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Schaubeder JB, Fürk P, Amering R, Gsöls L, Ravn J, Nypelö T, Spirk S. Deciphering heterogeneous enzymatic surface reactions on xylan using surface plasmon resonance spectroscopy. Carbohydr Polym 2024; 337:122137. [PMID: 38710567 DOI: 10.1016/j.carbpol.2024.122137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 03/07/2024] [Accepted: 04/05/2024] [Indexed: 05/08/2024]
Abstract
Xylans' unique properties make it attractive for a variety of industries, including paper, food, and biochemical production. While for some applications the preservation of its natural structure is crucial, for others the degradation into monosaccharides is essential. For the complete breakdown, the use of several enzymes is required, due to its structural complexity. In fact, the specificity of enzymatically-catalyzed reactions is guided by the surface, limiting or regulating accessibility and serving structurally encoded input guiding the actions of the enzymes. Here, we investigate enzymes at surfaces rich in xylan using surface plasmon resonance spectroscopy. The influence of diffusion and changes in substrate morphology is studied via enzyme surface kinetics simulations, yielding reaction rates and constants. We propose kinetic models, which can be applied to the degradation of multilayer biopolymer films. The most advanced model was verified by its successful application to the degradation of a thin film of polyhydroxybutyrate treated with a polyhydroxybutyrate-depolymerase. The herein derived models can be employed to quantify the degradation kinetics of various enzymes on biopolymers in heterogeneous environments, often prevalent in industrial processes. The identification of key factors influencing reaction rates such as inhibition will contribute to the quantification of intricate dynamics in complex systems.
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Affiliation(s)
- Jana B Schaubeder
- Graz University of Technology, Institute of Bioproducts and Paper Technology (BPTI), Inffeldgasse 23, 8010 Graz, Austria
| | - Peter Fürk
- Graz University of Technology, Institute for Chemistry and Technology of Materials (ICTM), Stremayrgasse 9, 8010 Graz, Austria
| | - Richard Amering
- Graz University of Technology, Institute of Bioproducts and Paper Technology (BPTI), Inffeldgasse 23, 8010 Graz, Austria
| | - Lena Gsöls
- Graz University of Technology, Institute of Molecular Biotechnology, Petersgasse 14, 8010 Graz, Austria; The COMET Center, Acib GmbH, Krenngasse 37, 8010 Graz, Austria
| | - Jonas Ravn
- Chalmers University of Technology, Department of Life Sciences, 412 96 Gothenburg, Sweden
| | - Tiina Nypelö
- Chalmers University of Technology, Department of Chemistry and Chemical Engineering, 412 96 Gothenburg, Sweden; Aalto University, Department of Bioproducts and Biosystems, Vuorimiehentie 1, 02150 Espoo, Finland
| | - Stefan Spirk
- Graz University of Technology, Institute of Bioproducts and Paper Technology (BPTI), Inffeldgasse 23, 8010 Graz, Austria.
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2
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Xylan-cellulose thin film platform for assessing xylanase activity. Carbohydr Polym 2022; 294:119737. [DOI: 10.1016/j.carbpol.2022.119737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/01/2022] [Accepted: 06/12/2022] [Indexed: 11/18/2022]
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3
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Agrawal AK, Ninawe A, Dhawan A. Nanostructured plasmonic chips employing nanopillar and nanoring hole arrays for enhanced sensitivity of SPR-based biosensing. RSC Adv 2021; 12:929-938. [PMID: 35425128 PMCID: PMC8978836 DOI: 10.1039/d1ra07937a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/12/2021] [Indexed: 01/12/2023] Open
Abstract
We present a theoretical analysis of the different nanostructured plasmonic sensor chips-consisting of plasmonic nanostructures present on the surface of plasmonic thin films-interrogated using the Kretschmann configuration for highly sensitive localized sensing, with high tunability from the visible to the infrared regions. Rigorous coupled-wave analysis is performed to analyze all the proposed nanostructured sensor chips and compare their sensing performance. The sensitivity parameters are defined to focus on the detection of a thin layer of biomolecules on the surface of nanostructures. The dimensions of the nanostructures and the incident angle shift the plasmon resonance wavelengths and can be used to tune the operating wavelength. The nanostructured films create local regions of high electric fields, which results in enhanced sensitivity of the proposed structures. The proposed sensors can be used in surface plasmon resonance imaging to detect multiple biomolecules in a single measurement. An extremely high surface sensitivity and figure of merit (FOMS) of 91 nm nm-1 and 0.59 nm-1 has been found, respectively, for one of the proposed nanostructured sensing platforms. Moreover, we demonstrate a very high differential reflectance of 55% per nm thickness of the biolayer.
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Affiliation(s)
- Ajay Kumar Agrawal
- Department of Electrical Engineering, Indian Institute of Technology Delhi Hauz Khas New Delhi 110016 India
| | - Akanksha Ninawe
- Department of Electrical Engineering, Indian Institute of Technology Delhi Hauz Khas New Delhi 110016 India
| | - Anuj Dhawan
- Department of Electrical Engineering, Indian Institute of Technology Delhi Hauz Khas New Delhi 110016 India
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4
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Immunosensors containing solution blow spun fibers of poly(lactic acid) to detect p53 biomarker. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 115:111120. [DOI: 10.1016/j.msec.2020.111120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 04/22/2020] [Accepted: 05/24/2020] [Indexed: 01/28/2023]
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5
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Ishihara R, Tanabe K, Inomata S, Matsui R, Kitane R, Hosokawa K, Maeda M, Kikuchi A. Fabrication of Storable Surface-Functionalized Power-Free Microfluidic Chip for Sensitive MicroRNA Detection Utilizing Ultraviolet Grafting. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c00620] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ryo Ishihara
- Department of Materials Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika, Tokyo 125-8585, Japan
| | - Kanta Tanabe
- Department of Materials Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika, Tokyo 125-8585, Japan
| | - Shoko Inomata
- Department of Materials Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika, Tokyo 125-8585, Japan
| | - Ryo Matsui
- Department of Materials Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika, Tokyo 125-8585, Japan
| | - Ryoichi Kitane
- Department of Materials Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika, Tokyo 125-8585, Japan
| | - Kazuo Hosokawa
- Cluster for Pioneering Research, Bioengineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mizuo Maeda
- Cluster for Pioneering Research, Bioengineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akihiko Kikuchi
- Department of Materials Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika, Tokyo 125-8585, Japan
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An N, Fleming AM, Rosecrans NC, Liao Y, Burrows CJ. Synthesis of Site-Specific Crown Ether Adducts to DNA Abasic Sites: 8-Oxo-7,8-Dihydro-2'-Deoxyguanosine and 2'-Deoxycytidine. Methods Mol Biol 2019; 1973:15-25. [PMID: 31016693 DOI: 10.1007/978-1-4939-9216-4_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Formation of adducts to DNA is of great benefit to DNA sequencing and damage detection technology and to enzymology. Here we describe the synthesis and characterization procedures of 18-crown-6 adducts formed to abasic (AP) sites, 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG), and 2'-deoxycytidine (C) residues in DNA oligodeoxynucleotides. These crown ether adducts were used as site-specific modifications to facilitate nanopore technology. The methods described can be readily expanded to attach other suitable primary amines of interest.
