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Pyrak E, Krajczewski J, Kowalik A, Kudelski A, Jaworska A. Surface Enhanced Raman Spectroscopy for DNA Biosensors-How Far Are We? Molecules 2019; 24:E4423. [PMID: 31817059 PMCID: PMC6943648 DOI: 10.3390/molecules24244423] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/20/2022] Open
Abstract
A sensitive and accurate identification of specific DNA fragments (usually containing a mutation) can influence clinical decisions. Standard methods routinely used for this type of detection are PCR (Polymerase Chain Reaction, and its modifications), and, less commonly, NGS (Next Generation Sequencing). However, these methods are quite complicated, requiring time-consuming, multi-stage sample preparation, and specially trained staff. Usually, it takes weeks for patients to obtain their results. Therefore, different DNA sensors are being intensively developed by many groups. One technique often used to obtain an analytical signal from DNA sensors is Raman spectroscopy. Its modification, surface-enhanced Raman spectroscopy (SERS), is especially useful for practical analytical applications due to its extra low limit of detection. SERS takes advantage of the strong increase in the efficiency of Raman signal generation caused by a local electric field enhancement near plasmonic (typically gold and silver) nanostructures. In this condensed review, we describe the most important types of SERS-based nanosensors for genetic studies and comment on their potential for becoming diagnostic tools.
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Affiliation(s)
- Edyta Pyrak
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland; (E.P.); (J.K.)
- Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland
| | - Jan Krajczewski
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland; (E.P.); (J.K.)
| | - Artur Kowalik
- Holy Cross Cancer Center, 3 Stefana Artwińskiego St., 25-734 Kielce, Poland
| | - Andrzej Kudelski
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland; (E.P.); (J.K.)
| | - Aleksandra Jaworska
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland; (E.P.); (J.K.)
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Duan Z, Zhang X, Ye T, Zhang X, Dong S, Liu J, Xiao X, Jiang C. Ultrasensitive Au Nanooctahedron Micropinball Sensor for Mercury Ions. ACS APPLIED MATERIALS & INTERFACES 2018; 10:25737-25743. [PMID: 29978695 DOI: 10.1021/acsami.8b04414] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Mercury ion (Hg2+) is one of the most toxic heavy metals that has severe adverse effects on the environment and human organs even at very low concentrations. Therefore, highly sensitive and selective detection of Hg2+ is desirable. Here, we introduce plasmonic micropinball constructed from Au nanooctahedron as a three-dimensional surface-enhanced Raman spectroscopy (SERS) platform, enabling ultrasensitive detection of trace Hg2+ ions. Typically, strong SERS signals could be obtained when the single-stranded DNA structure converts to the hairpin structure in the presence of Hg2+ ions, due to the formation of thymine (T)-Hg2+-T. As a result, the detection limit of Hg2+ ions is as low as 1 × 10-16 M, which is far below compared to that reported for conventional analytical strategies. Moreover, to achieve rapid multiple detection, we combine the micropinball sensors with microflow tube online detection. Our platform prevents cross-talk and tube contamination, allowing multiassay analysis, rapid identification, and quantification of different analytes and concentrations across separate phases.
