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Indumathi K, Abiram A, Praveena G. Effect of peptidic backbone on the nucleic acid dimeric strands. Mol Phys 2020. [DOI: 10.1080/00268976.2019.1584682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- K. Indumathi
- Department of Physics, PSGR Krishnammal College for Women, Coimbatore, India
| | - A. Abiram
- Department of Physics, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - G. Praveena
- Department of Physics, PSGR Krishnammal College for Women, Coimbatore, India
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Grześkowiak BF, Tuśnio K, Woźniak A, Szalata M, Lipiński D, Jurga S, Słomski R. Transgenic Plant Detection Using an AuNPs Based SPR Biosensor. BIOSENSORS-BASEL 2019; 9:bios9040116. [PMID: 31574896 PMCID: PMC6955715 DOI: 10.3390/bios9040116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/20/2019] [Accepted: 09/26/2019] [Indexed: 12/04/2022]
Abstract
The intensive development and commercialization of genetically modified plants observed over the last decade has led to the development of transgenic detection methods that are rapid and sensitive. Among the strategies used for the detection/monitoring of genetically modified organisms (GMOs), surface plasmon resonance (SPR) meets the necessary criteria. This optical technique measures the changes in the refractive index in the vicinity of thin metal layers (i.e., gold) in response to biomolecular interactions occurring at a flat metal‒solution interface. Additionally, it allows the application of functionalized gold nanoparticles (AuNPs) in SPR research to enhance the signal intensity. In the present study, an SPR method, enhanced by the application of AuNPs, was developed to detect transgenic tobacco plants carrying a Streptococcus mutans antigen. The basis for the detection of the target DNA was the hybridization between the genomic DNA isolated from the leaves, stems, and roots of the transgenic tobacco and the biotinylated oligonucleotide probes immobilized onto a streptavidin (SA) sensor chip. SA-functionalized AuNPs coated with a second type of biotinylated probe were applied to increase the sensitivity of the detection method. Analysis of the results indicated that the constructed SPR-based sensor chip can potentially recognize complementary standard fragments (nonamplified genomic DNA) at concentrations as low as 1 pM. Thus, nonamplified transgenic DNA was detected using a label-free and real-time AuNPs-enhanced SPR biosensing method. This unique approach could be used to detect GMOs with high efficiency, even at a low detection limit, high repeatability, and with less time and a lower cost needed for each analysis.
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Affiliation(s)
- Bartosz F Grześkowiak
- The NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland.
| | - Karol Tuśnio
- The NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland.
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznan, Poland.
| | - Anna Woźniak
- The NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland.
| | - Marlena Szalata
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznan, Poland.
| | - Daniel Lipiński
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznan, Poland.
| | - Stefan Jurga
- The NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland.
| | - Ryszard Słomski
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznan, Poland.
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Bellassai N, D'Agata R, Jungbluth V, Spoto G. Surface Plasmon Resonance for Biomarker Detection: Advances in Non-invasive Cancer Diagnosis. Front Chem 2019; 7:570. [PMID: 31448267 PMCID: PMC6695566 DOI: 10.3389/fchem.2019.00570] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/26/2019] [Indexed: 12/24/2022] Open
Abstract
Biomarker-based cancer analysis has great potential to lead to a better understanding of disease at the molecular level and to improve early diagnosis and monitoring. Unlike conventional tissue biopsy, liquid biopsy allows the detection of a large variety of circulating biomarkers, such as microRNA (miRNA), exosomes, circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and proteins, in an easily accessible and minimally invasive way. In this review, we describe and evaluate the relevance and applicability of surface plasmon resonance (SPR) and localized SPR (LSPR)-based platforms for the detection of different classes of cancer biomarkers in liquid biopsy samples. Firstly, we critically discuss unsolved problems and issues in capturing and analyzing biomarkers. Secondly, we highlight current challenges which need to be resolved in applying SPR biosensors into clinical practice. Then, we mainly focus on applications of SPR-based platforms that process a patient sample aiming to detect and quantify biomarkers as a minimally invasive liquid biopsy tool for cancer patients appearing over the last 5 years. Finally, we describe the analytical performances of selected SPR biosensor assays and their significant advantages in terms of high sensitivity and specificity as well as accuracy and workflow simplicity.
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Affiliation(s)
- Noemi Bellassai
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy
| | - Roberta D'Agata
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy
| | - Vanessa Jungbluth
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy
| | - Giuseppe Spoto
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy
- Istituto Nazionale di Biostrutture e Biosistemi, Università degli Studi di Catania, Catania, Italy
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4
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Chou WC, Hu WP, Yang YS, Chan HWH, Chen WY. Neutralized chimeric DNA probe for the improvement of GC-rich RNA detection specificity on the nanowire field-effect transistor. Sci Rep 2019; 9:11056. [PMID: 31363139 PMCID: PMC6667443 DOI: 10.1038/s41598-019-47522-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/12/2019] [Indexed: 12/15/2022] Open
Abstract
Silicon nanowire (SiNW) field-effect transistors (FETs) is a powerful tool in genetic molecule analysis because of their high sensitivity, short detection time, and label-free detection. In nucleic acid detection, GC-rich nucleic acid sequences form self- and cross-dimers and stem-loop structures, which can easily obtain data containing signals from nonspecific DNA binding. The features of GC-rich nucleic acid sequences cause inaccuracies in nucleic acid detection and hinder the development of precision medicine. To improve the inaccurate detection results, we used phosphate-methylated (neutral) nucleotides to synthesize the neutralized chimeric DNA oligomer probe. The probe fragment originated from a primer for the detection of hepatitis C virus (HCV) genotype 3b, and single-mismatched and perfect-matched targets were designed for single nucleotide polymorphisms (SNP) detection on the SiNW FET device. Experimental results revealed that the HCV-3b chimeric neutralized DNA (nDNA) probe exhibited better performance for SNP discrimination in 10 mM bis-tris propane buffer at 25 °C than a regular DNA probe. The SNP discrimination of the nDNA probe could be further improved at 40 °C on the FET device. Consequently, the neutralized chimeric DNA probe could successfully distinguish SNP in the detection of GC-rich target sequences under optimal operating conditions on the SiNW FET device.
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Affiliation(s)
- Wei-Cheng Chou
- Department of Chemical and Materials Engineering, National Central University, Jhong-Li, 32001, Taiwan
| | - Wen-Pin Hu
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, 41354, Taiwan
| | - Yuh-Shyong Yang
- Institute of Biological Science and Technology, National Chiao Tung University, Hsinchu, 30010, Taiwan
| | - Hardy Wai-Hong Chan
- Helios Bioelectronics, Inc. 3F., No. 2, Sec. 2, Shengyi Rd., Zhubei City, Hsinchu County, 302, Taiwan
| | - Wen-Yih Chen
- Department of Chemical and Materials Engineering, National Central University, Jhong-Li, 32001, Taiwan.
