and it is expected to find wide application in DNA mutation detection.
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Affiliation(s)
- E Mavrogiannopoulou
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - P S Petrou
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - G Koukouvinos
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - D Yannoukakos
- Molecular Diagnostics Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - A Siafaka-Kapadai
- Biochemistry Lab, Department of Chemistry, University of Athens, GR-15771 Panepistimiopolis, Athens, Greece
| | - K Fornal
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - K Awsiuk
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - A Budkowski
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - S E Kakabakos
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece.
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24
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Jia Y, Li J. Molecular assembly of Schiff Base interactions: construction and application. Chem Rev 2014; 115:1597-621. [PMID: 25543900 DOI: 10.1021/cr400559g] [Citation(s) in RCA: 286] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yi Jia
- Beijing National Laboratory for Molecular Sciences, CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing, 100190, China
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25
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Nimse SB, Song K, Sonawane MD, Sayyed DR, Kim T. Immobilization techniques for microarray: challenges and applications. SENSORS 2014; 14:22208-29. [PMID: 25429408 PMCID: PMC4299010 DOI: 10.3390/s141222208] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/24/2014] [Accepted: 11/11/2014] [Indexed: 02/03/2023]
Abstract
The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials) on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided.
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Affiliation(s)
- Satish Balasaheb Nimse
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Keumsoo Song
- Biometrix Technology, Inc. 202 BioVenture Plaza, Chuncheon 200-161, Korea.
| | - Mukesh Digambar Sonawane
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Danishmalik Rafiq Sayyed
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Taisun Kim
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
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26
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Gibriel A. Effect of Target Length on Specificity and Sensitivity of Oligonucleotide Microarrays: A Comparison between Dendrimer and Modified PCR based Labelling Methods. Open Biochem J 2014; 8:11-20. [PMID: 24551024 PMCID: PMC3927376 DOI: 10.2174/1874091x01408010011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 11/07/2013] [Accepted: 11/08/2013] [Indexed: 12/28/2022] Open
Abstract
DNA microarrays are widely used as end point detectors for gene expression analysis. Several methods have
been developed for target labelling to enable quantification but without taking target length into consideration. Here we
highlight the importance of choosing the optimum target length that would ensure specificity without compromising sensitivity
of the assay. For this, eight plasmids that are identical to each other except for a closely related 23 bp unique reporter
(UR) sequence were used to examine the hybridization efficiency for these URs. Targets of various lengths were
generated and labelled as follows: full length and 330 bases transcripts using a dendrimer labelling method, 120 bp amplicons
by the modified PCR end labelling method and synthetic labelled targets of 33 bases. This report also shows the advantages
of using the modified PCR method over other labelling methods in generating labelled amplicons of the desired
lengths to maximize hybridization efficiency.
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Affiliation(s)
- Abdullah Gibriel
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Ahram Canadian University (ACU) ; Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Ensafi AA, Heydari-Bafrooei E, Dinari M, Mallakpour S. Improved immobilization of DNA to graphite surfaces, using amino acid modified clays. J Mater Chem B 2014; 2:3022-3028. [DOI: 10.1039/c3tb21827a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A nano-sized biosensor containing valine amino acid organo-modified Cloisite as a bionanohybrid film for immobilization of DNA was developed.
