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Biofunctionalized silicon nitride platform for sensing applications. Biosens Bioelectron 2018; 102:497-503. [DOI: 10.1016/j.bios.2017.11.059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/15/2017] [Accepted: 11/22/2017] [Indexed: 11/20/2022]
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A Quasi-direct LC-MS/MS-based Targeted Proteomics Approach for miRNA Quantification via a Covalently Immobilized DNA-peptide Probe. Sci Rep 2017; 7:5669. [PMID: 28720752 PMCID: PMC5515972 DOI: 10.1038/s41598-017-05495-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/30/2017] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) play a vital role in regulating gene expression and are associated with a variety of cancers, including breast cancer. Their distorted and unique expression is a potential marker in clinical diagnoses and prognoses. Thus, accurate determination of miRNA expression levels is a prerequisite for their applications. However, the assays currently available for miRNA detection typically require pre-enrichment, amplification and labeling steps, and most of the assays are only semi-quantitative. Therefore, we developed a quasi-direct liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted proteomics approach to quantify target miRNA by innovatively converting the miRNA signal into the mass response of a reporter peptide via a covalently immobilized DNA-peptide probe. Specifically, the probe containing the targeted proteomics-selected substrate/reporter peptide, GDRAVQLGVDPFR/AVQLGVDPFR, and the DNA sequence complementary to the target miRNA (i.e., miR-21) was first immobilized on APMTS modified silica nanoparticles using PDITC. After the immobilized probe was recognized and hybridized with the target miRNA, the excess probe was degraded using MBN and followed by a trypsin digestion of the hybrids. The reporter peptide was released and quantified using LC-MS/MS. The obtained LOQ was 5 pM. Finally, the developed assay was used for the quantitative analysis of miR-21 in breast cells and tissue samples.
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Gállego I, Manning B, Prades JD, Mir M, Samitier J, Eritja R. DNA-Origami-Driven Lithography for Patterning on Gold Surfaces with Sub-10 nm Resolution. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1603233. [PMID: 28060403 DOI: 10.1002/adma.201603233] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 11/23/2016] [Indexed: 06/06/2023]
Abstract
Sub-10 nm lithography of DNA patterns is achieved using the DNA-origami stamping method. This new strategy utilizes DNA origami to bind a preprogrammed DNA ink pattern composed of thiol-modified oligonucleotides on gold surfaces. Upon denaturation of the DNA origami, the DNA ink pattern is exposed. The pattern can then be developed by hybridization with complementary strands carrying gold nanoparticles.
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Affiliation(s)
- Isaac Gállego
- Institute for Advanced Chemistry of Catalonia (IQAC), Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Spanish National Research Council (CSIC), Barcelona, 08034, Spain
| | - Brendan Manning
- Institute for Advanced Chemistry of Catalonia (IQAC), Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Spanish National Research Council (CSIC), Barcelona, 08034, Spain
| | - Joan Daniel Prades
- MIND-IN2UB, Department of Engineering: Electronics, University of Barcelona, Barcelona, 08028, Spain
| | - Mònica Mir
- Institute for Bioengineering of Catalonia (IBEC), Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, 08028, Spain
| | - Josep Samitier
- Institute for Bioengineering of Catalonia (IBEC), Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, 08028, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Spanish National Research Council (CSIC), Barcelona, 08034, Spain
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Brunet M, Aureau D, Chantraine P, Guillemot F, Etcheberry A, Gouget-Laemmel AC, Ozanam F. Etching and Chemical Control of the Silicon Nitride Surface. ACS APPLIED MATERIALS & INTERFACES 2017; 9:3075-3084. [PMID: 27977928 DOI: 10.1021/acsami.6b12880] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Silicon nitride is used for many technological applications, but a quantitative knowledge of its surface chemistry is still lacking. Native oxynitride at the surface is generally removed using fluorinated etchants, but the chemical composition of surfaces still needs to be determined. In this work, the thinning (etching efficiency) of the layers after treatments in HF and NH4F solutions has been followed by using spectroscopic ellipsometry. A quantitative estimation of the chemical bonds found on the surface is obtained by a combination of infrared absorption spectroscopy in ATR mode, X-ray photoelectron spectroscopy, and colorimetry. Si-F bonds are the majority species present at the surface after silicon nitride etching; some Si-OH and a few Si-NHx bonds are also present. No Si-H bonds are present, an unfavorable feature for surface functionalization in view of the interest of such mildly reactive groups for achieving stable covalent grafting. Mechanisms are described to support the experimental results, and two methods are proposed for generating surface SiH species: enriching the material in silicon, or submitting the etched surface to a H2 plasma treatment.