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5
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Saadati A, Hassanpour S, Guardia MDL, Mosafer J, Hashemzaei M, Mokhtarzadeh A, Baradaran B. Recent advances on application of peptide nucleic acids as a bioreceptor in biosensors development. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.02.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Fortunati S, Rozzi A, Curti F, Giannetto M, Corradini R, Careri M. Novel amperometric genosensor based on peptide nucleic acid (PNA) probes immobilized on carbon nanotubes-screen printed electrodes for the determination of trace levels of non-amplified DNA in genetically modified (GM) soy. Biosens Bioelectron 2019; 129:7-14. [PMID: 30682690 DOI: 10.1016/j.bios.2019.01.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/07/2019] [Accepted: 01/11/2019] [Indexed: 02/09/2023]
Abstract
A novel amperometric genosensor based on PNA probes covalently bound on the surface of Single Walled Carbon Nanotubes - Screen Printed Electrodes (SWCNT-SPEs) was developed and validated in samples of non-amplified genomic DNA extracted from genetically modified (GM)-Soy. The sandwich assay is based on a first recognition of a 20-mer portion of the target DNA by a complementary PNA Capture Probe (CP) and a second hybridization with a PNA Signalling Probe (SP), with a complementary sequence to a different portion of the target DNA. The SP was labelled with biotin to measure current signal by means of a final incubation of an Alkaline Phosphatase-streptavidin conjugate (ALP-Strp). The electrochemical detection was carried out using hydroquinone diphosphate (HQDP) as enzymatic substrate. The genoassay provided a linear range from 250 pM to 2.5 nM, LOD of 64 pM and LOQ of 215 pM Excellent selectivity towards one base mismatch (1-MM) or scrambled (SCR) sequences was obtained. A simple protocol for extraction and analysis of non-amplified soybean genomic DNA without sample treatment was developed and validated. Our study provides insight into how the outstanding recognition efficiency of PNAs can be combined with the unique properties of CNTs in terms of signal response enhancement for direct detection of genomic DNA samples at the level of interest without previous amplification.
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Affiliation(s)
- Simone Fortunati
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Andrea Rozzi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Federica Curti
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Marco Giannetto
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Roberto Corradini
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Maria Careri
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
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7
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Advanced methods for microRNA biosensing: a problem-solving perspective. Anal Bioanal Chem 2019; 411:4425-4444. [PMID: 30710205 DOI: 10.1007/s00216-019-01621-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/07/2019] [Accepted: 01/16/2019] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) present several features that make them more difficult to analyze than DNA and RNA. For this reason, efforts have been made in recent years to develop innovative platforms for the efficient detection of microRNAs. The aim of this review is to provide an overview of the sensing strategies able to deal with drawbacks and pitfalls related to microRNA detection. With a critical perspective of the field, we identify the main challenges to be overcome in microRNA sensing, and describe the areas where several innovative approaches are likely to come for managing those issues that put limits on improvement to the performances of the current methods. Then, in the following sections, we critically discuss the contribution of the most promising approaches based on the peculiar properties of nanomaterials or nanostructures and other hybrid strategies which are envisaged to support the adoption of these new methods useful for the detection of miRNA as biomarkers of practical clinical utility. Graphical abstract ᅟ.
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8
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Fathi F, Rashidi MR, Omidi Y. Ultra-sensitive detection by metal nanoparticles-mediated enhanced SPR biosensors. Talanta 2018; 192:118-127. [PMID: 30348366 DOI: 10.1016/j.talanta.2018.09.023] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/07/2018] [Accepted: 09/08/2018] [Indexed: 10/28/2022]
Abstract
Surface plasmon resonance (SPR), as an optical technique, has widely been used for the detection of biomarkers. Various investigations have been conducted to address the impacts of SPR on the kinetics of biological interactions between the ligand and its cognate bio-element. Up until now, different biofunctionalized metal nanoparticles (NPs) have been used for the ultrasensitive detection of biomarkers in the enhanced SPR. The enhancement of plasmonic properties and refractive index by means of metal NPs in SPR-based biosensors have significantly improved the diagnosis and monitoring of molecular markers in different disesaes including malignancies. In all the enhanced SPR systems utilized for the direct/sandwich assay, each NP is covalently modified with the analyte molecules like antibody (Ab) or a nucleic acid such as DNA/RNA aptamer (Ap) capable of interaction with the related biomarker(s). The increasing of density near the gold surface and plasmonic coupling of gold film and NPs can provide a large shift in the refractive index enhancing the plasmonic resonance because the SPR response unit is sensitive to alteration of the refractive index and the mass shifting onto the chip surface. In this study, we review the potential applications of two major NPs for enhancing the SPR signals for the detection of molecular biomarkers, including gold and magnetic NPs.
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Affiliation(s)
- Farzaneh Fathi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad-Reza Rashidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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9
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D'Agata R, Giuffrida MC, Spoto G. Peptide Nucleic Acid-Based Biosensors for Cancer Diagnosis. Molecules 2017; 22:E1951. [PMID: 29137122 PMCID: PMC6150339 DOI: 10.3390/molecules22111951] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/06/2017] [Accepted: 11/09/2017] [Indexed: 12/18/2022] Open
Abstract
The monitoring of DNA and RNA biomarkers freely circulating in the blood constitutes the basis of innovative cancer detection methods based on liquid biopsy. Such methods are expected to provide new opportunities for a better understanding of cancer disease at the molecular level, thus contributing to improved patient outcomes. Advanced biosensors can advance possibilities for cancer-related nucleic acid biomarkers detection. In this context, peptide nucleic acids (PNAs) play an important role in the fabrication of highly sensitive biosensors. This review provides an overview of recently described PNA-based biosensors for cancer biomarker detection. One of the most striking features of the described detection approaches is represented by the possibility to detect target nucleic acids at the ultra-low concentration with the capability to identify single-base mutations.
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Affiliation(s)
- Roberta D'Agata
- Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, I-95125 Catania, Italy.
| | - Maria Chiara Giuffrida
- Consorzio Interuniversitario "Istituto Nazionale di Biostrutture e Biosistemi", c/o Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, I-95125 Catania, Italy.
| | - Giuseppe Spoto
- Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, I-95125 Catania, Italy.