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Affiliation(s)
- Na An
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA
| | | | - Yi Liao
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA.
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7
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Boulade M, Morlay A, Piat F, Roupioz Y, Livache T, Charette PG, Canva M, Leroy L. Early detection of bacteria using SPR imaging and event counting: experiments withListeria monocytogenesandListeria innocua. RSC Adv 2019; 9:15554-15560. [PMID: 35514840 PMCID: PMC9064316 DOI: 10.1039/c9ra01466g] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022] Open
Abstract
Foodborne pathogens are of significant concern in the agrifood industry and the development of associated rapid detection and identification methods are of major importance. This paper describes the novel use of resolution-optimized prism-based surface plasmon resonance imaging (RO-SPRI) and data processing for the detection of the foodborne pathogens Listeria monocytogenes and Listeria innocua. With an imaging spatial resolution on the order of individual bacteria (2.7 ± 0.5 μm × 7.9 ± 0.6 μm) over a field of view 1.5 mm2, the RO-SPRI system enabled accurate counting of individual bacteria on the sensor surface. Using this system, we demonstrate the detection of two species of Listeria at an initial concentration of 2 × 102 CFU mL−1 in less than 7 hours. The surface density of bacteria at the point of positive detection was 15 ± 4 bacteria per mm2. Our approach offers great potential for the development of fast specific detection systems based on affinity monitoring. A dedicated SPR apparatus optimized for individual bacteria observation and a new strategy for early detection of microorganisms in growth.![]()
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Affiliation(s)
| | | | | | - Yoann Roupioz
- INAC-SyMMES
- Univ. Grenoble Alpes
- CEA
- CNRS
- 38000 Grenoble
| | | | - Paul G. Charette
- Laboratoire Nanotechnologies Nanosystèmes (LN2)
- CNRS UMI-3463
- Université de Sherbrooke
- UGA
- Canada
| | - Michael Canva
- Laboratoire Nanotechnologies Nanosystèmes (LN2)
- CNRS UMI-3463
- Université de Sherbrooke
- UGA
- Canada
| | - Loïc Leroy
- INAC-SyMMES
- Univ. Grenoble Alpes
- CEA
- CNRS
- 38000 Grenoble
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8
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Janissen R, Sahoo PK, Santos CA, da Silva AM, von Zuben AAG, Souto DEP, Costa ADT, Celedon P, Zanchin NIT, Almeida DB, Oliveira DS, Kubota LT, Cesar CL, Souza APD, Cotta MA. InP Nanowire Biosensor with Tailored Biofunctionalization: Ultrasensitive and Highly Selective Disease Biomarker Detection. NANO LETTERS 2017; 17:5938-5949. [PMID: 28895736 DOI: 10.1021/acs.nanolett.7b01803] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Electrically active field-effect transistors (FET) based biosensors are of paramount importance in life science applications, as they offer direct, fast, and highly sensitive label-free detection capabilities of several biomolecules of specific interest. In this work, we report a detailed investigation on surface functionalization and covalent immobilization of biomarkers using biocompatible ethanolamine and poly(ethylene glycol) derivate coatings, as compared to the conventional approaches using silica monoliths, in order to substantially increase both the sensitivity and molecular selectivity of nanowire-based FET biosensor platforms. Quantitative fluorescence, atomic and Kelvin probe force microscopy allowed detailed investigation of the homogeneity and density of immobilized biomarkers on different biofunctionalized surfaces. Significantly enhanced binding specificity, biomarker density, and target biomolecule capture efficiency were thus achieved for DNA as well as for proteins from pathogens. This optimized functionalization methodology was applied to InP nanowires that due to their low surface recombination rates were used as new active transducers for biosensors. The developed devices provide ultrahigh label-free detection sensitivities ∼1 fM for specific DNA sequences, measured via the net change in device electrical resistance. Similar levels of ultrasensitive detection of ∼6 fM were achieved for a Chagas Disease protein marker (IBMP8-1). The developed InP nanowire biosensor provides thus a qualified tool for detection of the chronic infection stage of this disease, leading to improved diagnosis and control of spread. These methodological developments are expected to substantially enhance the chemical robustness, diagnostic reliability, detection sensitivity, and biomarker selectivity for current and future biosensing devices.