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Affiliation(s)
- Ali A. Ensafi
- Department of Chemistry
- Isfahan University of Technology
- Isfahan 84156-83111, Iran
| | | | - Mohammad Dinari
- Department of Chemistry
- Isfahan University of Technology
- Isfahan 84156-83111, Iran
| | - S. Mallakpour
- Department of Chemistry
- Isfahan University of Technology
- Isfahan 84156-83111, Iran
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28
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De A, Souchelnytskyi S, van den Berg A, Carlen ET. Peptide nucleic acid (PNA)-DNA duplexes: comparison of hybridization affinity between vertically and horizontally tethered PNA probes. ACS APPLIED MATERIALS & INTERFACES 2013; 5:4607-4612. [PMID: 23668364 DOI: 10.1021/am4011429] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We compare the PNA-DNA duplex hybridization characteristics of vertically tethered and new horizontally tethered PNA probes on solid surfaces. The horizontal 15-mer PNA probe has been synthesized with linker molecules attached at three locations (γ-points) positioned along the PNA backbone that provides covalent attachment of the probe with the backbone aligned parallel to the surface, which is important for DNA hybridization assays that use electric field effect sensors for detection. A radioactive labeled assay and real-time surface plasmon resonance (SPR) biosensor are used to assess the probe surface density, nonspecific binding, and DNA hybridization affinity, respectively, of the new PNA probe configuration. The estimated equilibrium dissociation constants of the horizontally tethered duplex and the vertically tethered duplex are of the same order of magnitude (KD ≈ 5 nM), which indicates a sufficient hybridization affinity for many electronic biosensors that benefit from the horizontal alignment, which minimizes the effects of counterion screening.
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Sobek J, Aquino C, Weigel W, Schlapbach R. Drop drying on surfaces determines chemical reactivity - the specific case of immobilization of oligonucleotides on microarrays. BMC BIOPHYSICS 2013; 6:8. [PMID: 23758982 PMCID: PMC3694035 DOI: 10.1186/2046-1682-6-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 02/13/2013] [Indexed: 12/13/2022]
Abstract
BACKGROUND Drop drying is a key factor in a wide range of technical applications, including spotted microarrays. The applied nL liquid volume provides specific reaction conditions for the immobilization of probe molecules to a chemically modified surface. RESULTS We investigated the influence of nL and μL liquid drop volumes on the process of probe immobilization and compare the results obtained to the situation in liquid solution. In our data, we observe a strong relationship between drop drying effects on immobilization and surface chemistry. In this work, we present results on the immobilization of dye labeled 20mer oligonucleotides with and without an activating 5'-aminoheptyl linker onto a 2D epoxysilane and a 3D NHS activated hydrogel surface. CONCLUSIONS Our experiments identified two basic processes determining immobilization. First, the rate of drop drying that depends on the drop volume and the ambient relative humidity. Oligonucleotides in a dried spot react unspecifically with the surface and long reaction times are needed. 3D hydrogel surfaces allow for immobilization in a liquid environment under diffusive conditions. Here, oligonucleotide immobilization is much faster and a specific reaction with the reactive linker group is observed. Second, the effect of increasing probe concentration as a result of drop drying. On a 3D hydrogel, the increasing concentration of probe molecules in nL spotting volumes accelerates immobilization dramatically. In case of μL volumes, immobilization depends on whether the drop is allowed to dry completely. At non-drying conditions, very limited immobilization is observed due to the low oligonucleotide concentration used in microarray spotting solutions. The results of our study provide a general guideline for microarray assay development. They allow for the initial definition and further optimization of reaction conditions for the immobilization of oligonucleotides and other probe molecule classes to different surfaces in dependence of the applied spotting and reaction volume.
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Affiliation(s)
- Jens Sobek
- Functional Genomics Center Zurich, ETH Zurich/ University of Zurich, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland.