- Consorzio Interuniversitario "Istituto Nazionale di Biostrutture e Biosistemi", c/o Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, I-95125 Catania, Italy.
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10
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Gupta A, Mishra A, Puri N. Peptide nucleic acids: Advanced tools for biomedical applications. J Biotechnol 2017; 259:148-159. [PMID: 28764969 PMCID: PMC7114329 DOI: 10.1016/j.jbiotec.2017.07.026] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 05/23/2017] [Accepted: 07/23/2017] [Indexed: 02/01/2023]
Abstract
Peptide Nucleic Acids − DNA/RNA analogues. Different Modifications on PNA backbone and their effects. Neutral backbone − remarkable hybridization properties. PNA based biosensors and their diverse biomedical applications. Potential antigene and antisense agents.
Peptide Nucleic Acids (PNAs) are the DNA/RNA analogues in which sugar-phosphate backbone is replaced by N-2-aminoethylglycine repeating units. PNA contains neutral backbone hence due to the absence of electrostatic repulsion, its hybridization shows remarkable stability towards complementary oligonucleotides. PNAs are highly resistant to cleavage by chemicals and enzymes due to the substrate specific nature of enzymes and therefore not degraded inside the cells. PNAs are emerging as new tools in the market due to their applications in antisense and antigene therapies by inhibiting translation and transcription respectively. Hence, several methods based on PNAs have been developed for designing various anticancer and antigene drugs, detection of mutations or modulation of PCR reactions. The duplex homopurine sequence of DNA may also be recognized by PNA, forming firm PNA/DNA/PNA triplex through strand invasion with a looped-out DNA strand. PNAs have also been found to replace DNA probes in varied investigative purposes. There are several disadvantages regarding cellular uptake of PNA, so modifications in PNA backbone or covalent coupling with cell penetrating peptides is necessary to improve its delivery inside the cells. In this review, hybridization properties along with potential applications of PNA in the field of diagnostics and pharmaceuticals are elaborated.
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Affiliation(s)
- Anjali Gupta
- Department of Chemistry, School of Basic and Applied Sciences, Galgotias University, Greater Noida, U.P., India.
| | - Anuradha Mishra
- School of Vocational Studies & Applied Sciences, Gautam Buddha University, Greater Noida, U.P., India
| | - Nidhi Puri
- Department of Applied Science & Humanities, I.T.S Engineering College, Greater Noida, U.P., India
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11
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D'Agata R, Palladino P, Spoto G. Streptavidin-coated gold nanoparticles: critical role of oligonucleotides on stability and fractal aggregation. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2017; 8:1-11. [PMID: 28144559 PMCID: PMC5238629 DOI: 10.3762/bjnano.8.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/08/2016] [Indexed: 05/12/2023]
Abstract
Gold nanoparticles (AuNPs) exhibit unique properties that can be modulated through a tailored surface functionalization, enabling their targeted use in biochemical sensing and medical diagnostics. In particular, streptavidin-modified AuNPs are increasingly used for biosensing purposes. We report here a study of AuNPs surface-functionalized with streptavidin-biotinylated oligonucleotide, focussing on the role played by the oligonucleotide probes in the stabilization/destabilization of the functionalized nanoparticle dispersion. The behaviour of the modified AuNP dispersion as a consequence of the competitive displacement of the biotinylated oligonucleotide has been investigated and the critical role of displaced oligonucletides in triggering the quasi one-dimensional aggregation of nanoparticles is demonstrated for the first time. The thorough understanding of the fundamental properties of bioconjugated AuNPs is of great importance for the design of highly sensitive and reliable functionalized AuNP-based assays.
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Affiliation(s)
- Roberta D'Agata
- Consorio Interuniversitario “Istituto Nazionale Biostrutture e Biosistemi”, c/o Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, I-95125, Catania, Italy
| | - Pasquale Palladino
- Consorio Interuniversitario “Istituto Nazionale Biostrutture e Biosistemi”, c/o Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, I-95125, Catania, Italy
| | - Giuseppe Spoto
- Consorio Interuniversitario “Istituto Nazionale Biostrutture e Biosistemi”, c/o Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, I-95125, Catania, Italy
- Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, I-95125, Catania, Italy
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12
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Sotnikov DV, Zherdev AV, Dzantiev BB. Detection of Intermolecular Interactions Based on Surface Plasmon Resonance Registration. BIOCHEMISTRY (MOSCOW) 2016; 80:1820-32. [PMID: 26878582 DOI: 10.1134/s0006297915130131] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Methods for registration of intermolecular interactions based on the phenomenon of surface plasmon resonance (SPR) have become one of the most efficient tools to solve fundamental and applied problems of analytical biochemistry. Nevertheless, capabilities of these methods are often insufficient to detect low concentrations of analytes or to screen large numbers of objects. That is why considerable efforts are directed at enhancing the sensitivity and efficiency of SPR-based measurements. This review describes the basic principles of the detection of intermolecular interactions using this method, provides a comparison of various types of SPR detectors, and classifies modern approaches to enhance sensitivity and efficiency of measurements.
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Affiliation(s)
- D V Sotnikov
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
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13
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Jana J, Ganguly M, Pal T. Enlightening surface plasmon resonance effect of metal nanoparticles for practical spectroscopic application. RSC Adv 2016. [DOI: 10.1039/c6ra14173k] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Pictorial depiction of applications of metal nanoparticles in different fields enlightening surface plasmon resonance effect.
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Affiliation(s)
- Jayasmita Jana
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
| | | | - Tarasankar Pal
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
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14
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Rajendran P, Kaufmann S, Vörös J, Zenobi-Wong M, Demkó L. Femtomolar oligonucleotide detection by a one-step gold nanoparticle-based assay. Colloids Surf B Biointerfaces 2015; 135:193-200. [PMID: 26263211 DOI: 10.1016/j.colsurfb.2015.07.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/20/2015] [Accepted: 07/13/2015] [Indexed: 12/11/2022]
Abstract
A sequence-specific oligonucleotide detection method based on the tail-to-tail aggregation of functionalized gold nanoparticles in the presence of target analytes is presented together with its optimization and capabilities for detection of single nucleotide polymorphisms (SNPs). In this single-step method, capture probes are freely accessible for hybridization, resulting in an improved assay performance compared to substrate-based assays. The analytes bring the nanoparticles close to each other via hybridization, causing a red shift of the nanoparticle plasmon peak detected by a spectrophotometer or CCD camera coupled to a darkfield imaging system. Optimal conditions for the assay were found to be (i) use of capture probes complementary to the target without any gap, (ii) maximum possible probe density on the gold nanoparticles, and (iii) 1M ionic strength buffer. The optimized assay has a 1 fM limit of detection and fM to 10 pM dynamic range, with detection of perfect match sequences being three orders of magnitude more sensitive than targets with single nucleotide mismatches.