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Affiliation(s)
- Richard Janissen
- "Gleb Wataghin" Physics Institute, University of Campinas , Campinas, São Paulo 13083-859, Brazil
- Kavli Institute of Nanoscience, Delft University of Technology , 2629 HZ Delft, The Netherlands
| | - Prasana K Sahoo
- "Gleb Wataghin" Physics Institute, University of Campinas , Campinas, São Paulo 13083-859, Brazil
| | - Clelton A Santos
- Center for Molecular Biology and Genetic Engineering, Biology Institute, University of Campinas , Campinas, São Paulo 13083-875, Brazil
| | - Aldeliane M da Silva
- "Gleb Wataghin" Physics Institute, University of Campinas , Campinas, São Paulo 13083-859, Brazil
| | - Antonio A G von Zuben
- "Gleb Wataghin" Physics Institute, University of Campinas , Campinas, São Paulo 13083-859, Brazil
| | - Denio E P Souto
- Chemistry Institute, University of Campinas , Campinas, São Paulo 13083-970, Brazil
| | - Alexandre D T Costa
- Oswaldo Cruz Foundation, Carlos Chagas Institute , Curitiba, Paraná 81310-020 Brazil
| | - Paola Celedon
- Molecular Biology Institute of Paraná , Curitiba, Paraná 81310-020 Brazil
| | - Nilson I T Zanchin
- Oswaldo Cruz Foundation, Carlos Chagas Institute , Curitiba, Paraná 81310-020 Brazil
| | - Diogo B Almeida
- "Gleb Wataghin" Physics Institute, University of Campinas , Campinas, São Paulo 13083-859, Brazil
| | - Douglas S Oliveira
- "Gleb Wataghin" Physics Institute, University of Campinas , Campinas, São Paulo 13083-859, Brazil
| | - Lauro T Kubota
- Chemistry Institute, University of Campinas , Campinas, São Paulo 13083-970, Brazil
| | - Carlos L Cesar
- "Gleb Wataghin" Physics Institute, University of Campinas , Campinas, São Paulo 13083-859, Brazil
| | - Anete P de Souza
- Center for Molecular Biology and Genetic Engineering, Biology Institute, University of Campinas , Campinas, São Paulo 13083-875, Brazil
| | - Monica A Cotta
- "Gleb Wataghin" Physics Institute, University of Campinas , Campinas, São Paulo 13083-859, Brazil
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9
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Hu F, Xu J, Chen Y. Surface Plasmon Resonance Imaging Detection of Sub-femtomolar MicroRNA. Anal Chem 2017; 89:10071-10077. [DOI: 10.1021/acs.analchem.7b02838] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Feichi Hu
- Key Laboratory of Analytical Chemistry for Living Biosystems; CAS
Research/Education Center for Excellence in Molecular Sciences; Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiying Xu
- Key Laboratory of Analytical Chemistry for Living Biosystems; CAS
Research/Education Center for Excellence in Molecular Sciences; Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yi Chen
- Key Laboratory of Analytical Chemistry for Living Biosystems; CAS
Research/Education Center for Excellence in Molecular Sciences; Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing National Laboratory for Molecular Science, Beijing 100190, China
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10
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Kim S, Lee HJ. Gold Nanostar Enhanced Surface Plasmon Resonance Detection of an Antibiotic at Attomolar Concentrations via an Aptamer-Antibody Sandwich Assay. Anal Chem 2017; 89:6624-6630. [PMID: 28520392 DOI: 10.1021/acs.analchem.7b00779] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A new sandwich assay for tetracycline (TC) involving a DNA aptamer and antibody pair is demonstrated in conjunction with gold nanostar (GNS) enhanced surface plasmon resonance (SPR) to achieve detection in the low attomolar range. GNS particles were covalently functionalized with the antibody probe (antiTC) and integrated into a surface sandwich assay in conjunction with a SPR gold chip modified with the TC-specific aptamer. After it was demonstrated that both affinity probes can bind simultaneously to TC, optimization of the assay was performed using either antiTC only or GNS-antiTC conjugates to interact with aptamer/TC complexes present on the chip surface. Target concentrations as low as 10 aM could be detected using GNS-antiTC's, which was >103 times greater in performance than when using antiTC only. In addition, good selectivity was achieved with respect to other tetracycline derivative antibiotics, such as oxytetracycline (OTC) and chlortetracycline (CTC), both which are structurally similar to TC. As a demonstration of trace antibiotic analysis in environmental samples, the GNS enhanced sandwich assay was applied to analyze TC added to aliquots of local river water and the results validated by comparing to conventional high-performance liquid chromatography (HPLC) analysis.
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Affiliation(s)
- Suhee Kim
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University , 80 Daehakro, Buk-gu, Daegu-city, 41566, Republic of Korea
| | - Hye Jin Lee
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University , 80 Daehakro, Buk-gu, Daegu-city, 41566, Republic of Korea
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11
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Castañeda AD, Brenes NJ, Kondajji A, Crooks RM. Detection of microRNA by Electrocatalytic Amplification: A General Approach for Single-Particle Biosensing. J Am Chem Soc 2017; 139:7657-7664. [DOI: 10.1021/jacs.7b03648] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Alma D. Castañeda
- Department of Chemistry and
Center for Electrochemistry, The University of Texas at Austin, 105 E. 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
| | - Nicholas J. Brenes
- Department of Chemistry and
Center for Electrochemistry, The University of Texas at Austin, 105 E. 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
| | - Aditya Kondajji
- Department of Chemistry and
Center for Electrochemistry, The University of Texas at Austin, 105 E. 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
| | - Richard M. Crooks
- Department of Chemistry and
Center for Electrochemistry, The University of Texas at Austin, 105 E. 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
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12
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Lee HK, Heo J, Myung S, Shin IS, Kim TH. Homogeneous Electrochemical Assay for Real-time Monitoring of Exonuclease III Activity Based on a Graphene Monolayer. ELECTROANAL 2017. [DOI: 10.1002/elan.201700006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Heon-Kyu Lee
- Department of Chemistry; Soonchunhyang University; Asan 31538 Republic of Korea
| | - Jihye Heo
- Department of Chemistry; Soonchunhyang University; Asan 31538 Republic of Korea
| | - Sung Myung
- Thin Film Materials Research Center; Korea Research Institute of Chemical Technology; Daejeon 34114 Republic of Korea
| | - Ik-Soo Shin
- Department of Chemistry; Soongsil University; Seoul 06978 Republic of Korea
| | - Tae Hyun Kim
- Department of Chemistry; Soonchunhyang University; Asan 31538 Republic of Korea
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13
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Castañeda AD, Robinson DA, Stevenson KJ, Crooks RM. Electrocatalytic amplification of DNA-modified nanoparticle collisions via enzymatic digestion. Chem Sci 2016; 7:6450-6457. [PMID: 28451102 PMCID: PMC5356041 DOI: 10.1039/c6sc02165d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 06/22/2016] [Indexed: 01/04/2023] Open
Abstract
We report a new and general approach that will be useful for adapting the method of electrocatalytic amplification (ECA) to biosensing applications. In ECA, individual collisions of catalytic nanoparticles with a noncatalytic electrode surface lead to bursts of current. In the work described here, the current arises from catalytic electrooxidation of N2H4 at the surface of platinum nanoparticles (PtNPs). The problem with using ECA for biosensing applications heretofore, is that it is necessary to immobilize a receptor, such as DNA (as in the case here) or an antibody on the PtNP surface. This inactivates the colliding NP, however, and leads to very small collision signatures. In the present article, we show that single-stranded DNA (ssDNA) present on the PtNP surface can be detected by selectively removing a fraction of the ssDNA using the enzyme Exonuclease I (Exo I). About half of the current associated with collisions of naked PtNPs can be recovered from fully passivated PtNPs after exposure to Exo I. Experiments carried out using both Au and Hg ultramicroelectrodes reveal some mechanistic aspects of the collision process before and after treatment of the ssDNA-modified PtNPs with Exo I.