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30
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Broderick AH, Carter MCD, Lockett MR, Smith LM, Lynn DM. Fabrication of oligonucleotide and protein arrays on rigid and flexible substrates coated with reactive polymer multilayers. ACS APPLIED MATERIALS & INTERFACES 2013; 5:351-9. [PMID: 23237360 PMCID: PMC3553252 DOI: 10.1021/am302285n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We report a top-down approach to the fabrication of oligonucleotide and protein arrays on surfaces coated with ultrathin, amine-reactive polymer multilayers fabricated by the covalent "layer-by-layer" (LbL) assembly of polyethyleneimine (PEI) and the amine-reactive, azlactone-functionalized polymer poly(2-vinyl-4,4-dimethylazlactone) (PVDMA). Manual spotting of amine-terminated oligonucleotide probe sequences on planar glass slides coated with PEI/PVDMA multilayers (~35 nm thick) yielded arrays of immobilized probes that hybridized fluorescently labeled complementary sequences with high signal intensities, high signal-to-noise ratios, and high sequence specificity. Treatment of residual azlactone functionality with the nonfouling small-molecule amine d-glucamine resulted in regions between the features of these arrays that resisted adsorption of protein and permitted hybridization in complex media containing up to 10 mg/mL protein. The residual azlactone groups in these films were also exploited to immobilize proteins on film-coated surfaces and fabricate functional arrays of proteins and enzymes. The ability to deposit PEI/PVDMA multilayers on substrates of arbitrary size, shape, and composition permitted the fabrication of arrays of oligonucleotides on the surfaces of multilayer-coated sheets of poly(ethylene terephthalate) and heat-shrinkable polymer film. Arrays fabricated on these flexible plastic substrates can be bent, cut, resized, and manipulated physically in ways that are difficult using more conventional rigid substrates. This approach could thus contribute to the development of new assay formats and new applications of biomolecule arrays. The methods described here are straightforward to implement, do not require access to specialized equipment, and should also be compatible with automated liquid-handling methods used to fabricate higher-density arrays of oligonucleotides and proteins on more traditional surfaces.
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Affiliation(s)
- Adam H Broderick
- Department of Chemical and Biological Engineering, 1415 Engineering Drive, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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31
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Qiao W, Kalachikov S, Liu Y, Levicky R. Charge-neutral morpholino microarrays for nucleic acid analysis. Anal Biochem 2012; 434:207-14. [PMID: 23246344 DOI: 10.1016/j.ab.2012.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 11/21/2012] [Accepted: 12/03/2012] [Indexed: 12/14/2022]
Abstract
A principal challenge in microarray experiments is to facilitate hybridization between probe strands on the array with complementary target strands from solution while suppressing any competing interactions that the probes and targets may experience. Synthetic DNA analogs, whose hybridization to targets can exhibit qualitatively different dependence on experimental conditions than for nucleic acid probes, open up an attractive alternative for improving selectivity of array hybridization. Morpholinos (MOs), a class of uncharged DNA analogs, are investigated as microarray probes instead of DNA. MO microarrays were fabricated by contact printing of amino-modified probes onto aldehyde slides. In addition to covalent immobilization, MOs were found to efficiently immobilize through physical adsorption; such physically adsorbed probes could be removed by post-printing washes with surfactant solutions. Hybridization of double-stranded DNA targets to MO microarrays revealed a hybridization maximum at intermediate ionic strengths. The decline in hybridization at lower ionic strengths was attributed to an electrostatic barrier accumulated from hybridized DNA targets, whereas at higher ionic strengths it was attributed to stabilization of target secondary structure in solution. These trends, which illustrate ionic strength tuning of forming on-array relative to solution secondary structure, were supported by a stability analysis of MO/DNA and DNA/DNA duplexes in solution.
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Affiliation(s)
- Wanqiong Qiao
- Department of Chemical and Biomolecular Engineering, Polytechnic Institute of New York University, Brooklyn, NY 11201, USA
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Yeh PY, Zhang Z, Lin M, Cao X. Nonfouling hydrophilic poly(ethylene glycol) engraftment strategy for PDMS/SU-8 heterogeneous microfluidic devices. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:16227-16236. [PMID: 23110374 DOI: 10.1021/la303196m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We report a novel nonfouling passivation method using poly(ethylene glycol) (PEG) engraftment on the surfaces of poly(dimethylsiloxane) (PDMS) microfluidic devices sealed with SU-8. To achieve bonding between the PDMS and SU-8 surfaces, the PDMS surface was first functionalized with amines by treatment with 3-aminopropyltrimethoxysilane (APTMS) for subsequent reaction with epoxide functional groups on SU-8 surfaces. To modify the heterogeneous surfaces of the resulting PDMS/SU-8 microfluidic device further, the remaining SU-8 surfaces were amino functionalized using ethylene diamine (EDA), followed by treating both amino-functionalized PDMS and SU-8 surfaces with mPEG-NHS (N-hydroxysuccinimide) through an amine-NHS reaction for facile PEG immobilizations, thus simultaneously modifying both PDMS and SU-8 surfaces in one reaction. Detailed surface analyses such as the water contact angle, X-ray photoelectron spectroscopy (XPS), and atomic force microscopy (AFM) were conducted to confirm the chemical reactions and characterize the resulting surface properties. To test the efficacy of this surface-modification strategy, we conducted nonspecific protein and particle binding tests using microfluidic devices with and without modifications. The PEG-modified PDMS/SU-8 device surfaces showed a 64.5% reduction in nonspecific bovine serum albumin (BSA) adsorption in comparison to that of the unmodified surfaces and 92.0 and 95.8% reductions in microbead adhesion under both stagnant and flowing conditions, respectively.