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Affiliation(s)
- Zhanxin Duan
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and Center for Ion Beam Application , Wuhan University , Wuhan 430072 , P. R. China
| | - Xingang Zhang
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and Center for Ion Beam Application , Wuhan University , Wuhan 430072 , P. R. China
| | - Tianyu Ye
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and Center for Ion Beam Application , Wuhan University , Wuhan 430072 , P. R. China
| | - Xiaolei Zhang
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and Center for Ion Beam Application , Wuhan University , Wuhan 430072 , P. R. China
| | - Shilian Dong
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and Center for Ion Beam Application , Wuhan University , Wuhan 430072 , P. R. China
| | - Jing Liu
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and Center for Ion Beam Application , Wuhan University , Wuhan 430072 , P. R. China
| | - Xiangheng Xiao
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and Center for Ion Beam Application , Wuhan University , Wuhan 430072 , P. R. China
| | - Changzhong Jiang
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and Center for Ion Beam Application , Wuhan University , Wuhan 430072 , P. R. China
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Wang Z, Zong S, Wang Z, Wu L, Chen P, Yun B, Cui Y. Microfluidic chip based micro RNA detection through the combination of fluorescence and surface enhanced Raman scattering techniques. NANOTECHNOLOGY 2017; 28:105501. [PMID: 28139463 DOI: 10.1088/1361-6528/aa527b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We present a novel microfluidic chip based method for the detection of micro RNA (miRNA) via the combination of fluorescence and surface enhanced Raman scattering (SERS) spectroscopies. First, silver nanoparticles (Ag NPs) are immobilized onto a glass slide, forming a SERS enhancing substrate. Then a specificially designed molecular beacon (MB) is attached to the SERS substrate. The 3' end of the MB is decorated with a thiol group to facilitate the attachment of the MB, while the 5' end of the MB is labeled with an organic dye 6-FAM, which is used both as the fluorophore and SERS reporter. In the absence of target miRNA, the MB will form a hairpin structure, making 6-FAM close to the Ag NPs. Hence, the fluorescence of 6-FAM will be quenched and the Raman signal of 6-FAM will be enhanced. On the contrary, with target miRNA present, hybridization between the miRNA and MB will unfold the MB and increase the distance between 6-FAM and the Ag NPs. Thus the fluorescence of 6-FAM will recover and the SERS signal of 6-FAM will decrease. So the target miRNA will simultaneously introduce opposite changing trends in the intensities of the fluorescence and SERS signals. By combining the opposite changes in the two optical spectra, an improved sensitivity and linearity toward the target miRNA is achieved as compared with using solely fluorescence or SERS. Moreover, introducing the microfluidic chip can reduce the reaction time, reagent dosage and complexity of detection. With the improved sensitivity and simplicity, we anticipate that the presented method can have great potential in the investigation of miRNA related diseases.
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Abstract
This review focuses on the recent advances in SERS and its potential to detect multiple biomolecules in clinical samples.
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Affiliation(s)
- Stacey Laing
- Centre for Molecular Nanometrology
- WestCHEM
- Pure and Applied Chemistry
- University of Strathclyde
- Technology and Innovation Centre
| | - Kirsten Gracie
- Centre for Molecular Nanometrology
- WestCHEM
- Pure and Applied Chemistry
- University of Strathclyde
- Technology and Innovation Centre
| | - Karen Faulds
- Centre for Molecular Nanometrology
- WestCHEM
- Pure and Applied Chemistry
- University of Strathclyde
- Technology and Innovation Centre
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5
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Graham D, Faulds K. Surface-enhanced Raman scattering as a detection technique for molecular diagnostics. Expert Rev Mol Diagn 2014; 9:537-9. [DOI: 10.1586/erm.09.37] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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6