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Affiliation(s)
- Alma D Castañeda
- Department of Chemistry , Center for Electrochemistry, and the Center for Nano- and Molecular Science and Technology , The University of Texas at Austin , 105 E. 24th St., Stop A5300 , Austin , TX 78712-1224 , USA . ; Tel: +1-512-475-8674
| | - Donald A Robinson
- Department of Chemistry , Center for Electrochemistry, and the Center for Nano- and Molecular Science and Technology , The University of Texas at Austin , 105 E. 24th St., Stop A5300 , Austin , TX 78712-1224 , USA . ; Tel: +1-512-475-8674
| | - Keith J Stevenson
- Department of Chemistry , Center for Electrochemistry, and the Center for Nano- and Molecular Science and Technology , The University of Texas at Austin , 105 E. 24th St., Stop A5300 , Austin , TX 78712-1224 , USA . ; Tel: +1-512-475-8674
| | - Richard M Crooks
- Department of Chemistry , Center for Electrochemistry, and the Center for Nano- and Molecular Science and Technology , The University of Texas at Austin , 105 E. 24th St., Stop A5300 , Austin , TX 78712-1224 , USA . ; Tel: +1-512-475-8674
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14
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15
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Fasoli J, Corn RM. Surface Enzyme Chemistries for Ultrasensitive Microarray Biosensing with SPR Imaging. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:9527-9536. [PMID: 25641598 PMCID: PMC4564839 DOI: 10.1021/la504797z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/30/2015] [Indexed: 06/01/2023]
Abstract
The sensitivity and selectivity of surface plasmon resonance imaging (SPRI) biosensing with nucleic acid microarrays can be greatly enhanced by exploiting various nucleic acid ligases, nucleases, and polymerases that manipulate the surface-bound DNA and RNA. We describe here various examples from each of these different classes of surface enzyme chemistries that have been incorporated into novel detection strategies that either drastically enhance the sensitivity of or create uniquely selective methods for the SPRI biosensing of proteins and nucleic acids. A dual-element generator-detector microarray approach that couples a bioaffinity adsorption event on one microarray element to nanoparticle-enhanced SPRI measurements of nucleic acid hybridization adsorption on a different microarray element is used to quantitatively detect DNA, RNA, and proteins at femtomolar concentrations. Additionally, this dual-element format can be combined with the transcription and translation of RNA from surface-bound double-stranded DNA (dsDNA) templates for the on-chip multiplexed biosynthesis of aptamer and protein microarrays in a microfluidic format; these microarrays can be immediately used for real-time SPRI bioaffinity sensing measurements.
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16
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Abstract
Protein measurements are essential to many fields ranging from fundamental biochemistry to clinical diagnostics. The ability to make measurements of proteins with ultra-sensitivity will enable early diagnosis of diseases by accessing a concentration regime below the detection limit of present protein assay methods. Furthermore, while single cell analysis is becoming an essential tool, most single cell analytical methods are aimed at measuring genetic targets. Single cell protein measurements will be critical to obtaining a complete picture of the cell. Microwells and microwell arrays are powerful platforms for making protein measurements. Confining molecules and cells to small volumes creates high local concentrations. This Insight discusses the present status of microwell arrays for making protein measurements and describes some of the fundamental challenges as well as opportunities for using microwells in the future.
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Affiliation(s)
- David R Walt
- Tufts University, Department of Chemistry, Medford, MA 02155, USA.
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17
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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: 215] [Impact Index Per Article: 21.5] [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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18
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Noor MO, Petryayeva E, Tavares AJ, Uddayasankar U, Algar WR, Krull UJ. Building from the “Ground” Up: Developing interfacial chemistry for solid-phase nucleic acid hybridization assays based on quantum dots and fluorescence resonance energy transfer. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2013.08.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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19
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Gray CJ, Weissenborn MJ, Eyers CE, Flitsch SL. Enzymatic reactions on immobilised substrates. Chem Soc Rev 2014; 42:6378-405. [PMID: 23579870 DOI: 10.1039/c3cs60018a] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This review gives an overview of enzymatic reactions that have been conducted on substrates attached to solid surfaces. Such biochemical reactions have become more important with the drive to miniaturisation and automation in chemistry, biology and medicine. Technical aspects such as choice of solid surface and analytical methods are discussed and examples of enzyme reactions that have been successful on these surfaces are provided.
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Affiliation(s)
- Christopher J Gray
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Road, Manchester, M1 7DN, UK
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20
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Improving surface plasmon resonance imaging of DNA by creating new gold and silver based surface nanostructures. Mikrochim Acta 2013. [DOI: 10.1007/s00604-013-1023-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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21
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Anne A, Demaille C. Kinetics of enzyme action on surface-attached substrates: a practical guide to progress curve analysis in any kinetic situation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:14665-14671. [PMID: 22978617 DOI: 10.1021/la3030827] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In the present work, exact kinetic equations describing the action of an enzyme in solution on a substrate attached to a surface have been derived in the framework of the Michaelis-Menten mechanism but without resorting to the often-used steady-state approximation. The here-derived kinetic equations are cast in a workable format, allowing us to introduce a simple and universal procedure for the quantitative analysis of enzyme surface kinetics that is valid for any kinetic situation. The results presented here should allow experimentalists studying the kinetics of enzyme action on immobilized substrates to analyze their data in a perfectly rigorous way.
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Affiliation(s)
- Agnès Anne
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
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22
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Zelzer M, Todd SJ, Hirst AR, McDonald TO, Ulijn RV. Enzyme responsive materials: design strategies and future developments. Biomater Sci 2012; 1:11-39. [PMID: 32481995 DOI: 10.1039/c2bm00041e] [Citation(s) in RCA: 227] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Enzyme responsive materials (ERMs) are a class of stimuli responsive materials with broad application potential in biological settings. This review highlights current and potential future design strategies for ERMs and provides an overview of the present state of the art in the area.
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Affiliation(s)
- Mischa Zelzer
- WestCHEM, Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, U.K..
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23
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Guo X. Surface plasmon resonance based biosensor technique: a review. JOURNAL OF BIOPHOTONICS 2012; 5:483-501. [PMID: 22467335 DOI: 10.1002/jbio.201200015] [Citation(s) in RCA: 170] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 03/10/2012] [Accepted: 03/11/2012] [Indexed: 05/12/2023]
Abstract
Optical Surface plasmon resonance (SPR) biosensors represent the most advanced and developed optical label-free biosensor technology. Optical SPR biosensors are a powerful detection and analysis tool that has vast applications in environmental protection, biotechnology, medical diagnostics, drug screening, food safety and security. This article reviews the recent development of SPR biosensor techniques, including bulk SPR and localized SPR (LSPR) biosensors, for detecting interactions between an analyte of interest in solution and a biomolecular recognition. The concepts of bulk and localized SPs and the working principles of both sensing techniques are introduced. Major sensing advances on biorecognition elements, measurement formats, and sensing platforms are presented. Finally, the discussions on both biosensor techniques as well as comparison of both SPR sensing techniques are made.