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Affiliation(s)
- Po Ying Yeh
- Department of Chemical and Biological Engineering, University of Ottawa, Ottawa, Ontario, Canada
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Rao AN, Rodesch CK, Grainger DW. Real-time fluorescent image analysis of DNA spot hybridization kinetics to assess microarray spot heterogeneity. Anal Chem 2012; 84:9379-87. [PMID: 23043216 DOI: 10.1021/ac302165h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Current microarray assay technology predominately uses fluorescence as a detectable signal end point. This study assessed real-time in situ surface hybridization capture kinetics for single printed DNA microspots on solid array surfaces using fluorescence. The influence of the DNA target and probe cyanine dye position on oligo-DNA duplex formation behavior was compared in solution versus surface-hybridized single DNA printed spots using fluorescence resonance energy transfer (FRET) analysis. Fluorophore Cy3/Cy5 fluorescence intensities were analyzed both through the printed hybridized DNA spot thickness and radially across single-spot surfaces. Confocal single-spot imaging shows that real-time in situ hybridization kinetics with constant target concentrations changes as a function of the printed probe density. Target-specific imaging in single spots exhibits a heterogeneous printed probe radial density that influences hybridization spatially and temporally via radial hemispherical diffusion of dye-labeled target from the outside edge of the spot to the interior. FRET of the surface-captured target occurs irrespective of the probe/target fluorophore position, resulting from excess printed probe density and spot thickness. Both heterogeneous probe density distributions in printed spots and the fluorophore position on short DNA oligomers influence duplex formation kinetics, hybridization efficiencies, and overall fluorescence intensity end points in surface-capture formats. This analysis is important to understanding, controlling, and quantifying the array assay signal essential to reliable application of the surface-capture format.
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Affiliation(s)
- Archana N Rao
- Department of Pharmaceutics and Pharmaceutical Chemistry, School of Medicine, University of Utah, Salt Lake City, Utah 84112, United States
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Wen J, Shi X, He Y, Zhou J, Li Y. Novel plastic biochips for colorimetric detection of biomolecules. Anal Bioanal Chem 2012; 404:1935-44. [DOI: 10.1007/s00216-012-6297-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 07/20/2012] [Accepted: 07/23/2012] [Indexed: 12/30/2022]
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Xu J, Asatekin A, Gleason KK. The design and synthesis of hard and impermeable, yet flexible, conformal organic coatings. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2012; 24:3692-3696. [PMID: 22689327 DOI: 10.1002/adma.201201197] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 04/13/2012] [Indexed: 06/01/2023]
Abstract
A new design paradigm for conformal, all-organic coatings that retain their flexibility and chemical functionality while displaying exceptional mechanical hardness and barrier properties is presented. Initiated chemical vapor deposition is used to synthesize a novel alternating copolymer thin film. Upon annealing, films display elastic moduli exceeding 20 GPa, excellent scratch resistance and flexibility, and very low oxygen permeability.