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Piantanida L, Naumenko D, Lazzarino M. Highly efficient gold nanoparticle dimer formation via DNA hybridization. RSC Adv 2014. [DOI: 10.1039/c3ra47478j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Yazdi SH, Giles KL, White IM. Multiplexed detection of DNA sequences using a competitive displacement assay in a microfluidic SERRS-based device. Anal Chem 2013; 85:10605-11. [PMID: 24125433 DOI: 10.1021/ac402744z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate sensitive and multiplexed detection of DNA sequences through a surface enhanced resonance Raman spectroscopy (SERRS)-based competitive displacement assay in an integrated microsystem. The use of the competitive displacement scheme, in which the target DNA sequence displaces a Raman-labeled reporter sequence that has lower affinity for the immobilized probe, enables detection of unlabeled target DNA sequences with a simple single-step procedure. In our implementation, the displacement reaction occurs in a microporous packed column of silica beads prefunctionalized with probe-reporter pairs. The use of a functionalized packed-bead column in a microfluidic channel provides two major advantages: (i) immobilization surface chemistry can be performed as a batch process instead of on a chip-by-chip basis, and (ii) the microporous network eliminates the diffusion limitations of a typical biological assay, which increases the sensitivity. Packed silica beads are also leveraged to improve the SERRS detection of the Raman-labeled reporter. Following displacement, the reporter adsorbs onto aggregated silver nanoparticles in a microfluidic mixer; the nanoparticle-reporter conjugates are then trapped and concentrated in the silica bead matrix, which leads to a significant increase in plasmonic nanoparticles and adsorbed Raman reporters within the detection volume as compared to an open microfluidic channel. The experimental results reported here demonstrate detection down to 100 pM of the target DNA sequence, and the experiments are shown to be specific, repeatable, and quantitative. Furthermore, we illustrate the advantage of using SERRS by demonstrating multiplexed detection. The sensitivity of the assay, combined with the advantages of multiplexed detection and single-step operation with unlabeled target sequences makes this method attractive for practical applications. Importantly, while we illustrate DNA sequence detection, the SERRS-based competitive displacement assay is applicable to detection of a variety of biological macromolecules, including proteins and proteolytic enzymes.
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Affiliation(s)
- Soroush H Yazdi
- Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
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Harper MM, McKeating KS, Faulds K. Recent developments and future directions in SERS for bioanalysis. Phys Chem Chem Phys 2013; 15:5312-28. [PMID: 23318580 DOI: 10.1039/c2cp43859c] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The ability to develop new and sensitive methods of biomolecule detection is crucial to the advancement of pre-clinical disease diagnosis and effective patient specific treatment. Surface enhanced Raman scattering (SERS) is an optical spectroscopy amenable to this goal, as it is capable of extremely sensitive biomolecule detection and multiplexed analysis. This perspective highlights where SERS has been successfully used to detect target biomolecules, specifically DNA and proteins, and where in vivo analysis has been successfully utilised. The future of SERS development is discussed and emphasis is placed on the steps required to transport this novel technique from the research laboratory to a clinical setting for medical diagnostics.
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Affiliation(s)
- Mhairi M Harper
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
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9
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Ding X, Kong L, Wang J, Fang F, Li D, Liu J. Highly sensitive SERS detection of Hg2+ ions in aqueous media using gold nanoparticles/graphene heterojunctions. ACS APPLIED MATERIALS & INTERFACES 2013; 5:7072-7078. [PMID: 23855919 DOI: 10.1021/am401373e] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Gold nanoparticles (AuNPs)/reduced graphene oxide (rGO) heterojunctions were synthesized directly on SiO2/Si substrates via a seed-assisted growth process. The in situ chemical fabrication strategy has been proven to be quite simple and efficient for generating highly active surface-enhanced Raman scattering (SERS) substrates due to synergistic enhanced protocol from rGO and AuNPs. The SERS substrates with AuNPs/rGO heterojunctions have been utilized for trace analysis of mercury(II) ions via thymine-Hg(2+)-thymine coordination. Thereby, very low limits of detection, i.e., 0.1 nM or 20 ppt for Hg(2+), can be achieved in contrast with some other SERS subsrtates, which suggests that the heterojunctions are appropriate as versatile surface-enhanced substrates applied in chemical sensing or biosensing.