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Affiliation(s)
- Xiaowei Guo
- School of Electrical Engineering and Computer Science, and College of Engineering, Seoul National University, 599 Gwanangno, Gwanak-gu, Seoul 151-744, South Korea.
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24
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Anne A, Chovin A, Demaille C. Optimizing electrode-attached redox-peptide systems for kinetic characterization of protease action on immobilized substrates. Observation of dissimilar behavior of trypsin and thrombin enzymes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:8804-8813. [PMID: 22591015 DOI: 10.1021/la301316r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this work, we experimentally address the issue of optimizing gold electrode attached ferrocene (Fc)-peptide systems for kinetic measurements of protease action. Considering human α-thrombin and bovine trypsin as proteases of interest, we show that the recurring problem of incomplete cleavage of the peptide layer by these enzymes can be solved by using ultraflat template-stripped gold, instead of polished polycrystalline gold, as the Fc-peptide bearing electrode material. We describe how these fragile surfaces can be mounted in a rotating disk configuration so that enzyme mass transfer no longer limits the overall measured cleavage kinetics. Finally, we demonstrate that, once the system has been optimized, in situ real-time cyclic voltammetry monitoring of the protease action can yield high-quality kinetic data, showing no sign of interfering effects. The cleavage progress curves then closely match the Langmuirian variation expected for a kinetically controlled surface process. Global fit of the progress curves yield accurate values of the peptide cleavage rate for both trypsin and thrombin. It is shown that, whereas trypsin action on the surface-attached peptide closely follows Michaelis-Menten kinetics, thrombin displays a specific and unexpected behavior characterized by a nearly enzyme-concentration-independent cleavage rate in the subnanomolar enzyme concentration range. The reason for this behavior has still to be clarified, but its occurrence may limit the sensitivity of thrombin sensors based on Fc-peptide layers.
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Affiliation(s)
- Agnès Anne
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Univ Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France.
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25
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Kong DH, Jung SH, Lee ST, Kim YM, Ha KS. Monitoring of proteolytic enzyme activity using phase transition-based peptide arrays. Biosens Bioelectron 2012; 36:147-53. [DOI: 10.1016/j.bios.2012.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 03/18/2012] [Accepted: 04/09/2012] [Indexed: 02/01/2023]
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26
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Okabe Y, Chen Y, Purohit R, Corn RM, Lee AP. Piezoelectrically driven vertical cavity acoustic transducers for the convective transport and rapid detection of DNA and protein binding to DNA microarrays with SPR imaging—A parametric study. Biosens Bioelectron 2012; 35:37-43. [DOI: 10.1016/j.bios.2012.01.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 12/08/2011] [Accepted: 01/19/2012] [Indexed: 10/14/2022]
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27
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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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28
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Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance. JOURNAL OF AMINO ACIDS 2012; 2012:816032. [PMID: 22500214 PMCID: PMC3303711 DOI: 10.1155/2012/816032] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 11/07/2011] [Indexed: 01/04/2023]
Abstract
Several proteins, like transcription factors, bind to certain DNA sequences, thereby regulating biochemical pathways that determine the fate of the corresponding cell. Due to these key positions, it is indispensable to analyze protein-DNA interactions and to identify their mode of action. Surface plasmon resonance is a label-free method that facilitates the elucidation of real-time kinetics of biomolecular interactions. In this article, we focus on this biosensor-based method and provide a detailed guide how SPR can be utilized to study binding of proteins to oligonucleotides. After a description of the physical phenomenon and the instrumental realization including fiber-optic-based SPR and SPR imaging, we will continue with a survey of immobilization methods. Subsequently, we will focus on the optimization of the experiment, expose pitfalls, and introduce how data should be analyzed and published. Finally, we summarize several interesting publications of the last decades dealing with protein-DNA and RNA interaction analysis by SPR.
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Akbay N, Lakowicz JR, Ray K. Distance-dependent intrinsic fluorescence of proteins on aluminum nanostructures. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2012; 8234:823417. [PMID: 24027612 PMCID: PMC3767003 DOI: 10.1117/12.928379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In the past several years we have demonstrated the metal-enhanced fluorescence (MEF) and the significant changes in the photophysical properties of fluorophores in the presence of metallic nanostructures and nanoparticles using ensemble spectroscopic studies. In the represented study, we explored the distance effect on intrinsic fluorescence of proteins adsorbed on our layer-by-layer assembled metallic nanostructures. The study is expected to provide more information on the importance of positioning the proteins at a particular distance for enhanced fluorescence from metallic structures. For the present study, we considered using easy and inexpensive LbL technique to provide well-defined distance from metallic surface. The explored proteins were adsorbed on different numbers of alternate layers of poly(styrene sulfonate) (PSS) and poly(allylamine hydrochloride) (PAH). SA and BSA were electrostatically attached to the positively charged PAH layer. We obtained a maximum of ~11-fold and 9-fold increase in fluorescence intensity from SA and BSA, respectively. And also we observed ~3-fold decrease in BSA lifetime on metallic nanostructures than those on bare control quartz slides. This study reveals the distance dependence of protein fluorescence.
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Affiliation(s)
- Nuriye Akbay
- ; phone 1 410 706 7500; fax 1 410 706 8408; http://cfs.umbi.umd.edu
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30
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Affiliation(s)
- Francisco Zaera
- Department of Chemistry, University of California, Riverside, California 92521, United States
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31
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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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32
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Zhou WJ, Halpern AR, Seefeld TH, Corn RM. Near infrared surface plasmon resonance phase imaging and nanoparticle-enhanced surface plasmon resonance phase imaging for ultrasensitive protein and DNA biosensing with oligonucleotide and aptamer microarrays. Anal Chem 2011; 84:440-5. [PMID: 22126812 DOI: 10.1021/ac202863k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The techniques of surface plasmon resonance-phase imaging (SPR-PI) and nanoparticle-enhanced SPR-PI have been implemented for the multiplexed bioaffinity detection of proteins and nucleic acids. The SPR-PI experiments utilized a near-infrared 860 nm light emitting diode (LED) light source and a wedge depolarizer to create a phase grating on a four-element single-stranded DNA (ssDNA) microarray; bioaffinity adsorption onto the various microarray elements was detected via multiplexed real time phase shift measurements. In a first set of demonstration experiments, an ssDNA aptamer microarray was used to directly detect thrombin at concentrations down to 100 pM with SPR-PI. Two different ssDNA aptamers were used in these experiments with two different Langmuir adsorption coefficients, K(A1) = 4.4 × 10(8) M(-1) and K(A2) = 1.2 × 10(8) M(-1). At concentrations below 1 nM, the equilibrium phase shifts observed upon thrombin adsorption vary linearly with concentration with a slope that is proportional to the appropriate Langmuir adsorption coefficient. The observed detection limit of 100 pM is approximately 20 times more sensitive than that observed previously with SPRI. In a second set of experiments, two short ssDNA oligonucleotides (38mers) were simultaneously detected at concentrations down to 25 fM using a three-sequence hybridization format that employed 120 nm DNA-modified silica nanoparticles to enhance the SPR-PI signal. In this first demonstration of nanoparticle-enhanced SPR-PI, the adsorbed silica nanoparticles provided a greatly enhanced phase shift upon bioaffinity adsorption due to a large increase in the real component of the interfacial refractive index from the adsorbed nanoparticle. As in the case of SPR-PI, the detection limit of 25 fM for nanoparticle-enhanced SPR-PI is approximately 20 times more sensitive than that observed previously with nanoparticle-enhanced SPRI.