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Affiliation(s)
- Jingjing Xu
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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36
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Kojima N, Komatsu Y. Synthesis and application of highly reactive amino linkers for functional oligonucleotides. ACTA ACUST UNITED AC 2012; Chapter 4:Unit 4.48.1-23. [PMID: 22395967 DOI: 10.1002/0471142700.nc0448s48] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Oligonucleotides are functionalized by conjugation with a variety of molecules, and aliphatic amino linkers have been frequently used as a tether for their modifications. This unit describes the syntheses and applications of novel amino linkers having a carbamate structure. Two major chemical properties of the primary amine are induced by the neighboring effect of the carbamate group, which are found to be optimum in an aminoethyl carbamate structure. First, the hydrophobic monomethoxytrityl group can be rapidly removed from the aminoethyl carbamate under very mild acidic conditions, while the deprotection is not completed in standard aliphatic amines even under high acid concentration. This significant feature enables the convenient purification of amino-modified oligonucleotides by using the hydrophobic interaction of the monomethoxytrityl group with a reverse-phase resin. Second, the introduction of the carbamate linkage reduces the pK(a) value of the neighboring primary amine, resulting in an increase in the conjugation yields with various functional molecules, such as those having active esters. The novel amino linkers that have an aminoethyl carbamate linkage indicate potent activity and are applicable for the preparation of various functional oligonucleotides.
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Affiliation(s)
- Naoshi Kojima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
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37
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Tsougeni K, Koukouvinos G, Petrou PS, Tserepi A, Kakabakos SE, Gogolides E. High-capacity and high-intensity DNA microarray spots using oxygen-plasma nanotextured polystyrene slides. Anal Bioanal Chem 2012; 403:2757-64. [DOI: 10.1007/s00216-012-6058-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 04/11/2012] [Accepted: 04/16/2012] [Indexed: 10/28/2022]
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38
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Abstract
The field of microfluidics has exploded in the past decade, particularly in the area of chemical and biochemical analysis systems. Borrowing technology from the solid-state electronics industry and the production of microprocessor chips, researchers working with glass, silicon, and polymer substrates have fabricated macroscale laboratory components in miniaturized formats. These devices pump nanoliter volumes of liquid through micrometer-scale channels and perform complex chemical reactions and separations. The detection of reaction products is typically done fluorescently with off-chip optical components, and the analysis time from start to finish can be significantly shorter than that of conventional techniques. In this review we describe these microfluidic analysis systems, from the original continuous flow systems relying on electroosmotic pumping for liquid motion to the large diversity of microarray chips currently in use to the newer droplet-based devices and segmented flow systems. Although not currently widespread, microfluidic systems have the potential to become ubiquitous.
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Affiliation(s)
- Eric Livak-Dahl
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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39
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Ulianas A, Heng LY, Hanifah SA, Ling TL. An electrochemical DNA microbiosensor based on succinimide-modified acrylic microspheres. SENSORS 2012; 12:5445-60. [PMID: 22778594 PMCID: PMC3386693 DOI: 10.3390/s120505445] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Revised: 03/26/2012] [Accepted: 04/11/2012] [Indexed: 11/28/2022]
Abstract
An electrochemical microbiosensor for DNA has been fabricated based on new acrylic microspheres modified with reactive N-acryloxysuccinimide (NAS) functional groups. Hydrophobic poly(n-butylacrylate-N-acryloxysuccinimide) microspheres were synthesized in an emulsion form with a simple one-step photopolymerization technique. Aminated DNA probe was attached to the succinimde functional group of the acrylic microspheres via covalent bonding. The hybridization of the immobilized DNA probe with the complementary DNA was studied by differential pulse voltametry using anthraquninone-2-sulfonic acid monohydrate sodium salt (AQMS) as the electroactive hybridization label. The influences of many factors such as duration of DNA probe immobilization and hybridization, pH, type of ions, buffer concentrations, ionic strength, operational temperature and non-complementary DNA on the biosensor performance were evaluated. Under optimized conditions, the DNA microbiosensor demonstrated a linear response range to target DNA over a wide concentration range of 1.0 × 10−16 and 1.0 × 10−8 M with a lower limit of detection (LOD) of 9.46 × 10−17 M (R2 = 0.97). This DNA microbiosensor showed good reproducibility with 2.84% RSD (relative standard deviation) (n = 3). Application of the NAS-modified acrylic microspheres in the construction of DNA microbiosensor had improved the overall analytical performance of the resultant DNA microbiosensor when compared with other reported DNA biosensors using other nano-materials for membranes and microspheres as DNA immobilization matrices.