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Affiliation(s)
- Xiaofeng Ding
- Research Center for Biomimetic Functional Materials and Sensing Devices, Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui 230031, China
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Wei X, Su S, Guo Y, Jiang X, Zhong Y, Su Y, Fan C, Lee ST, He Y. A molecular beacon-based signal-off surface-enhanced Raman scattering strategy for highly sensitive, reproducible, and multiplexed DNA detection. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:2493-2652. [PMID: 23359560 DOI: 10.1002/smll.201202914] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 01/04/2013] [Indexed: 06/01/2023]
Affiliation(s)
- Xinpan Wei
- Institute of Functional Nano & Soft Materials-FUNSOM and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, PR China
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11
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van Lierop D, Larmour IA, Faulds K, Graham D. SERS primers and their mode of action for pathogen DNA detection. Anal Chem 2013; 85:1408-14. [PMID: 23311662 DOI: 10.1021/ac302254h] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
SERS primers have been used to directly detect specific PCR products utilizing the difference in adsorption of single-stranded and double-stranded DNA onto nanoparticle surfaces. Herein, seven parameters important for improved positive SERS assays for real applications were investigated. First, we applied a model system for optimization experiments, followed by a PCR assay to detect pathogen DNA, and then the introduction of a new assay that utilizes the 5'→3' exonuclease activity of Taq DNA polymerase to partly digest the SERS probe, generating dye-labeled single-stranded DNA increasing the SERS signals for detection of pathogen DNA. Applying the model system, it was found that uni-molecular SERS primers perform better than bi-molecular SERS primers. However, within the PCR assays, it was found that uni- and bi-molecular SERS primers performed very similarly, and the most reproducible results were obtained using the 5'→3' exonuclease digestion assay. These SERS-based assays offer new routes over conventional fluorescence-based techniques without compromising sensitivity or selectivity.
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Affiliation(s)
- Danny van Lierop
- Centre for Molecular Nanometrology, WestCHEM, Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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12
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Abstract
SERRS (surface-enhanced resonance Raman scattering) is a vibrational technique, whereby a relatively weak Raman scattering effect is enhanced through the use of a visible chromophore and a roughened metal surface. The direct analysis of DNA by SERRS requires the modification of a nucleic acid sequence to incorporate a chromophore, and adsorption of the modified sequence on to a roughened metal surface. Aggregated metallic nanoparticles are commonly used in the analysis of dye-labelled DNA by SERRS, allowing for detection levels that rival those gained from standard fluorescence-based techniques. In the present paper, we report on how SERRS can be exploited for the analysis of clinically relevant DNA samples. We also report on the ability of nanoparticles to aggregate as the result of a biologically significant event, as opposed to the use of an external charge-modifying agent. The self-assembly of metallic nanoparticles is shown to be a promising new technique in the move towards extremely sensitive methods of DNA analysis by SERRS.
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13
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Kode K, Shachaf C, Elchuri S, Nolan G, Paik DS. Raman Labeled Nanoparticles: Characterization of Variability and Improved Method for Unmixing. JOURNAL OF RAMAN SPECTROSCOPY : JRS 2012; 43:895-905. [PMID: 24833814 PMCID: PMC4019428 DOI: 10.1002/jrs.3114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Raman spectroscopy can differentiate the spectral fingerprints of many molecules, resulting in potentially high multiplexing capabilities of Raman-tagged nanoparticles. However, accurate quantitative unmixing of Raman spectra is challenging because of potential overlaps between Raman peaks from each molecule as well as slight variations in the location, height and width of the very narrow peaks. If not accounted for properly, even minor fluctuations in the spectra may produce significant error which will ultimately result in poor unmixing accuracy. The objective of our study was to develop and validate a mathematical model of the Raman spectra of nanoparticles to unmix the contributions from each nanoparticle allowing simultaneous quantitation of several nanoparticle concentrations during sample characterization. We developed and evaluated an algorithm for quantitative unmixing of the spectra, called Narrow Peak Spectral Algorithm (NPSA) . Using NPSA, we were able to successfully unmix Raman spectra from up to 7 Raman nanoparticles after correcting for the spectral variations of 30% in intensity and shifts in peak locations of up to 10 cm-1 which is equivalent to 50% of the full width at half maximum (FWHM). We compared the performance of NPSA to the conventional least squares analysis (LS), error in NPSA is approximately 50% lower than LS. The error in estimating the relative contributions of each nanoparticle using NPSA are in the range of 10-16% for equal ratios and 13-19% for unequal ratios for unmixing of 7 composite organic - inorganic nanoparticles (COINs) whereas the errors using the traditional least squares approach were in the range of 25-38% for equal ratios and 45-68% for unequal ratios. Here, we report for the first time, the quantitative unmixing of 7 nanoparticles with maximum RMS % error less than 20%.