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Affiliation(s)
- Prayanka Rajendran
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Silvan Kaufmann
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, CH-8092 Zurich, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Marcy Zenobi-Wong
- Cartilage Engineering and Regeneration, Department of Health Sciences and Technology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - László Demkó
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, CH-8092 Zurich, Switzerland.
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15
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Okumura S, Kuroda R, Inouye K. Single Nucleotide Polymorphism Typing with a Surface Plasmon Resonance-Based Sensor Using Hybridization Enhancement Blockers. Appl Biochem Biotechnol 2014; 174:494-505. [DOI: 10.1007/s12010-014-1072-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 07/21/2014] [Indexed: 11/30/2022]
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16
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Bertucci A, Manicardi A, Candiani A, Giannetti S, Cucinotta A, Spoto G, Konstantaki M, Pissadakis S, Selleri S, Corradini R. Detection of unamplified genomic DNA by a PNA-based microstructured optical fiber (MOF) Bragg-grating optofluidic system. Biosens Bioelectron 2014; 63:248-254. [PMID: 25104434 DOI: 10.1016/j.bios.2014.07.047] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 07/16/2014] [Indexed: 12/22/2022]
Abstract
Microstructured optical fibers containing microchannels and Bragg grating inscribed were internally functionalized with a peptide nucleic acid (PNA) probe specific for a gene tract of the genetically modified Roundup Ready soy. These fibers were used as an optofluidic device for the detection of DNA by measuring the shift in the wavelength of the reflected IR light. Enhancement of optical read-out was obtained using streptavidin coated gold-nanoparticles interacting with the genomic DNA captured in the fiber channels (0%, 0.1%, 1% and 10% RR-Soy), enabling to achieve statistically significant, label-free, and amplification-free detection of target DNA in low concentrations, low percentages, and very low sample volumes. Computer simulations of the fiber optics based on the finite element method (FEM) were consistent with the formation of a layer of organic material with an average thickness of 39 nm for the highest percentage (10% RR soy) analysed.
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Affiliation(s)
- Alessandro Bertucci
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Alex Manicardi
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Alessandro Candiani
- Dipartimento di Ingegneria dell'Informazione, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Sara Giannetti
- Dipartimento di Ingegneria dell'Informazione, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Annamaria Cucinotta
- Dipartimento di Ingegneria dell'Informazione, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Giuseppe Spoto
- Dipartimento di Chimica, Università di Catania, Via Andrea Doria 6, 95125 Catania, Italy
| | - Maria Konstantaki
- Foundation for Research and Technology Hellas (FORTH), Institute of Electronic Structure and Laser (IESL), P.O. Box 1385, Heraklion 71 110, Greece
| | - Stavros Pissadakis
- Foundation for Research and Technology Hellas (FORTH), Institute of Electronic Structure and Laser (IESL), P.O. Box 1385, Heraklion 71 110, Greece
| | - Stefano Selleri
- Dipartimento di Ingegneria dell'Informazione, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Roberto Corradini
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
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17
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Shen J, Li Y, Gu H, Xia F, Zuo X. Recent development of sandwich assay based on the nanobiotechnologies for proteins, nucleic acids, small molecules, and ions. Chem Rev 2014; 114:7631-77. [PMID: 25115973 DOI: 10.1021/cr300248x] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Juwen Shen
- Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST) , Wuhan 430074, China
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18
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Tokel O, Inci F, Demirci U. Advances in plasmonic technologies for point of care applications. Chem Rev 2014; 114:5728-52. [PMID: 24745365 PMCID: PMC4086846 DOI: 10.1021/cr4000623] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Onur Tokel
- Demirci
Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical
School, Cambridge, Massachusetts 02139, United States
| | - Fatih Inci
- Demirci
Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical
School, Cambridge, Massachusetts 02139, United States
- Demirci
Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Canary Center at Stanford
for Cancer Early Detection, Palo
Alto, California 94304, United States
| | - Utkan Demirci
- Demirci
Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical
School, Cambridge, Massachusetts 02139, United States
- Division of Infectious Diseases, Brigham
and Women’s Hospital, Harvard Medical
School, Boston, Massachusetts 02115, United States
- Harvard-MIT
Health Sciences and Technology, Cambridge, Massachusetts 02139, United States
- Demirci
Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Canary Center at Stanford
for Cancer Early Detection, Palo
Alto, California 94304, United States
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19
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Ermini ML, Mariani S, Scarano S, Minunni M. Bioanalytical approaches for the detection of single nucleotide polymorphisms by Surface Plasmon Resonance biosensors. Biosens Bioelectron 2014; 61:28-37. [PMID: 24841091 DOI: 10.1016/j.bios.2014.04.052] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 04/23/2014] [Indexed: 11/16/2022]
Abstract
The mapping of specific single nucleotide polymorphisms (SNPs) in patients' genome is a main goal in theranostics, aiming to the development of therapies based on personalized medicine. In this review, Surface Plasmon Resonance (SPR) and Surface Plasmon Resonance imaging (SPRi) biosensors applied to the recognition of SNPs were reviewed, since these technologies are emerging in clinical diagnosis as powerful tools thanks to their analytical features, mainly the real-time and label-free monitoring based on array format for parallel analysis. Since the literature is heterogeneous, a critical classification and a systemic comparison of the analytical performances of published methods were here reviewed on the basis of the analytical strategy and the assay design. In particular, the use of helping agents (i.e. proteins, nanoparticles (NPs), intercalating agents) or artificial DNAs, often coupled to SPR to achieve allele discrimination and/or enhanced sensitivity, were here revised and classified. Finally, the real suitability of SPR biosensors to clinical diagnostics for SNPs detection was addressed by comparing their features and performances with those of other biosensors based on other techniques (e.g. electrochemical biosensors).
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Affiliation(s)
- Maria Laura Ermini
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, via della Lastruccia 3-13, 50019 Sesto Fiorentino, FI, Italy
| | - Stefano Mariani
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, via della Lastruccia 3-13, 50019 Sesto Fiorentino, FI, Italy
| | - Simona Scarano
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, via della Lastruccia 3-13, 50019 Sesto Fiorentino, FI, Italy
| | - Maria Minunni
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, via della Lastruccia 3-13, 50019 Sesto Fiorentino, FI, Italy; Consorzio Sistemi a Grande Interfase, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, FI, Italy.