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Affiliation(s)
- Alizar Ulianas
- School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; E-Mails: (A.U.); (S.A.H.)
| | - Lee Yook Heng
- School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; E-Mails: (A.U.); (S.A.H.)
- Author to whom correspondence should be addressed; E-Mail: ; Fax: +60-3-8921-5410
| | - Sharina Abu Hanifah
- School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; E-Mails: (A.U.); (S.A.H.)
| | - Tan Ling Ling
- Industrial Chemistry Programme, Faculty of Industrial Sciences & Technology, Universiti Malaysia Pahang, 26300 Gambang, Kuantan, Pahang, Malaysia; E-Mail:
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40
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Ruslinda AR, Penmatsa V, Ishii Y, Tajima S, Kawarada H. Highly sensitive detection of platelet-derived growth factor on a functionalized diamond surface using aptamer sandwich design. Analyst 2012; 137:1692-7. [PMID: 22349046 DOI: 10.1039/c2an15933c] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aptamer-based fluorescence detection of platelet-derived growth factor (PDGF) on a functionalized diamond surface was demonstrated. In this work, a sandwich design based on the ability of PDGF to bind with aptamers at its two available binding sites was employed. It was found that this sandwich design approach significantly increases the fluorescence signal intensity, and thereby a very low detection limit of 4 pM was achieved. The effect of the ionic strength of MgCl(2) buffer solution was also investigated, and the most favourable binding for PDGF-BB occurred at a Mg(2+) concentration of 5.5 mM. Since the aptamers bind to the target PDGF with high affinity, fluorescence detection exhibited high selectivity towards different biomolecules. The high reproducibility of detection was confirmed by performing three cycles of measurements over a period of three days.
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Affiliation(s)
- A Rahim Ruslinda
- School of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku, Tokyo 169-8555, Japan.
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41
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Kabeláč M, Kroutil O, Předota M, Lankaš F, Šíp M. Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study. Phys Chem Chem Phys 2012; 14:4217-29. [PMID: 22354557 DOI: 10.1039/c2cp23540d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Molecular dynamics (MD) simulations of single-stranded (ss) and double-stranded (ds) oligonucleotides anchored via an aliphatic linker to a graphene surface were performed in order to investigate the role of the surface charge density in the structure and orientation of attached DNA. Two types of interactions of DNA with the surface are crucial for the stabilisation of the DNA-surface system. Whereas for a surface with a zero or low positive charge density the dispersion forces between the base(s) and the surface dominate, the higher charge densities applied on the surface lead to a strong electrostatic interaction between the phosphate groups of DNA, the surface and the ions. At high-charge densities, the interaction of the DNA with the surface is strongly affected by the formation of a low-mobility layer of counterions compensating for the charge of the surface. A considerable difference in the behaviour of the ds-DNA and ss-DNA anchored to the layer was observed. The ds-DNA interacts with the surface at low- and zero-charge densities exclusively by the nearest base pair. It keeps its geometry close to the canonical B-DNA form, even at surfaces with high-charge densities. The ss-DNA, owing to its much higher flexibility, has a tendency to maximise the attraction to the surface exploiting more bases for the interaction. The interaction of the polar amino group(s) of the base(s) of ss-DNA with a negatively charged surface also contributes significantly to the system stability.