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Affiliation(s)
- Marine Brunet
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, Université Paris-Saclay , 91128 Palaiseau, France
- Saint-Gobain Recherche , 39 quai Lucien Lefranc, 93303 Aubervilliers, France
| | - Damien Aureau
- Institut Lavoisier, UVSQ-CNRS UMR 8180 , 78035 Versailles, France
| | - Paul Chantraine
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, Université Paris-Saclay , 91128 Palaiseau, France
| | - François Guillemot
- Saint-Gobain Recherche , 39 quai Lucien Lefranc, 93303 Aubervilliers, France
| | | | - Anne Chantal Gouget-Laemmel
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, Université Paris-Saclay , 91128 Palaiseau, France
| | - François Ozanam
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, Université Paris-Saclay , 91128 Palaiseau, France
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Abstract
An assay was developed for measuring the active-site concentration, activity, and thereby the catalytic turnover rate (kcat) of an immobilized dihydrofolate reductase model system (Singh et al., (2015), Anal. Biochem). This data article contains a calibration plot for the developed assay. In the calibration plot rate is plotted as a function of DHFR concentration and shows linear relationship. The concentration of immobilized enzyme was varied by using 5 different size mica chips. The dsDNA concentration was the same for all chips, assuming that the surface area of the mica chip dictates the resulting amount of bound enzyme (i.e. larger sized chip would have more bound DHFR). The activity and concentration of each chip was measured.
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González-Guerrero AB, Alvarez M, Castaño AG, Domínguez C, Lechuga LM. A comparative study of in-flow and micro-patterning biofunctionalization protocols for nanophotonic silicon-based biosensors. J Colloid Interface Sci 2013; 393:402-10. [DOI: 10.1016/j.jcis.2012.10.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 10/18/2012] [Accepted: 10/19/2012] [Indexed: 01/24/2023]
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7
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Abstract
There is a large interest in the use of nucleic acids covalently bound to surfaces for a variety of biomedical uses: biosensors, microarrays, drug delivery, lab-on-chip devices, and gene therapy, etc. Most of these applications require the covalent attachment of oligonucleotides via specific reactive groups on both modified oligonucleotide and/or surface. The purpose of this chapter is to provide experimental protocols for the synthesis of oligonucleotides and for the immobilization of these synthetic oligonucleotides onto surfaces such as gold and silicon oxide.
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Caballero D, Martinez E, Bausells J, Errachid A, Samitier J. Impedimetric immunosensor for human serum albumin detection on a direct aldehyde-functionalized silicon nitride surface. Anal Chim Acta 2012; 720:43-8. [PMID: 22365119 DOI: 10.1016/j.aca.2012.01.031] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 01/14/2012] [Accepted: 01/17/2012] [Indexed: 10/14/2022]
Abstract
In this work we report the fabrication and characterization of a label-free impedimetric immunosensor based on a silicon nitride (Si(3)N(4)) surface for the specific detection of human serum albumin (HSA) proteins. Silicon nitride provides several advantages compared with other materials commonly used, such as gold, and in particular in solid-state physics for electronic-based biosensors. However, few Si(3)N(4)-based biosensors have been developed; the lack of an efficient and direct protocol for the integration of biological elements with silicon-based substrates is still one of its the main drawbacks. Here, we use a direct functionalization method for the direct covalent binding of monoclonal anti-HSA antibodies on an aldehyde-functionalized Si-p/SiO(2)/Si(3)N(4) structure. This methodology, in contrast with most of the protocols reported in literature, requires less chemical reagents, it is less time-consuming and it does not need any chemical activation. The detection capability of the immunosensor was tested by performing non-faradaic electrochemical impedance spectroscopy (EIS) measurements for the specific detection of HSA proteins. Protein concentrations within the linear range of 10(-13)-10(-7) M were detected, showing a sensitivity of 0.128 Ω μM(-1) and a limit of detection of 10(-14) M. The specificity of the sensor was also addressed by studying the interferences with a similar protein, bovine serum albumin. The results obtained show that the antibodies were efficiently immobilized and the proteins detected specifically, thus, establishing the basis and the potential applicability of the developed silicon nitride-based immunosensor for the detection of proteins in real and more complex samples.
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Affiliation(s)
- David Caballero
- Nanobioengineering group-IBEC, Barcelona Science Park, C/ Baldiri Reixach 10-12, 08028 Barcelona, Spain.