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20
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Mariani S, Minunni M. Surface plasmon resonance applications in clinical analysis. Anal Bioanal Chem 2014; 406:2303-23. [PMID: 24566759 PMCID: PMC7080119 DOI: 10.1007/s00216-014-7647-5] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 01/20/2014] [Accepted: 01/21/2014] [Indexed: 12/20/2022]
Abstract
In the last 20 years, surface plasmon resonance (SPR) and its advancement with imaging (SPRi) emerged as a suitable and reliable platform in clinical analysis for label-free, sensitive, and real-time monitoring of biomolecular interactions. Thus, we report in this review the state of the art of clinical target detection with SPR-based biosensors in complex matrices (e.g., serum, saliva, blood, and urine) as well as in standard solution when innovative approaches or advanced instrumentations were employed for improved detection. The principles of SPR-based biosensors are summarized first, focusing on the physical properties of the transducer, on the assays design, on the immobilization chemistry, and on new trends for implementing system analytical performances (e.g., coupling with nanoparticles (NPs). Then we critically review the detection of analytes of interest in molecular diagnostics, such as hormones (relevant also for anti-doping control) and biomarkers of interest in inflammatory, cancer, and heart failure diseases. Antibody detection is reported in relation to immune disorder diagnostics. Subsequently, nucleic acid targets are considered for revealing genetic diseases (e.g., point mutation and single nucleotides polymorphism, SNPs) as well as new emerging clinical markers (microRNA) and for pathogen detection. Finally, examples of pathogen detection by immunosensing were also analyzed. A parallel comparison with the reference methods was duly made, indicating the progress brought about by SPR technologies in clinical routine analysis.
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Affiliation(s)
- Stefano Mariani
- Dipartimento di Chimica Ugo Schiff, Università di Firenze, via della Lastruccia 3-13, 50019 Sesto Fiorentino, FI Italy
| | - Maria Minunni
- Dipartimento di Chimica Ugo Schiff, Università di Firenze, via della Lastruccia 3-13, 50019 Sesto Fiorentino, FI Italy
- Istituto Nazionale Biostrutture e Biosistemi, Consorzio Interuniversitario, 50019 Sesto Fiorentino, FI Italy
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21
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Guo S, Du D, Tang L, Ning Y, Yao Q, Zhang GJ. PNA-assembled graphene oxide for sensitive and selective detection of DNA. Analyst 2013; 138:3216-20. [PMID: 23598429 DOI: 10.1039/c3an00266g] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA detection based on peptide nucleic acid (PNA)-DNA hybridization is emerging as an important method in the area of DNA microarrays and biosensors because PNA shows remarkable hybridization properties. In this work, we provide a novel, simple, sensitive, and selective strategy based on a PNA-graphene oxide (GO) assembled biosensor for fluorescence turn-on detection of DNA, in which the new nanomaterial GO was used as a scaffold for PNA and a quencher for the fluorophore. The PNA-GO assembled biosensor is capable of distinguishing sequence specificity including complementary, one-base mismatched and non-complementary targets. Moreover, the results show that the biosensor is able to detect target DNA down to hundreds of picomolar. This sensing platform has been demonstrated to be highly sensitive and specific, and we expect that it will find great applications in the field of biomedicine and disease diagnostics.
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Affiliation(s)
- Shuang Guo
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
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22
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Zanoli LM, Licciardello M, D'Agata R, Lantano C, Calabretta A, Corradini R, Marchelli R, Spoto G. Peptide nucleic acid molecular beacons for the detection of PCR amplicons in droplet-based microfluidic devices. Anal Bioanal Chem 2013; 405:615-24. [PMID: 22212864 DOI: 10.1007/s00216-011-5638-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 12/05/2011] [Accepted: 12/05/2011] [Indexed: 11/26/2022]
Abstract
The use of droplet-based microfluidics and peptide nucleic acid molecular beacons for the detection of polymerase chain reaction (PCR)-amplified DNA sequences within nanoliter-sized droplets is described in this work. The nanomolar-attomolar detection capabilities of the method were preliminarily tested by targeting two different single-stranded DNA sequences from the genetically modified Roundup Ready soybean and the Olea europaea genomes and detecting the fluorescence generated by peptide nucleic acid molecular beacons with fluorescence microscopy. Furthermore, the detection of 10 nM solutions of PCR amplicon of DNA extracted from leaves of O. europaea L. encapsulated in nanoliter-sized droplets was performed to demonstrate that peptide nucleic acid molecular beacons can discriminate O. europaea L. cultivar species carrying different single-nucleotide polymorphisms.
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Affiliation(s)
- Laura Maria Zanoli
- Scuola Superiore di Catania, c/o Dipartimento di Scienze Chimiche, Università di Catania, Catania, Italy
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23
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Abstract
Surface plasmon resonance imaging (SPRI) is a powerful tool for simple, fast and cheap nucleic acid detection. Great efforts have been made during the last decade with the aim of developing even more sensitive and specific SPRI-based methods to be used for the direct detection of DNA and RNA. Here, after a description of the fundamentals of SPRI, the state of the art of recent platform and assay developments is presented, with special attention given to advances in SPRI signal enhancement procedures.
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Affiliation(s)
- Roberta D'Agata
- Dipartimento di Scienze Chimiche, Università di Catania, Catania, Italy
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24
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Grasso G, Spoto G. Plasmonics for the study of metal ion–protein interactions. Anal Bioanal Chem 2012; 405:1833-43. [DOI: 10.1007/s00216-012-6421-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/10/2012] [Accepted: 09/12/2012] [Indexed: 12/19/2022]
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25
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Abstract
This Perspective discusses recent advances in the field of surface plasmon resonance imaging (SPRi) for the label-free, multiplex, and sensitive study of biomolecular systems. Large efforts have been made during the past decade with the aim of developing even more sensitive and specific SPRi-based platforms. Metal nanostructures have been used to enhance SPRi sensitivity and to build a specific SPR-active surface, while special effects such as long-range SPR have been investigated to develop more effective SPRi platforms. Here, we review some of the significant work performed with SPRi for the ultrasensitive detection of biomolecular systems and provide a perspective on the challenges that need to be overcome to enable the wide use of SPRi in emerging key areas such as health diagnostics and antidoping controls.