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Affiliation(s)
- Kranthi Kode
- Deparment of Radiology, Stanford University School of Medicine ; Computational and Mathematical Engineering, Stanford University School of Engineering
| | - Cathy Shachaf
- Deparment of Radiology, Stanford University School of Medicine ; Deparment of Microbiology and Immunology, Stanford University School of Medicine
| | - Sailaja Elchuri
- Deparment of Microbiology and Immunology, Stanford University School of Medicine
| | - Garry Nolan
- Deparment of Microbiology and Immunology, Stanford University School of Medicine
| | - David S Paik
- Deparment of Radiology, Stanford University School of Medicine
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14
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The effect of base-pair sequence on electrochemically driven denaturation. Bioelectrochemistry 2012; 85:7-13. [DOI: 10.1016/j.bioelechem.2011.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 11/17/2011] [Accepted: 11/18/2011] [Indexed: 11/18/2022]
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15
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Santiago-Cordoba M, Topal Ö, Allara DL, Kalkan AK, Demirel MC. Stimuli responsive release of metalic nanoparticles on semiconductor substrates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:5975-5980. [PMID: 22428723 DOI: 10.1021/la3002256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Optically active metal nanoparticles have been of recent and broad interest for applications to biomarker detection because of their ability to enable high sensitivity enhancements in various optical detection techniques. Here, we report stimuli responsive release of metallic nanoparticles on a semiconductor thin film array structure based on pH change. The metallic nanoparticles are obtained by a simple redox procedure on the semiconductor surface. This approach allows controlling nanoparticle surface coatings in situ for biomolecule conjugation, such as DNA probes on nanoparticles, and rapid stimuli responsive release of these nanoparticles upon pH change.
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Affiliation(s)
- Miguel Santiago-Cordoba
- Materials Research Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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van Lierop D, Faulds K, Graham D. Separation Free DNA Detection Using Surface Enhanced Raman Scattering. Anal Chem 2011; 83:5817-21. [DOI: 10.1021/ac200514e] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Danny van Lierop
- Centre for Molecular Nanometrology, WestCHEM, Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, United Kingdom
| | - Karen Faulds
- Centre for Molecular Nanometrology, WestCHEM, Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, United Kingdom
| | - Duncan Graham
- Centre for Molecular Nanometrology, WestCHEM, Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, United Kingdom
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Hu J, Zhang CY. Sensitive Detection of Nucleic Acids with Rolling Circle Amplification and Surface-Enhanced Raman Scattering Spectroscopy. Anal Chem 2010; 82:8991-7. [DOI: 10.1021/ac1019599] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Juan Hu
- Institute of Biomedical Engineering and Health Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Chun-yang Zhang
- Institute of Biomedical Engineering and Health Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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Drake P, Huang HY, Lin YJ. Design of a peptide linker group to increase the surface enhanced Raman spectroscopy signal intensity of a rhodamine-nanoparticle system. JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1134/s1061934810060109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Sun L, Irudayaraj J. PCR-free quantification of multiple splice variants in a cancer gene by surface-enhanced Raman spectroscopy. J Phys Chem B 2010; 113:14021-5. [PMID: 19780515 DOI: 10.1021/jp908225f] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate a surface-enhanced Raman spectroscopy (SERS) based array platform to monitor gene expression in cancer cells in a multiplex and quantitative format without amplification steps. A strategy comprising DNA/RNA hybridization, S1 nuclease digestion, and alkaline hydrolysis was adopted to obtain DNA targets specific to two splice junction variants, Delta(9,10) and Delta(5), of the breast cancer susceptibility gene 1 from MCF-7 and MDA-MB-231 breast cancer cell lines. These two targets were identified simultaneously, and their absolute quantities were estimated by a SERS strategy utilizing the inherent plasmon-phonon Raman mode of gold nanoparticle probes as a self-referencing standard to correct for the variability in surface enhancement. The results were then validated by reverse-transcription polymerase chain reaction. Our proposed methodology could be expanded to a higher level of multiplexing for quantitative gene expression analysis of any gene without any amplification steps.