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Reusable chromium-coated quartz crystal microbalance for immunosensing. Colloids Surf B Biointerfaces 2011; 88:191-5. [DOI: 10.1016/j.colsurfb.2011.06.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 05/27/2011] [Accepted: 06/22/2011] [Indexed: 11/20/2022]
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Sung D, Shin DH, Jon S. Toward immunoassay chips: Facile immobilization of antibodies on cyclic olefin copolymer substrates through pre-activated polymer adlayers. Biosens Bioelectron 2011; 26:3967-72. [DOI: 10.1016/j.bios.2011.03.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 02/17/2011] [Accepted: 03/08/2011] [Indexed: 01/10/2023]
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11
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Dawson K, Baudequin M, O'Riordan A. Single on-chip gold nanowires for electrochemical biosensing of glucose. Analyst 2011; 136:4507-13. [DOI: 10.1039/c1an15279c] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Caballero D, Samitier J, Bausells J, Errachid A. Direct patterning of anti-human serum albumin antibodies on aldehyde-terminated silicon nitride surfaces for HSA protein detection. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2009; 5:1531-1534. [PMID: 19296562 DOI: 10.1002/smll.200801735] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- David Caballero
- Nanobioengineering group, Institute for Bioengineering of Catalonia, Barcelona Science Park, c/ Baldiri Reixac 10-12, 08028 Barcelona, Spain.
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Raj J, Herzog G, Manning M, Volcke C, MacCraith BD, Ballantyne S, Thompson M, Arrigan DW. Surface immobilisation of antibody on cyclic olefin copolymer for sandwich immunoassay. Biosens Bioelectron 2009; 24:2654-8. [DOI: 10.1016/j.bios.2009.01.026] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Revised: 01/19/2009] [Accepted: 01/20/2009] [Indexed: 01/10/2023]
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Abstract
Among the parameters which influence the success of a microarray experiment, the attachment of the nucleic acid captures to the support surface plays a decisive role.This article attempts to review the main concepts and ideas of the multiple variants which exist in terms of the immobilization chemistries used in nucleic acid microarray technology. Starting from the attachment of unmodified nucleic acids to modified glass slides by adsorption, further strategies for the coupling of nucleic acid capture molecules to a variety of support materials are surveyed with a focus on the reactive groups involved in the respective process.After a brief introduction, an overview is given about microarray substrates with special emphasis on the approaches used for the activation of these - usually chemically inert - materials. In the next sections strategies for the "undefined" and "defined" immobilization of captures on the substrates are described. While the latter approach tries to accomplish the coupling via a defined reactive moiety of the molecule to be immobilized, the former mentioned techniques involve multiply occurring reactive groups in the capture.The article finishes with an example for microarray manufacture, the production of aminopropyltriethoxysilane (APTES) functionalized glass substrates to which PDITC homobifunctional linker molecules are coupled; on their part providing reactive functional groups for the covalent immobilization of pre-synthesized, amino-modified oligonucleotides.This survey does not seek to be comprehensive rather it tries to present and provide key examples for the basic techniques, and to enable orientation if more detailed studies are needed. This review should not be considered as a guide to how to use the different chemistries described, but instead as a presentation of various principles and approaches applied in the still evolving field of nucleic acid microarray technology.
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Affiliation(s)
- Sascha Todt
- Center for Applied Genesensor-Technology, University of Bremen, , Bremen, Germany
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16
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Baek TJ, Park PY, Han KN, Kwon HT, Seong GH. Development of a photodiode array biochip using a bipolar semiconductor and its application to detection of human papilloma virus. Anal Bioanal Chem 2008; 390:1373-8. [DOI: 10.1007/s00216-007-1814-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Revised: 12/07/2007] [Accepted: 12/12/2007] [Indexed: 12/28/2022]
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Arafat A, Giesbers M, Rosso M, Sudhölter EJR, Schroën K, White RG, Yang L, Linford MR, Zuilhof H. Covalent biofunctionalization of silicon nitride surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:6233-44. [PMID: 17455968 DOI: 10.1021/la7007045] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Covalently attached organic monolayers on etched silicon nitride (SixN4; x >/= 3) surfaces were prepared by reaction of SixN4-coated wafers with neat or solutions of 1-alkenes and 1-alkynes in refluxing mesitylene. The surface modification was monitored by measurement of the static water contact angle, XPS, IRRAS, AFM, and ToF-SIMS, and evidence for the formation of Si-C bonds is presented. The etching can be achieved by dilute HF solutions and yields both Si-H and N-H moieties. The resulting etched SixN4 surfaces are functionalized by terminal carboxylic acid groups in either of two ways: (a) via attachment of a 10-undecenoic acid 2,2,2-trifluoroethyl ester (trifluoro ethanol ester) and subsequent thermal acid hydrolysis; (b) through attachment of a photocleavable ester, and subsequent photochemical cleavage, as this would allow photopatterned functionalized SixN4. The carboxylic acids are successfully used for the attachment of oligopeptides (aspartame) and complete proteins using EDC/NHS chemistry. Finally, an amino-terminated organic monolayer can be formed by reaction of HF-treated SixN4 surfaces with a N-(omega-undecylenyl)phthalimide, which yields an amino-terminated surface upon deprotection with hydrazine.