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Affiliation(s)
- Giuseppe Spoto
- †Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
- ‡Istituto Nazionale di Biostrutture e Biosistemi, Catania, Italy
| | - Maria Minunni
- §Dipartimento di Chimica e CSGI, Università di Firenze, Via della Lastruccia, 3 50019 Sesto F.no (FI), Italy
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26
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Lee JH, Hwang JH, Nam JM. DNA-tailored plasmonic nanoparticles for biosensing applications. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2012; 5:96-109. [DOI: 10.1002/wnan.1196] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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27
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Bonifazi D, Carloni LE, Corvaglia V, Delforge A. Peptide nucleic acids in materials science. ARTIFICIAL DNA, PNA & XNA 2012; 3:112-22. [PMID: 22925824 PMCID: PMC3581510 DOI: 10.4161/adna.21941] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review highlights the recent methods to prepare PNA-based materials through a combination of self-assembly and self-organization processes. The use of these methods allows easy and versatile preparation of structured hybrid materials showing specific recognition properties and unique physicochemical properties at the nano- and micro-scale levels displaying potential applications in several directions, ranging from sensors and microarrays to nanostructured devices for biochips.
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Affiliation(s)
- Davide Bonifazi
- Namur Research College, Department of Chemistry, University of Namur, Namur, Belgium.
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28
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Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development. Anal Bioanal Chem 2012; 402:3071-89. [PMID: 22297860 DOI: 10.1007/s00216-012-5742-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 01/12/2012] [Indexed: 01/06/2023]
Abstract
Nucleic acid biosensors have a growing number of applications in genetics and biomedicine. This contribution is a critical review of the current state of the art concerning the use of nucleic acid analogues, in particular peptide nucleic acids (PNA) and locked nucleic acids (LNA), for the development of high-performance affinity biosensors. Both PNA and LNA have outstanding affinity for natural nucleic acids, and the destabilizing effect of base mismatches in PNA- or LNA-containing heterodimers is much higher than in double-stranded DNA or RNA. Therefore, PNA- and LNA-based biosensors have unprecedented sensitivity and specificity, with special applicability in DNA genotyping. Herein, the most relevant PNA- and LNA-based biosensors are presented, and their advantages and their current limitations are discussed. Some of the reviewed technology, while promising, still needs to bridge the gap between experimental status and the harder reality of biotechnological or biomedical applications.
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29
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Rossi S, Calabretta A, Tedeschi T, Sforza S, Arcioni S, Baldoni L, Corradini R, Marchelli R. Selective recognition of DNA from olive leaves and olive oil by PNA and modified-PNA microarrays. ARTIFICIAL DNA, PNA & XNA 2012; 3:63-72. [PMID: 22772038 PMCID: PMC3429532 DOI: 10.4161/adna.20603] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
PNA probes for the specific detection of DNA from olive oil samples by microarray technology were developed. The presence of as low as 5% refined hazelnut (Corylus avellana) oil in extra-virgin olive oil (Olea europaea L.) could be detected by using a PNA microarray. A set of two single nucleotide polymorphisms (SNPs) from the Actin gene of Olive was chosen as a model for evaluating the ability of PNA probes for discriminating olive cultivars. Both unmodified and C2-modified PNAs bearing an arginine side-chain were used, the latter showing higher sequence specificity. DNA extracted from leaves of three different cultivars (Ogliarola leccese, Canino and Frantoio) could be easily discriminated using a microarray with unmodified PNA probes, whereas discrimination of DNA from oil samples was more challenging, and could be obtained only by using chiral PNA probes.
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Affiliation(s)
- Stefano Rossi
- Dipartimento di Chimica Organica e Industriale, Università di Parma, Parma, Italy
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30
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Abstract
The combined use of surface plasmon resonance (SPR) and modified or mimic oligonucleotides have expanded diagnostic capabilities of SPR-based biosensors and have allowed detailed studies of molecular recognition processes. This review summarizes the most significant advances made in this area over the past 15 years. Functional and conformationally restricted DNA analogs (e.g., aptamers and PNAs) when used as components of SPR biosensors contribute to enhance the biosensor sensitivity and selectivity. At the same time, the SPR technology brings advantages that allows forbetter exploration of underlying properties of non-natural nucleic acid structures such us DNAzymes, LNA and HNA.
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Affiliation(s)
- Roberta D'Agata
- Dipartimento di Scienze Chimiche, Università di Catania, Catania, Italy
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31
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Li YC, Chiou CC, Luo JD, Chen WJ, Su LC, Chang YF, Chang YS, Lai CS, Lee CC, Chou C. Sensitive detection of unlabeled oligonucleotides using a paired surface plasma waves biosensor. Biosens Bioelectron 2012; 35:342-348. [PMID: 22480779 DOI: 10.1016/j.bios.2012.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 03/08/2012] [Accepted: 03/09/2012] [Indexed: 02/02/2023]
Abstract
Detection of unlabeled oligonucleotides using surface plasmon resonance (SPR) is difficult because of the oligonucleotides' relatively lower molecular weight compared with proteins. In this paper, we describe a method for detecting unlabeled oligonucleotides at low concentration using a paired surface plasma waves biosensor (PSPWB). The biosensor uses a sensor chip with an immobilized probe to detect a target oligonucleotide via sequence-specific hybridization. PSPWB measures the demodulated amplitude of the heterodyne signal in real time. In the meantime, the ratio of the amplitudes between the detected output signal and reference can reduce the excess noise from the laser intensity fluctuation. Also, the common-path propagation of p and s waves cancels the common phase noise induced by temperature variation. Thus, a high signal-to-noise ratio (SNR) of the heterodyne signal is detected. The sequence specificity of oligonucleotide hybridization ensures that the platform is precisely discriminating between target and non-target oligonucleotides. Under optimized experimental conditions, the detected heterodyne signal increases linearly with the logarithm of the concentration of target oligonucleotide over the range 0.5-500 pM. The detection limit is 0.5 pM in this experiment. In addition, the non-target oligonucleotide at concentrations of 10 pM and 10nM generated signals only slightly higher than background, indicating the high selectivity and specificity of this method. Different length of perfectly matched oligonucleotide targets at 10-mer, 15-mer and 20-mer were identified at the concentration of 150 pM.