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Affiliation(s)
- Wen-Juan Zhou
- Department of Chemistry, University of California-Irvine, Irvine, California 92697, USA
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33
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Real-time monitoring of matrix metalloproteinase-9 collagenolytic activity with a surface plasmon resonance biosensor. Anal Biochem 2011; 419:53-60. [DOI: 10.1016/j.ab.2011.07.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 07/23/2011] [Accepted: 07/25/2011] [Indexed: 11/18/2022]
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34
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Abstract
The convergence of terahertz spectroscopy and single molecule experimentation offers significant promise of enhancement in sensitivity and selectivity in molecular recognition, identification and quantitation germane to military and security applications. This paper provides a brief overview of the constraints set by single molecule recognition systems and reports the results of experiments which address fundamental barriers to the integration of large, patterned bio-compatible molecular opto-electronic systems with silicon based microelectronic systems. Central to this thrust is an approach involving sequential epitaxy on surface bound single stranded DNA one-dimensional substrates. The challenge of producing highly structured macromolecular substrates, which are necessary in order to implement molecular nanolithography, has been addressed experimentally by combining “designer” synthetic DNA with biosynthetically derived plasmid components. By design, these one dimensional templates are composed of domains which contain sites which are recognized, and therefore addressable by either complementary DNA sequences and/or selected enzymes. Such design is necessary in order to access the nominal 2 nm linewidth potential resolution of nanolithography on these one-dimensional substrates. The recognition and binding properties of DNA ensure that the lithographic process is intrinsically self-organizing, and therefore self-aligning, a necessity for assembly processes at the requisite resolution. Another requirement of this molecular epitaxy approach is that the substrate must be immobilized. The challenge of robust surface immobilization is being addressed via the production of the equivalent of molecular tube sockets. In this application, multi-valent core-shell fluorescent quantum dots provide a mechanism to prepare surface attachment sites with a pre-determined 1:1 attachment site : substrate (DNA) molecule ratio.
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Affiliation(s)
- Michael Norton
- Department of Chemistry, Marshall University, 1 John Marshall Drive, Huntington, WV 25755, USA
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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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Chowdhury MH, Chakraborty S, Lakowicz JR, Ray K. Feasibility of Using Bimetallic Plasmonic Nanostructures to Enhance the Intrinsic Emission of Biomolecules. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2011; 115:16879-16891. [PMID: 21984954 PMCID: PMC3185356 DOI: 10.1021/jp205108s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Detection of the intrinsic fluorescence from proteins is important in bio-assays because it can potentially eliminate the labeling of external fluorophores to proteins. This is advantageous because using external fluorescent labels to tag biomolecules requires chemical modification and additional incubation and washing steps which can potentially perturb the native functionality of the biomolecules. Hence the external labeling steps add expense and complexity to bio-assays. In this paper, we investigate for the first time the feasibility of using bimetallic nanostructures made of silver (Ag) and aluminum (Al) to implement the metal enhanced fluorescence (MEF) phenomenon for enhancing the intrinsic emission of biomolecules in the ultra-violet (UV) spectral region. Fluorescence intensities and lifetimes of a tryptophan analogue N-acetyl-L-tryptophanamide (NATA) and a tyrosine analogue N-acetyl-L-tyrosinamide (NATA-tyr) were measured. Increase in fluorescence intensities of upto 10-fold and concurrent decrease in lifetimes for the amino acids were recorded in the presence of the bimetallic nanostructures when compared to quartz controls. We performed a model protein assay involving biotinylated bovine serum albumin (bt-BSA) and streptavidin on the bimetallic nanostructured substrate to investigate the distance dependent effects on the extent of MEF from the bimetallic nanostructures and found a maximum enhancement of over 15-fold for two layers of bt-BSA and streptavidin. We also used finite difference time domain (FDTD) calculations to explore how bimetallic nanostructures interact with plane waves and excited state fluorophores in the UV region and demonstrate that the bimetallic substrates are an effective platform for enhancing the intrinsic emission of proteins and other biomolecules.
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Affiliation(s)
| | | | | | - Krishanu Ray
- Corresponding author: , Phone: 1-410-706-7500; Fax: 1-410-706-8408
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37
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Yang CJ, Cui L, Huang J, Yan L, Lin X, Wang C, Zhang WY, Kang H. Linear molecular beacons for highly sensitive bioanalysis based on cyclic Exo III enzymatic amplification. Biosens Bioelectron 2011; 27:119-24. [PMID: 21764287 DOI: 10.1016/j.bios.2011.06.027] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 06/11/2011] [Accepted: 06/21/2011] [Indexed: 12/21/2022]
Abstract
Sensitive analysis or monitoring of biomolecules and small molecules is very important for many biological researches, clinical diagnosis and forensic investigations. As a sequence-independent exonuclease, Exonuclease III (Exo III) has been widely used for amplified detection of proteins and nucleic acids where displacing probes or molecular beacons are used as the signaling probes. However, displacing probes suffer slow hybridization rate and high background signal and molecular beacons are difficult to design and prone to undesired nonspecific interactions. Herein, we report a new type of probes called linear molecular beacons (LMBs) for use in Exo III amplification assays to improve hybridization kinetics and reduce background noises. LMBs are linear oligonucleotide probes with a fluorophore and quencher attached to 3' terminal and penultimate nucleotides, respectively. Compared to conventional molecular beacons and displacing probes, LMBs are easy to design and synthesize. More importantly, LMBs have a much lower background noise and allow faster reaction rates. Using LMBs in cyclic Exo III amplification assay, ultrasensitive nucleic acid detection methods were developed with a detection limit of less than 120fM, which is 2 orders of magnitude lower than that of conventional molecular beacons or displacing probes-based Exo III amplification assays. Furthermore, LMBs can be extended as universal probes for detection of non-nucleic acid molecules such as cocaine with high sensitivity. These results demonstrate that the combination of Exo III amplification and LMB signaling provides a general method for ultrasensitive and selective detection of a wide range of targets.