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Affiliation(s)
- M Kabeláč
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
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42
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Mueller A, Eber FJ, Azucena C, Petershans A, Bittner AM, Gliemann H, Jeske H, Wege C. Inducible site-selective bottom-up assembly of virus-derived nanotube arrays on RNA-equipped wafers. ACS NANO 2011; 5:4512-4520. [PMID: 21591634 DOI: 10.1021/nn103557s] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Tobacco mosaic virus (TMV) is a tube-shaped, exceptionally stable plant virus, which is among the biomolecule complexes offering most promising perspectives for nanotechnology applications. Every viral nanotube self-assembles from a single RNA strand and numerous identical coat protein (CP) subunits. Here we demonstrate that biotechnologically engineered RNA species containing the TMV origin of assembly can be selectively attached to solid surfaces via one end and govern the bottom-up growth of surface-linked TMV-like nanotubes in situ on demand. SiO(2) wafers patterned by polymer blend lithography were modified in a chemically selective manner, which allowed positioning of in vitro produced RNA scaffolds into predefined patches on the 100-500 nm scale. The RNA operated as guiding strands for the self-assembly of spatially ordered nanotube 3D arrays on the micrometer scale. This novel approach may promote technically applicable production routes toward a controlled integration of multivalent biotemplates into miniaturized devices to functionalize poorly accessible components prior to use. Furthermore, the results mark a milestone in the experimental verification of viral nucleoprotein complex self-assembly mechanisms.
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Affiliation(s)
- Anna Mueller
- Department of Molecular Biology and Virology of Plants, Institute of Biology, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
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43
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Schulze H, Ross AJ, Ember SWJ, Luby J, Khondoker M, Giraud G, Ciani I, Tlili C, Papale D, Terry JG, Mount AR, Walton AJ, Crain J, Ghazal P, Bachmann TT, Campbell CJ. Peptide-tags for enhanced DNA microarray performance. Faraday Discuss 2011; 149:201-10; discussion 227-45. [PMID: 21413182 DOI: 10.1039/c005491g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA microarrays are powerful tools for gene expression analysis and genotyping studies in research and diagnostic applications. A high sensitivity and short time-to-result are prerequisites for their practical application in the clinic. The hybridization efficiency of DNA microarrays depends on the probe density and the probe orientation and thus their accessibility for target molecules. In order to find an optimal probe immobilization procedure a set of different oligonucleotide modifications was tested on epoxy silane functionalized glass slides. It was found that histidine-tagged oligonucleotides resulted in the highest amount of bound probe and by far the best hybridization efficiencies. The detection limit obtained with histidine-tagged probes was up to two orders of magnitude lower compared to commonly used probe modifications. In order to further investigate the binding mechanism of histidine-tags towards functionalized glass substrates a set of different peptide-tags with and without free terminal amino-groups and with different amino acid compositions was tested. The results indicate an impact of the terminal amino group on the covalent surface binding and of aromatic amino acid residues on the enhanced hybridisation efficiency.
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Affiliation(s)
- Holger Schulze
- Division of Pathway Medicine, College of Medicine and Veterinary Medicine, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, Scotland.
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44
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Silanization of silica and glass slides for DNA microarrays by impregnation and gas phase protocols: A comparative study. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2011. [DOI: 10.1016/j.msec.2010.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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45
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Schopf E, Liu Y, Deng JC, Yang S, Cheng G, Chen Y. tuberculosis detection via rolling circle amplification. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2011; 3:267-273. [PMID: 32938023 DOI: 10.1039/c0ay00529k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hybridization-based assays for DNA detection often use single-stranded DNA (ssDNA) probes to capture ssDNA targets in solution. Unfortunately, these assays are often not able to detect double-stranded DNA (dsDNA). Here, we achieve highly sensitive dsDNA target detection by including short oligonucleotide sequences during denaturing and cooling. After performing an isothermal nucleic acid amplification technique (Rolling Circle Amplification, RCA), these captured dsDNA targets are labeled, allowing single amplified molecules to be imaged and counted. This detection method was first applied to the detection of PCR-generated (polymerase chain reaction) dsDNA targets, yielding a limit of detection of 4.25 fM. As an application of the developed assay, the detection of extracted Mycobacterium tuberculosis (M. tb.) genomic DNA was attempted. A M. tb.-specific target was detected with high specificity compared to similar bacteria, and a detection limit of 10 000 colony forming units (cfu) ml-1 was achieved, close to the sensitivity required for clinical diagnosis.