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Affiliation(s)
- Ying-Chang Li
- Department of Optics and Photonics, National Central University, Taoyuan, 320, Taiwan; Graduate Institute of Electro-Optical Engineering, Chang Gung University, Taoyuan, 333, Taiwan
| | - Chiuan-Chian Chiou
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, 333, Taiwan
| | - Ji-Dung Luo
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, 333, Taiwan
| | - Wei-Ju Chen
- Graduate Institute of Electro-Optical Engineering, Chang Gung University, Taoyuan, 333, Taiwan
| | - Li-Chen Su
- Department of Optics and Photonics, National Central University, Taoyuan, 320, Taiwan; Graduate Institute of Electro-Optical Engineering, Chang Gung University, Taoyuan, 333, Taiwan
| | - Ying-Feng Chang
- Graduate Institute of Electro-Optical Engineering, Chang Gung University, Taoyuan, 333, Taiwan; Molecular Medicine Research Center, Chang Gung University, Taoyuan, 333, Taiwan
| | - Yu-Sun Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, 333, Taiwan; Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, 333, Taiwan
| | - Chao-Sung Lai
- Department of Electronic Engineering, Chang Gung University, Taoyuan, 333, Taiwan; Biomedical Engineering Research Center, Chang Gung University, Taoyuan, 333, Taiwan
| | - Cheng-Chung Lee
- Department of Optics and Photonics, National Central University, Taoyuan, 320, Taiwan
| | - Chien Chou
- Department of Optics and Photonics, National Central University, Taoyuan, 320, Taiwan; Graduate Institute of Electro-Optical Engineering, Chang Gung University, Taoyuan, 333, Taiwan; Biomedical Engineering Research Center, Chang Gung University, Taoyuan, 333, Taiwan.
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32
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Kwon MJ, Lee J, Wark AW, Lee HJ. Nanoparticle-Enhanced Surface Plasmon Resonance Detection of Proteins at Attomolar Concentrations: Comparing Different Nanoparticle Shapes and Sizes. Anal Chem 2012; 84:1702-7. [DOI: 10.1021/ac202957h] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Min Jeong Kwon
- Department
of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu,
Daegu-city, 702-701, Republic of Korea
| | - Jaeyoung Lee
- Ertl Center for Electrochemistry and Catalysis/RISE & School of Environmental Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Alastair W. Wark
- Centre
for Molecular Nanometrology,
WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow,
U.K. G1 1XL
| | - Hye Jin Lee
- Department
of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu,
Daegu-city, 702-701, Republic of Korea
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33
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D’Agata R, Spoto G. Surface Plasmon Resonance-Based Methods. DETECTION OF NON-AMPLIFIED GENOMIC DNA 2012. [DOI: 10.1007/978-94-007-1226-3_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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34
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Miura S, Nishizawa S, Suzuki A, Fujimoto Y, Ono K, Gao Q, Teramae N. DNA-Binding Small-Ligand-Immobilized Surface Plasmon Resonance Biosensor for Detecting Thymine-Related Single-Nucleotide Polymorphisms. Chemistry 2011; 17:14104-10. [DOI: 10.1002/chem.201101290] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Indexed: 01/28/2023]
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35
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D'Agata R, Breveglieri G, Zanoli LM, Borgatti M, Spoto G, Gambari R. Direct detection of point mutations in nonamplified human genomic DNA. Anal Chem 2011; 83:8711-7. [PMID: 21978174 DOI: 10.1021/ac2021932] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultrasensitive detection protocols not requiring polymerase chain reaction (PCR)-mediated target DNA amplification are expected to significantly improve our possibilities in several research and diagnostic applications for which minute cell quantities are available. For this reason we have tested a nanoparticle-enhanced surface plasmon resonance imaging (SPRI) sensing strategy to detect point mutations in nonamplified genomic DNA. We have used genomic DNAs, not subject to costly, time-consuming, and prone to contamination PCR-based amplification procedures, obtained from both healthy individuals and homozygous or heterozygous patients affected by β-thalassemia, in order to demonstrate the specificity and the sensitivity of the described sensing strategy. The assay we describe is ultrasensitive and convenient. Attomolar concentrations of target genomic DNA are detected, DNAs from healthy individuals and homozygous or heterozygous patients affected by β-thalassemia are discriminated, and only simple manipulations of the genetic samples are required before the analysis. The proposed ultrasensitive detection of DNA point mutations involved in genomic disorders possibly represents an important advantage in several biomedical applications.
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Affiliation(s)
- Roberta D'Agata
- Dipartimento di Scienze Chimiche, Università di Catania, Catania, Italy
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36
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Zanoli LM, D’Agata R, Spoto G. Functionalized gold nanoparticles for ultrasensitive DNA detection. Anal Bioanal Chem 2011; 402:1759-71. [DOI: 10.1007/s00216-011-5318-3] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 07/13/2011] [Accepted: 08/04/2011] [Indexed: 12/18/2022]
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37
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Malic L, Sandros MG, Tabrizian M. Designed biointerface using near-infrared quantum dots for ultrasensitive surface plasmon resonance imaging biosensors. Anal Chem 2011; 83:5222-9. [PMID: 21604742 DOI: 10.1021/ac200465m] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The surface plasmon resonance imaging chip biointerface is fully designed using near-infrared (NIR) quantum dots (QDs) for the enhancement of surface plasmon resonance imaging (SPRi) signals in order to extend their application for medical diagnostics. The measured SPRi detection signal following the QD binding to the surface was amplified 25-fold for a 1 nM concentration of single-stranded DNA (ssDNA) and 50-fold for a 1 μg/mL concentration of prostate-specific antigen (PSA), a cancer biomarker, thus substantiating their wide potential to study interactions of a diverse set of small biomolecules. This significant enhancement is attributed to the QD's mass-loading effect and spontaneous emission coupling with propagating surface plasmons, which allowed the SPRi limit of detection to be reduced to 100 fM and 100 pg/mL for ssDNA and PSA, respectively. Furthermore, this study illustrates the potential of SPRi to be easily integrated with fluorescent imaging for advanced correlative surface-interaction analysis.
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Affiliation(s)
- Lidija Malic
- Department of Biomedical Engineering, McGill University, 3775 University Street, Montreal, Quebec, Canada H3A 2B4
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Calabretta A, Wasserberg D, Posthuma-Trumpie GA, Subramaniam V, van Amerongen A, Corradini R, Tedeschi T, Sforza S, Reinhoudt DN, Marchelli R, Huskens J, Jonkheijm P. Patterning of peptide nucleic acids using reactive microcontact printing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:1536-1542. [PMID: 20799750 DOI: 10.1021/la102756k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
PNAs (peptide nucleic acids) have been immobilized onto surfaces in a fast, accurate way by employing reactive microcontact printing. Surfaces have been first modified with aldehyde groups to react with the amino end of the synthesized PNAs. When patterning fluorescein-labeled PNAs by reactive microcontact printing using oxygen-oxidized polydimethylsiloxane stamps, homogeneous arrays were fabricated and characterized using optical methods. PNA-patterned surfaces were hybridized with complementary and mismatched dye-labeled oligonucleotides to test their ability to recognize DNA sequences. The stability and selectivity of the PNA-DNA duplexes on surfaces have been verified by fluorescence microscopy, and the melting curves have been recorded. Finally, the technique has been applied to the fabrication of chips by spotting a PNA microarray onto a flat PDMS stamp and reproducing the same features onto many slides. The chips were finally applied to single nucleotide polymorphism detection on oligonucleotides.