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Affiliation(s)
- Lan Sun
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center and Birck Nanotechnology Center, Purdue University, 225 S. University Street, West Lafayette, Indiana 47907, USA.
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20
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Prigodich AE, Seferos DS, Massich MD, Giljohann DA, Lane BC, Mirkin CA. Nano-flares for mRNA regulation and detection. ACS NANO 2009; 3:2147-52. [PMID: 19702321 PMCID: PMC2742376 DOI: 10.1021/nn9003814] [Citation(s) in RCA: 184] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
We build off the previously described concept of a nanoflare to develop an oligonucleotide gold nanoparticle conjugate that is capable of both detecting and regulating intracellular levels of mRNA. We characterize the binding rate and specificity of these materials using survivin, a gene associated with the diagnosis and treatment of cancer, as a target. The nanoconjugate enters cells and binds mRNA, thereby decreasing the relative abundance of mRNA in a dose- and sequence-dependent manner, resulting in a fluorescent response. This represents the first demonstration of a single material capable of both mRNA regulation and detection. Further, we investigate the intracellular biochemistry of the nanoconjugate, elucidating its mechanism of gene regulation. This work is important to the study of biologically active nanomaterials such as the nanoflare and is a first step toward the development of an mRNA responsive "theranostic".
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Affiliation(s)
- Andrew E Prigodich
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
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21
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Surface-enhanced Raman scattering as a tool to probe cytochrome P450-catalysed substrate oxidation. Anal Bioanal Chem 2009; 394:1797-801. [DOI: 10.1007/s00216-009-2866-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 05/24/2009] [Accepted: 05/26/2009] [Indexed: 10/20/2022]
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Mahajan S, Richardson J, Brown T, Bartlett PN. SERS-Melting: A New Method for Discriminating Mutations in DNA Sequences. J Am Chem Soc 2008; 130:15589-601. [DOI: 10.1021/ja805517q] [Citation(s) in RCA: 150] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sumeet Mahajan
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - James Richardson
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Tom Brown
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Philip N. Bartlett
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
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23
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Deb SK, Davis B, Ben-Amotz D, Davisson VJ. Accurate concentration measurements using surface-enhanced Raman and deuterium exchanged dye pairs. APPLIED SPECTROSCOPY 2008; 62:1001-1007. [PMID: 18801239 DOI: 10.1366/000370208785793290] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Quantitative applications of surface-enhanced resonance Raman scattering (SERRS) are often limited by the reproducibility of SERRS intensities, given the difficulty of controlling analyte-substrate interactions and the associated local field enhancement. As demonstrated here, SERRS from dye molecules even within the same structural class that compete with similar substrates display distinct spectral intensities that are not proportional to analyte concentrations, which limits their use as internal standardization probes and/or for multiplex analysis. Recently, we demonstrated that isotopic variants of rhodamine 6G (R6G), namely R6G-d0 and R6G-d4, can be used for internal standards in SERRS experiments with a linear optical response from picomolar to micromolar concentrations (of total analytes). Here we extend these results by describing a straightforward method for obtaining isotopomeric pairs of other Raman active dyes by hydrogen-deuterium exchange conditions for substitution at electron rich aromatic heterocycles. Most of the known SERRS active probes can be converted into the corresponding isotopomeric molecule by this exchange method, which significantly expands the scope of the isotopic edited internal standard (IEIS) approach. The relative quantification using IEIS enables accurate, reproducible (residual standard deviation+/-2.2%) concentration measurements over a range of 200 pM to 2 microM. These studies enable easy access to a variety of isotopically substituted Raman active dyes and establish the generality of the methodology for quantitative SERRS measurements. For the first time, three rhodamine 6G isotopomers have been created and show distinct Raman spectra, demonstrating the principle of the approach for application as a multiplex technique in biomolecular detection/quantification.