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Affiliation(s)
- Ahmed Arafat
- Laboratory of Organic Chemistry, Wageningen University, Dreijenplein 8, 6703 HB Wageningen, The Netherlands
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18
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Stine R, Cole CL, Ainslie KM, Mulvaney SP, Whitman LJ. Formation of primary amines on silicon nitride surfaces: a direct, plasma-based pathway to functionalization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:4400-4. [PMID: 17323989 DOI: 10.1021/la0635653] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Silicon nitride is the most commonly used passivation layer in biosensor applications where electronic components must be interfaced with ionic solutions. Unfortunately, the predominant method for functionalizing silicon nitride surfaces, silane chemistry, suffers from a lack of reproducibility. As an alternative, we have developed a silane-free pathway that allows for the direct functionalization of silicon nitride through the creation of primary amines formed by exposure to a radio frequency glow discharge plasma fed with humidified air. The aminated surfaces can then be further functionalized by a variety of methods; here we demonstrate using glutaraldehyde as a bifunctional linker to attach a robust NeutrAvidin (NA) protein layer. Optimal amine formation, based on plasma exposure time, was determined by labeling treated surfaces with an amine-specific fluorinated probe and characterizing the coverage using X-ray photoelectron spectroscopy (XPS). XPS and radiolabeling studies also reveal that plasma-modified surfaces, as compared with silane-modified surfaces, result in similar NA surface coverage, but notably better reproducibility.
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Affiliation(s)
- Rory Stine
- Naval Research Laboratory, Washington, DC 20375, USA
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Harnett EM, Alderman J, Wood T. The surface energy of various biomaterials coated with adhesion molecules used in cell culture. Colloids Surf B Biointerfaces 2007; 55:90-7. [PMID: 17207976 DOI: 10.1016/j.colsurfb.2006.11.021] [Citation(s) in RCA: 179] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Revised: 11/15/2006] [Accepted: 11/15/2006] [Indexed: 10/23/2022]
Abstract
This study calculates the surface energy of polystyrene tissue culture plastic, silicon, silicon dioxide and indium tin oxide, all of which have applications in tissue culture. The adhesion molecules: collagen, fibronectin, poly-L-ornithine and poly-D-lysine, were coated onto these various surfaces, and the surface energy of the coated substrates calculated. Coating with fibronectin was found to produce a monopolar acidic surface while poly-D-lysine, poly-L-ornithine and collagen coatings were found to produce monopolar basic surfaces. The calculated surface energy components of the coated materials were then used to give a quantitative determination of the magnitude of their hydrophobicity. It was concluded that collagen, polylysine and polyornithine could provide a hydrophobic or hydrophilic surface depending on the underlying substrates they were coated on. The measurement obtained for fibronectin, unlike the other adhesion molecules, was independent of the underlying surface and remained hydrophobic on all substrates tested. Wetting experiments were carried out on the coated substrates, using the tissue culture medium Dulbeccos modified eagles medium, both containing and not containing serum proteins, and saline solution. These liquids that are commonly used in tissue culture, were then used to provide information how these liquids behave on various substrates coated with the adhesion molecules. Results show that fibronectin coated surfaces represent the most phobic surface for all three liquids. The findings of this study can be used in cell manipulation studies and provide a valuable data set for the biomedical and research industries.