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Affiliation(s)
- Alessandro Calabretta
- Molecular Nanofabrication and Biophysical Engineering, Department of Science and Technology, University of Twente, PEnschede, The Netherlands
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Hu R, Zhang XB, Kong RM, Zhao XH, Jiang J, Tan W. Nucleic acid-functionalized nanomaterials for bioimaging applications. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm12588e] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Sforza S, Corradini R, Tedeschi T, Marchelli R. Food analysis and food authentication by peptide nucleic acid (PNA)-based technologies. Chem Soc Rev 2010; 40:221-32. [PMID: 20882238 DOI: 10.1039/b907695f] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
This tutorial review will address the issue of DNA determination in food by using Peptide Nucleic Acid (PNA) probes with different technological platforms, with a particular emphasis on the applications devoted to food authentication. After an introduction aimed at describing PNAs structure, binding properties and their use as genetic probes, the review will then focus specifically on the use of PNAs in the field of food analysis. In particular, the following issues will be considered: detection of genetically modified organisms (GMOs), of hidden allergens, of microbial pathogens and determination of ingredient authenticity. Finally, the future perspectives for the use of PNAs in food analysis will be briefly discussed according to the most recent developments.
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Affiliation(s)
- Stefano Sforza
- Department of Organic and Industrial Chemistry, University of Parma, Parco Area delle Scienze 17a, University Campus, I-43124, Parma, Italy.
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41
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Scarano S, Scuffi C, Mascini M, Minunni M. Surface plasmon resonance imaging (SPRi)-based sensing: a new approach in signal sampling and management. Biosens Bioelectron 2010; 26:1380-5. [PMID: 20692144 DOI: 10.1016/j.bios.2010.07.056] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 07/05/2010] [Accepted: 07/15/2010] [Indexed: 10/19/2022]
Abstract
Surface plasmon resonance imaging (SPRi) is at the forefront of optical sensing, allowing real-time and label free simultaneous multi-analyte measurements. It represents an interesting technology for studying a broad variety of affinity interactions with impact in chemistry, both in fundamental and applied research. Signal sampling and management is a key step in SPRi measurements to achieve successful performances. This work aims to develop a strategy for selecting the sensing areas, called Regions of Interest (ROIs), to be sampled for recording SPRi signals that could results in improved sensor performances. The approach has been evaluated using antigen-antibody interaction: anti-human IgGs are immobilized on the chip surface in an array format, while the specific ligand (hIgG antigen) is in solution. This approach has general applicability and demonstrates that rational selection of sensitive areas and standard management of SPRi data has dramatic impact on sensor behaviour. The criteria of the method are: (a) creation of high density maps of ROIs, (b) evaluation of the SPRi binding signals on all the ROIs during a pre-analysis step, (c) 3D elaboration of the results, and (d) ranking of the ROIs for their final selection in further biosensor analysis. Using standard solution of antigen, three different ROIs selection approaches have been compared for their analytical performances. The proposed innovative method results to be the best one for SPRi-based sensing applications.
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Affiliation(s)
- Simona Scarano
- Dipartimento di Chimica Ugo Schiff, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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D'Agata R, Corradini R, Ferretti C, Zanoli L, Gatti M, Marchelli R, Spoto G. Ultrasensitive detection of non-amplified genomic DNA by nanoparticle-enhanced surface plasmon resonance imaging. Biosens Bioelectron 2010; 25:2095-100. [PMID: 20227870 DOI: 10.1016/j.bios.2010.02.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 02/05/2010] [Accepted: 02/12/2010] [Indexed: 11/27/2022]
Abstract
Technologies today available for the DNA detection rely on a combination of labeled probes hybridized to target sequences which are amplified by polymerase chain reaction (PCR). Direct detection methods that eliminate the requirement for both PCR and labeling steps could afford faster, cheaper and simpler devices for the analysis of small amounts of unamplified DNA. In this work we describe the results obtained in the ultrasensitive detection of non-amplified genomic DNA. We analyzed certified reference materials containing different amounts of genetically modified DNA by using a detection method which combines the nanoparticle-enhanced surface plasmon resonance imaging (SPRI) biosensing to the peptide nucleic acids (PNAs) improved selectivity and sensitivity in targeting complementary DNA sequences. The method allowed us to obtain a 41 zM sensitivity in targeting genomic DNA even in the presence of a large excess of non-complementary DNA.
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Affiliation(s)
- Roberta D'Agata
- Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, I-95125 Catania, Italy
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Bell NM, Micklefield J. Chemical modification of oligonucleotides for therapeutic, bioanalytical and other applications. Chembiochem 2010; 10:2691-703. [PMID: 19739190 DOI: 10.1002/cbic.200900341] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Neil M Bell
- School of Chemistry, The University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, UK
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Grasso G, D'Agata R, Zanoli L, Spoto G. Microfluidic networks for surface plasmon resonance imaging real-time kinetics experiments. Microchem J 2009. [DOI: 10.1016/j.microc.2009.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Pedersen LN, Herrmann B, Møller JK. Typing Chlamydia trachomatis: from egg yolk to nanotechnology. ACTA ACUST UNITED AC 2009; 55:120-30. [PMID: 19281564 DOI: 10.1111/j.1574-695x.2008.00526.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A historical review is provided of the various methods used for half a century to differentiate and type Chlamydia trachomatis strains. Typing of C. trachomatis is an important tool for revealing transmission patterns in sexual networks, and enabling association with clinical manifestations and pathogenicity. Serotyping using the major outer membrane protein (MOMP) has been the mainstay of epidemiological work for several decades. However, the development of nucleic acid amplification techniques (NAAT) and easy access to sequencing have shifted the focus from MOMP serotypes to omp1 genotypes. However, insufficient epidemiological resolution is achieved by characterization of both MOMP and omp1. This calls for new high-resolution genotyping methods applying for example a multilocus variable number tandem repeat assay (MLVA) or multilocus sequence typing (MLST). The futuristic nanotechnology already seems at hand to further simplify and automate the high-resolution genotyping method based on NAAT and sequencing of various targets in the C. trachomatis genome. Thereby, a high throughput can be achieved and more epidemiological information can be obtained. However, it is important to realize that culture of C. trachomatis may still be needed to detect and characterize new variants of C. trachomatis.
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