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Affiliation(s)
- Chaoyong James Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, PR China.
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38
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Sheppard G, Oseki T, Baba A, Patton D, Kaneko F, Mao L, Locklin J. Thiolene-based microfluidic flow cells for surface plasmon resonance imaging. BIOMICROFLUIDICS 2011; 5:26501. [PMID: 21731900 PMCID: PMC3129337 DOI: 10.1063/1.3596395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 05/01/2011] [Indexed: 05/08/2023]
Abstract
Thiolene-based microfluidic devices have been coupled with surface plasmon resonance imaging (SPRI) to provide an integrated platform to study interfacial interactions in both aqueous and organic solutions. In this work, we develop a photolithographic method that interfaces commercially available thiolene resin to gold and glass substrates to generate microfluidic channels with excellent adhesion that leave the underlying sensor surface free from contamination and readily available for surface modification through self-assembly. These devices can sustain high flow rates and have excellent solvent compatibility even with several organic solvents. To demonstrate the versatility of these devices, we have conducted nanomolar detection of streptavidin-biotin interactions using in situ SPRI.
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39
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Seefeld TH, Zhou WJ, Corn RM. Rapid microarray detection of DNA and proteins in microliter volumes with surface plasmon resonance imaging measurements. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:6534-40. [PMID: 21488682 PMCID: PMC3093654 DOI: 10.1021/la200649n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
A four-chamber microfluidic biochip is fabricated for the rapid detection of multiple proteins and nucleic acids from microliter volume samples with the technique of surface plasmon resonance imaging (SPRI). The 18 mm × 18 mm biochip consists of four 3 μL microfluidic chambers attached to an SF10 glass substrate, each of which contains three individually addressable SPRI gold thin film microarray elements. The 12-element (4 × 3) SPRI microarray consists of gold thin film spots (1 mm(2) area; 45 nm thickness), each in individually addressable 0.5 μL volume microchannels. Microarrays of single-stranded DNA and RNA (ssDNA and ssRNA, respectively) are fabricated by either chemical and/or enzymatic attachment reactions in these microchannels; the SPRI microarrays are then used to detect femtomole amounts (nanomolar concentrations) of DNA and proteins (ssDNA binding protein and thrombin via aptamer-protein bioaffinity interactions). Microarrays of ssRNA microarray elements are also used for the ultrasensitive detection of zeptomole amounts (femtomolar concentrations) of DNA via the technique of RNase H-amplified SPRI. Enzymatic removal of ssRNA from the surface due to the hybridization adsorption of target ssDNA is detected as a reflectivity decrease in the SPR imaging measurements. The observed reflectivity loss is proportional to the log of the target ssDNA concentration with a detection limit of 10 fM or 30 zeptomoles (18 000 molecules). This enzymatic amplified ssDNA detection method is not limited by diffusion of ssDNA to the interface, and thus is extremely fast, requiring only 200 s in the microliter volume format.
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40
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Zhou WJ, Chen Y, Corn RM. Ultrasensitive microarray detection of short RNA sequences with enzymatically modified nanoparticles and surface plasmon resonance imaging measurements. Anal Chem 2011; 83:3897-902. [PMID: 21524060 DOI: 10.1021/ac200422u] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A novel multiplexed method for short RNA detection that employs an enzymatic capture reaction onto DNA-modified silica nanoparticles (SiNPs) followed by nanoparticle-enhanced surface plasmon resonance imaging (SPRI) is demonstrated. SiNPs functionalized with 5'-phosphorylated single stranded DNA (ssDNA) are used with T4 RNA ligase to capture various short 20-24 base single-stranded RNA (ssRNA) oligonucleotides from a target solution. The ssRNA-modified SiNPs are collected from the target solution, specifically adsorbed onto a cDNA microarray and then detected with SPRI. The use of DNA-modified SiNPs to capture ssRNA for profiling has several advantages as compared to a planar SPRI surface bioaffinity adsorption format: (i) the target solution is exposed to a larger total surface area for the RNA ligation reaction; (ii) the SiNPs enhance the diffusion rate of the ssRNA to the surface; (iii) the SiNPs can be collected, washed, and preconcentrated prior to detection; and (iv) the ssRNA-modified SiNPs give an enhanced SPRI signal upon hybridization adsorption to the microarray. Our initial measurements demonstrate that this detection method can be used to detect multiple ssRNA sequences at concentrations as low as 100 fM in 500 μL.
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Affiliation(s)
- Wen-Juan Zhou
- Department of Chemistry, University of California-Irvine, Irvine, California 92697, USA
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41
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Sendroiu IE, Gifford LK, Lupták A, Corn RM. Ultrasensitive DNA microarray biosensing via in situ RNA transcription-based amplification and nanoparticle-enhanced SPR imaging. J Am Chem Soc 2011; 133:4271-3. [PMID: 21391582 DOI: 10.1021/ja2005576] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA microarrays are invaluable tools for the detection and identification of nucleic acids in biosensing applications. The sensitivity and selectivity of multiplexed single-stranded DNA (ssDNA) surface bioaffinity sensing can be greatly enhanced when coupled to a surface enzymatic reaction. Herein we describe a novel method where the specific sequence-dependent adsorption of a target ssDNA template molecule onto an ssDNA-modified gold microarray is followed with the generation of multiple copies of ssRNA via in situ surface transcription by RNA polymerase. The RNA created on this "generator" element is then detected by specific adsorption onto a second adjacent "detector" element of ssDNA that is complementary to one end of the ssRNA transcript. SPR imaging is then used to detect the subsequent hybridization of cDNA-coated gold nanoparticles with the surface-bound RNA. This RNA transcription-based, dual element amplification method is used to detect ssDNA down to a concentration of 1 fM in a volume of 25 μL (25 zeptomoles).