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Affiliation(s)
- Elaine M Harnett
- Tyndall National Institute, Life Science Interface, Lee Maltings, Prospect Row, Cork, Ireland
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Lillis B, Manning M, Hurley E, Berney H, Duane R, Mathewson A, Sheehan MM. Investigation into the effect that probe immobilisation method type has on the analytical signal of an EIS DNA biosensor. Biosens Bioelectron 2007; 22:1289-95. [PMID: 16806891 DOI: 10.1016/j.bios.2006.05.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2005] [Revised: 05/22/2006] [Accepted: 05/22/2006] [Indexed: 10/24/2022]
Abstract
The analytical performance of an enhanced surface area electrolyte insulator semiconductor (EIS) device was investigated for DNA sensor development. The work endeavored to advance EIS performance by monitoring the effect of DNA probe layers have on the impedimetric signal during target hybridisation detection. Two universally employed covalent chemistries, direct and spacer-mediated attachment of amino modified probe molecules to amino-functionalised surfaces were investigated. Relative areal densities of immobilised probe were measured on planar and enhanced surface area substrates using epi-fluorescence microscopy. The reproducibility of the each immobilisation method was seen to have a direct effect on the reproducibility of the impedimetric signal. The sensitivity and selectivity was seen to be dependent on the type of immobilisation method. Real time, impedimetric detection of target DNA hybridisation concentrations as low as 25 and 1 nM were possible. The impact that probe concentration had on the impedimetric signal for selective and non-selective interactions was also investigated.
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Affiliation(s)
- Brian Lillis
- Tyndall National Institute, Prospect Row, Cork, Ireland
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Terry JG, Campbell CJ, Ross AJ, Livingston AD, Buck AH, Dickinson P, Mountford CP, Evans SAG, Mount AR, Beattie JS, Crain J, Ghazal P, Walton AJ. Improved silicon nitride surfaces for next-generation microarrays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:11400-4. [PMID: 17154632 DOI: 10.1021/la060489v] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
This work reports how the use of a standard integrated circuit (IC) fabrication process can improve the potential of silicon nitride layers as substrates for microarray technology. It has been shown that chemical mechanical polishing (CMP) substantially improves the fluorescent intensity of positive control gene and test gene microarray spots on both low-pressure chemical vapor deposition (LPCVD) and plasma-enhanced chemical vapor deposition (PECVD) silicon nitride films, while maintaining a low fluorescent background. This results in the improved discrimination of low expressing genes. The results for the PECVD silicon nitride, which has been previously reported as unsuitable for microarray spotting, are particularly significant for future devices that hope to incorporate microelectronic control and analysis circuitry, due to the film's use as a final passivating layer.
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Affiliation(s)
- Jonathan G Terry
- Institute for Integrated Micro and Nano Systems, University of Edinburgh, Scottish Microelectronics Centre, West Mains Road, Edinburgh EH9 3JF, UK.
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Li Y, Lee HJ, Corn RM. Fabrication and characterization of RNA aptamer microarrays for the study of protein-aptamer interactions with SPR imaging. Nucleic Acids Res 2006; 34:6416-24. [PMID: 17130155 PMCID: PMC1702490 DOI: 10.1093/nar/gkl738] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RNA microarrays were created on chemically modified gold surfaces using a novel surface ligation methodology and employed in a series of surface plasmon resonance imaging (SPRI) measurements of DNA-RNA hybridization and RNA aptamer-protein binding. Various unmodified single-stranded RNA (ssRNA) oligonucleotides were ligated onto identical 5'-phosphate-terminated ssDNA microarray elements with a T4 RNA ligase surface reaction. A combination of ex situ polarization modulation FTIR measurements of the RNA monolayer and in situ SPRI measurements of DNA hybridization adsorption onto the surface were used to determine an ssRNA surface density of 4.0 x 10(12) molecules/cm2 and a surface ligation efficiency of 85 +/- 10%. The surface ligation methodology was then used to create a five-component RNA microarray of potential aptamers for the protein factor IXa (fIXa). The relative surface coverages of the different aptamers were determined through a novel enzymatic method that employed SPRI measurements of a surface RNase H hydrolysis reaction. SPRI measurements were then used to correctly identify the best aptamer to fIXa, which was previously determined from SELEX measurements. A Langmuir adsorption coefficient of 1.6 x 10(7) M(-1) was determined for fIXa adsorption to this aptamer. Single-base variations from this sequence were shown to completely destroy the aptamer-fIXa binding interaction.