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Affiliation(s)
- Shirshendu K Deb
- Department of Medicinal Chemistry and Molecular Pharmacology, Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907, USA
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Hering KK, Möller R, Fritzsche W, Popp J. Microarray-Based Detection of Dye-Labeled DNA by SERRS Using Particles Formed by Enzymatic Silver Deposition. Chemphyschem 2008; 9:867-72. [PMID: 18386261 DOI: 10.1002/cphc.200700591] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Melvin T. Optical biosensing: future possibilities. EXPERT REVIEW OF OPHTHALMOLOGY 2007. [DOI: 10.1586/17469899.2.6.883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abu-Hatab NA, John JF, Oran JM, Sepaniak MJ. Multiplexed microfluidic surface-enhanced Raman spectroscopy. APPLIED SPECTROSCOPY 2007; 61:1116-22. [PMID: 17958963 DOI: 10.1366/000370207782217842] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Over the past few decades, surface-enhanced Raman spectroscopy (SERS) has garnered respect as an analytical technique with significant chemical and biological applications. SERS is important for the life sciences because it can provide trace level detection, a high level of structural information, and enhanced chemical detection. However, creating and successfully implementing a sensitive, reproducible, and robust SERS active substrate continues to be a challenging task. Herein, we report a novel method for SERS that is based upon using multiplexed microfluidics (MMFs) in a polydimethylsiloxane platform to perform parallel, high throughput, and sensitive detection/identification of single or various analytes under easily manipulated conditions. A facile passive pumping method is used to deliver Ag colloids and analytes into the channels where SERS measurements are done under nondestructive flowing conditions. With this approach, SERS signal reproducibility is found to be better than 7%. Utilizing a very high numerical aperture microscope objective with a confocal-based Raman spectrometer, high sensitivity is achieved. Moreover, the long working distance of this objective coupled with an appreciable channel depth obviates normal alignment issues expected with translational multiplexing. Rapid evaluation of the effects of anion activators and the type of colloid employed on SERS performance are used to demonstrate the efficiency and applicability of the MMF approach. SERS spectra of various pesticides were also obtained. Calibration curves of crystal violet (non-resonant enhanced) and Mitoxantrone (resonant enhanced) were generated, and the major SERS bands of these analytes were observable down to concentrations in the low nM and sub-pM ranges, respectively. While conventional random morphology colloids were used in most of these studies, unique cubic nanoparticles of silver were synthesized with different sizes and studied using visible wavelength optical extinction spectrometry, scanning electron microscopy, and the MMF-SERS approach.