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Affiliation(s)
- Iuliana E Sendroiu
- Department of Chemistry, University of California-Irvine, Irvine, California 92697, USA
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42
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Hall WP, Ngatia SN, Van Duyne RP. LSPR Biosensor Signal Enhancement Using Nanoparticle-Antibody Conjugates. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2011; 115:1410-1414. [PMID: 21660207 PMCID: PMC3109750 DOI: 10.1021/jp106912p] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
A method to amplify the wavelength shift observed from localized surface plasmon resonance (LSPR) bioassays is developed using gold nanoparticle-labeled antibodies. The technique, which involves detecting surface-bound analytes using gold nanoparticle conjugated antibodies, provides a way to enhance LSPR shifts for more sensitive detection of low-concentration analytes. Using the biotin and antibiotin binding pair as a model, we demonstrate up to a 400% amplification of the shift upon antibody binding to analyte. In addition, the antibody-nanoparticle conjugate improves the observed binding constant by 2 orders of magnitude, and the limit of detection by nearly 3 orders of magnitude. This amplification strategy provides a way to improve the sensitivity of plasmon-based bioassays, paving the way for single molecule-based detection and clinically relevant diagnostics.
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Larmour IA, Graham D. Surface enhanced optical spectroscopies for bioanalysis. Analyst 2011; 136:3831-53. [DOI: 10.1039/c1an15452d] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Nanostructured digital microfluidics for enhanced surface plasmon resonance imaging. Biosens Bioelectron 2011; 26:2053-9. [DOI: 10.1016/j.bios.2010.09.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Revised: 07/30/2010] [Accepted: 09/01/2010] [Indexed: 01/08/2023]
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Wang J, Munir A, Zhu Z, Zhou HS. Magnetic nanoparticle enhanced surface plasmon resonance sensing and its application for the ultrasensitive detection of magnetic nanoparticle-enriched small molecules. Anal Chem 2010; 82:6782-9. [PMID: 20704367 DOI: 10.1021/ac100812c] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Magnetic nanoparticles (MNPs) have been frequently used in bioseparation, but their applicability in bioassays is limited due to their extremely small size so that sensitive detection is difficult to achieve using a general technique. Here, we present an amplification technique using MNPs for an enhanced surface plasmon resonance (SPR) bioassay. The amplification effect of carboxyl group modified Fe(3)O(4) MNPs of two sizes on SPR spectroscopy is first demonstrated by assembling MNPs on amino group modified SPR gold substrate. To further evaluate the feasibility of the use of Fe(3)O(4) MNPs in enhancing a SPR bioassay, a novel SPR sensor based on an indirect competitive inhibition assay (ICIA) is developed for detecting adenosine by employing Fe(3)O(4) MNP-antiadenosine aptamer conjugates as the amplification reagent. The results confirm that Fe(3)O(4) MNPs can be used as a powerful amplification agent to provide a sensitive approach to detect adenosine by SPR within the range of 10-10,000 nM, which is much superior to the detection result obtained by a general SPR sensor. Importantly, the present detection methodology could be easily extended to detect other biomolecules of interest by changing the corresponding aptamer in Fe(3)O(4) MNP-aptamer conjugates. This novel technique not only explores the possibility of the use of SPR spectroscopy in a highly sensitive detection of an MNP-based separation product but also offers a new direction in the use of Fe(3)O(4) MNPs as an amplification agent to design high performance SPR biosensors.
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Affiliation(s)
- Jianlong Wang
- Department of Chemical Engineering, Worcester Polytechnic Institute, 100 Institute Road, Worcester, Massachusetts 01609, USA
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In situ imaging of micropatterned phospholipid membranes by surface plasmon fluorescence microscopy. Colloids Surf B Biointerfaces 2010; 81:447-51. [DOI: 10.1016/j.colsurfb.2010.07.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 07/14/2010] [Accepted: 07/16/2010] [Indexed: 11/24/2022]
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Shen Y, Kim H, Tong M, Li Q. Influence of solution chemistry on the deposition and detachment kinetics of RNA on silica surfaces. Colloids Surf B Biointerfaces 2010; 82:443-9. [PMID: 21030219 DOI: 10.1016/j.colsurfb.2010.09.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 09/21/2010] [Accepted: 09/23/2010] [Indexed: 11/17/2022]
Abstract
The deposition kinetics of RNA extracted from both virus and bacteria on silica surfaces were examined in both monovalent (NaCl) and divalent (CaCl(2)) solutions under a wide range of environmentally relevant ionic strength and pH conditions by utilizing a quartz crystal microbalance with dissipation (QCM-D). To better understand the RNA deposition mechanisms, QCM-D data were complemented by diffusion coefficients and zeta potentials of RNA as a function of examined solution chemistry conditions. Favorable deposition of RNA on poly-l-lysine-coated (positively charged) silica surfaces was governed by the convective-diffusive transport of RNA to the surfaces. The deposition kinetics of RNA on bare silica surfaces were controlled by classic Derjaguin-Landau-Verwey-Overbeek (DLVO) interactions. The presence of divalent cations (Ca(2+)) in solutions greatly enhanced the deposition kinetics of RNA on silica surfaces. Solution pH also affected the deposition behavior of RNA on silica surfaces. Release experiments showed that detachment of RNA from silica surfaces was significant in NaCl solutions, whereas, the deposited RNA on silica surfaces in CaCl(2) solutions was more likely to be irreversible.
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Affiliation(s)
- Yun Shen
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Yi He Yuan Road #5, Haidian District, Beijing 100871, PR China
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Gifford LK, Sendroiu IE, Corn RM, Lupták A. Attomole detection of mesophilic DNA polymerase products by nanoparticle-enhanced surface plasmon resonance imaging on glassified gold surfaces. J Am Chem Soc 2010; 132:9265-7. [PMID: 20565098 DOI: 10.1021/ja103043p] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA microarrays are invaluable tools for biosensing applications such as diagnostic detection of DNA and analysis of gene expression. Surface plasmon resonance imaging can detect unlabeled oligonucleotide targets adsorbed to the array elements. The variety of biosensing applications can be expanded by enzymatic manipulation of DNA microarray elements, and the sensitivity of detection can be enhanced with the use of oligonucleotide immobilized onto a gold nanoparticle surface. We describe a novel method that couples a template-directed polymerase extension of a surface array element with nanoparticle-enhanced detection of the reaction product. Using this technique, it is possible to see as little as 10-100 amol of polymerase product, representing as little as 0.25% of a monolayer. This sensitivity would allow for the detection of a specific DNA target that is present in low amounts in a sample and with partially unknown sequence. One application of this method would be to identify the presence of the aberrantly recombined DNA sequences, such as those found in the fragile sites of chromosomes.
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Affiliation(s)
- Lida K Gifford
- Department of Chemistry, University of California, Irvine, California 92697, USA
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Manimozhi P, Rajendran L. Derivation of nonsteady-state analytical solution for surface enzyme kinetics. J Electroanal Chem (Lausanne) 2010. [DOI: 10.1016/j.jelechem.2010.05.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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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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