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Affiliation(s)
- Eric Schopf
- Department of Mechanical and Aerospace Engineering, California NanoSystems Institute, University of California, Los Angeles, California 90095, USA.
| | - Yang Liu
- Department of Mechanical and Aerospace Engineering, California NanoSystems Institute, University of California, Los Angeles, California 90095, USA.
| | - Jane C Deng
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Siyin Yang
- Department of Mechanical and Aerospace Engineering, California NanoSystems Institute, University of California, Los Angeles, California 90095, USA.
| | - Genhong Cheng
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Yong Chen
- Department of Mechanical and Aerospace Engineering, California NanoSystems Institute, University of California, Los Angeles, California 90095, USA.
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46
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Cao R, Lu Z, Duan D, Zhao Z, Du X, Li J. Dextran-silane coating chemistry for SiO2-based suspension array system. Polym Chem 2011. [DOI: 10.1039/c1py00279a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Jiang KR, Huang JL, Chen CC, Su HJ, Wu JC. Effect of co-axially hybridized gene targets on hybridization efficiency of microarrayed DNA probes. J Taiwan Inst Chem Eng 2011; 42:5-12. [PMID: 32362954 PMCID: PMC7185593 DOI: 10.1016/j.jtice.2010.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 04/19/2010] [Accepted: 04/25/2010] [Indexed: 11/25/2022]
Abstract
The effect of relative size of two co-axially hybridized gene targets on the hybridization efficiency was studied for two DNA probe configurations and various probe concentrations. Each of two sets of microarrayed probes contained a pair of DNA probes and a pair of their complementary samples labeled with two distinct fluorescent dyes. The sequence of each probe is especially designed so that two targets are simultaneously complementary to two adjacent sections of the probe. The molecular steric effect on the hybridization efficiency is investigated by comparing the dye signals between configurations of one-target and two-target hybridization scenarios. The results show that a low probe concentration gives better hybridization efficiency and the first-hybridization conducted by a shorter-size DNA target improves the hybridization efficiency of the second target coupling onto the same probe.
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Affiliation(s)
- Kai Ren Jiang
- Chemical Engineering Department, Chung Yuan Christian University, Chung Li, Tao Yuan 32023, Taiwan
| | - Jie-Len Huang
- Biomedical Engineering Center, Industrial Technology Research Institute, Chu Tung, Hsin Chu 31040, Taiwan
| | - Chia-Chun Chen
- Biomedical Engineering Center, Industrial Technology Research Institute, Chu Tung, Hsin Chu 31040, Taiwan
| | - Hung-Ju Su
- Biomedical Engineering Center, Industrial Technology Research Institute, Chu Tung, Hsin Chu 31040, Taiwan
| | - Jui-Chuang Wu
- Chemical Engineering Department, Chung Yuan Christian University, Chung Li, Tao Yuan 32023, Taiwan
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48
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Gooding JJ, Ciampi S. The molecular level modification of surfaces: from self-assembled monolayers to complex molecular assemblies. Chem Soc Rev 2011; 40:2704-18. [DOI: 10.1039/c0cs00139b] [Citation(s) in RCA: 390] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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49
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Ham HO, Liu Z, Lau KHA, Lee H, Messersmith PB. Facile DNA immobilization on surfaces through a catecholamine polymer. Angew Chem Int Ed Engl 2010; 50:732-6. [PMID: 21226165 DOI: 10.1002/anie.201005001] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 10/05/2010] [Indexed: 11/09/2022]
Affiliation(s)
- Hyun Ok Ham
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208, USA
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50
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Ham HO, Liu Z, Lau KHA, Lee H, Messersmith PB. Facile DNA Immobilization on Surfaces through a Catecholamine Polymer. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201005001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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