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Affiliation(s)
- Nahla A Abu-Hatab
- University of Tennessee-Knoxville, Department of Chemistry, 552 Buehler Hall, Knoxville, Tennessee 37996-1600, USA
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Jung J, Chen L, Lee S, Kim S, Seong GH, Choo J, Lee EK, Oh CH, Lee S. Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel. Anal Bioanal Chem 2007; 387:2609-15. [PMID: 17318519 DOI: 10.1007/s00216-007-1158-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2006] [Revised: 01/23/2007] [Accepted: 01/26/2007] [Indexed: 10/23/2022]
Abstract
A new DNA hybridization analytical method using a microfluidic channel and a molecular beacon-based probe (MB-probe) is described. A stem-loop DNA oligonucleotide labeled with two fluorophores at the 5' and 3' termini (a donor dye, TET, and an acceptor dye, TAMRA, respectively) was used to carry out a fast and sensitive DNA analysis. The MB-probe utilized the specificity and selectivity of the DNA hairpin-type probe DNA to detect a specific target DNA of interest. The quenching of the fluorescence resonance energy transfer (FRET) signal between the two fluorophores, caused by the sequence-specific hybridization of the MB-probe and the target DNA, was used to detect a DNA hybridization reaction in a poly(dimethylsiloxane) (PDMS) microfluidic channel. The azoospermia gene, DYS 209, was used as the target DNA to demonstrate the applicability of the method. A simple syringe pumping system was used for quick and accurate analysis. The laminar flow along the channel could be easily controlled by the 3-D channel structure and flow speed. By injecting the MB-probe and target DNA solutions into a zigzag-shaped PDMS microfluidic channel, it was possible to detect their sequence-specific hybridization. Surface-enhanced Raman spectroscopy (SERS) was also used to provide complementary evidence of the DNA hybridization. Our data show that this technique is a promising real-time detection method for label-free DNA targets in the solution phase. Figure FRET-based DNA hybridization detection using a molecular beacon in a zigzag-shaped PDMS microfluidic channel.
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Affiliation(s)
- Jaehyun Jung
- Department of Applied Chemistry, Hanyang University, Ansan 426-791, South Korea
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McGuinness CD, Macmillan AM, Karolin J, Smith WE, Graham D, Pickup JC, Birch DJS. Single molecule level detection of allophycocyanin by surface enhanced resonance Raman scattering. Analyst 2007; 132:633-4. [PMID: 17592580 DOI: 10.1039/b706409h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single molecule level detection of the near-infrared fluorescent protein allophycocyanin (APC) has been achieved using surface enhanced resonance Raman scattering (SERRS). The detection limit using the peak height of the 440 cm(-1) band was 1 x 10(-13) mol l(-1), compared to 2 x 10(-12) mol l(-1) for the fluorescence peak at 660 nm.
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Affiliation(s)
- Colin D McGuinness
- Unit for Metabolic Medicine, Thomas Guy House, Guy's Hospital, St. Thomas' Street, London, UK SE1 9RT.
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Jockusch S, Martí AA, Turro NJ, Li Z, Li X, Ju J, Stevens N, Akins DL. Spectroscopic investigation of a FRET molecular beacon containing two fluorophores for probing DNA/RNA sequences. Photochem Photobiol Sci 2006; 5:493-8. [PMID: 16685327 DOI: 10.1039/b600213g] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the design, synthesis, and characterization of a molecular beacon (MB) consisting of two fluorescent dyes (Alexa 488 and RedX) for DNA and RNA analysis. In the absence of the target DNA or RNA the MB is in its stem-closed form and shows efficient energy transfer from the donor (Alexa) to the acceptor (RedX), generating mostly fluorescence from RedX. In the presence of the complementary target DNA the MB opened efficiently, hybridizes with the target DNA, and energy transfer is blocked in the stem-open form. This attachment to the target generates a fluorescence signature, which is clearly distinguishable from the fluorescence signature of the stem-closed form, allowing for ratiometric analysis of the fluorescence signal. In addition to steady-state fluorescence analysis, time resolved fluorescence (ps time range) and fluorescence depolarization studies were performed. We show that fluorescence lifetime and fluorescence depolarization measurements are useful analytical tools to optimize the MB design.
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Affiliation(s)
- Steffen Jockusch
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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Graham D, Faulds K, Smith WE. Biosensing using silver nanoparticles and surface enhanced resonance Raman scattering. Chem Commun (Camb) 2006:4363-71. [PMID: 17057846 DOI: 10.1039/b607904k] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Silver nanoparticles can be used to provide excellent surface enhanced resonance Raman scattering. Control of the surface chemistry and the use of appropriate protocols enables effective sensing of biomolecules.
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Affiliation(s)
- Duncan Graham
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UKG1 1XL.
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