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Affiliation(s)
| | | | - Robert M. Corn
- To whom correspondence should be addressed. Tel: +1 949 824 1746; Fax: +1 949 824 8571;
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Oh SJ, Hong BJ, Choi KY, Park JW. Surface Modification for DNA and Protein Microarrays. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2006; 10:327-43. [PMID: 17069511 DOI: 10.1089/omi.2006.10.327] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Microarrays of biomolecules are emerging as powerful tools for genomics, proteomics, and clinical assays, since they make it possible to screen biologically important binding events in a parallel and high throughput fashion. Because the microarrays are fabricated on a solid support, coating of the surface and immobilization strategy of the biomolecules are major issues for successful microarray fabrication. This review deals with both DNA microarrays and protein microarrays, and focuses on the various modification approaches for the two-dimensional surface materials and three-dimensional ones. In addition, the immobilization strategies including adsorption, covalent attachment, physical entrapment, and affinity attachment of the biomolecules are summarized, and advantage and limitation of representative efforts are discussed.
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Affiliation(s)
- Soon Jin Oh
- Department of Biomedical Science and Technology, Institute of Biomedical Science and Technology, Konkuk University, Seoul, Korea.
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Spehar-Deleze AM, Suomi J, Jiang Q, de Rooij N, Koudelka-Hep M, Kulmala S. Heterogeneous oligonucleotide-hybridization assay based on hot electron-induced electrochemiluminescence of a rhodamine label at oxide-coated aluminum and silicon electrodes. Electrochim Acta 2006. [DOI: 10.1016/j.electacta.2006.02.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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25
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Lillis B, Manning M, Berney H, Hurley E, Mathewson A, Sheehan MM. Dual polarisation interferometry characterisation of DNA immobilisation and hybridisation detection on a silanised support. Biosens Bioelectron 2006; 21:1459-67. [PMID: 16112566 DOI: 10.1016/j.bios.2005.06.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Revised: 06/16/2005] [Accepted: 06/17/2005] [Indexed: 11/21/2022]
Abstract
Dual polarisation interferometry is an analytical technique that allows the simultaneous determination of thickness, density and mass of a biological layer on a sensing waveguide surface in real time. We evaluated, for the first time, the ability of this technique to characterise the covalent immobilisation of single stranded probe DNA and the selective detection of target DNA hybridisation on a silanised support. Two immobilisation strategies have been evaluated: direct attachment of the probe molecule and a more complex chemistry employing a 1,2 homobifunctional crosslinker molecule. With this technique we demonstrate it was possible to determine probe orientation and measure probe coverage at different stages of the immobilisation process in real time and in a single experiment. In addition, by measuring simultaneously changes in thickness and density of the probe layer upon hybridisation of target DNA, it was possible to directly elucidate the impact that probe mobility had on hybridisation efficiency. Direct covalent attachment of an amine modified 19 mer resulted in a thickness change of 0.68 nm that was consistent with multipoint attachment of the probe molecule to the surface. Blocking with BSA formed a dense layer of protein molecules that absorbed between the probe molecules on the surface. The observed hybridisation efficiency to target DNA was approximately 35%. No further significant reorientation of the probe molecule occurred upon hybridisation. The initial thickness of the probe layer upon attachment to the crosslinker molecule was 0.5 nm. Significant reorientation of the probe molecule surface normal occurred upon hybridisation to target DNA. This indicated that the probe molecule had greater mobility to hybridise to target DNA. The observed hybridisation efficiency for target DNA was approximately 85%. The results show that a probe molecule attached to the surface via a crosslinker group is better able to hybridise to target DNA due to its greater mobility.
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Affiliation(s)
- B Lillis
- Tyndall Institute, Lee Maltings, Prospect Row, Cork, Ireland
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Wu P, Hogrebe P, Grainger DW. DNA and protein microarray printing on silicon nitride waveguide surfaces. Biosens Bioelectron 2006; 21:1252-63. [PMID: 16002276 DOI: 10.1016/j.bios.2005.05.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Revised: 05/18/2005] [Accepted: 05/23/2005] [Indexed: 11/26/2022]
Abstract
Sputtered silicon nitride optical waveguide surfaces were silanized and modified with a hetero-bifunctional crosslinker to facilitate thiol-reactive immobilization of contact-printed DNA probe oligonucleotides, streptavidin and murine anti-human interleukin-1 beta capture agents in microarray formats. X-ray photoelectron spectroscopy (XPS) was used to characterize each reaction sequence on the native silicon oxynitride surface. Thiol-terminated DNA probe oligonucleotides exhibited substantially higher surface printing immobilization and target hybridization efficiencies than non-thiolated DNA probe oligonucleotides: strong fluorescence signals from target DNA hybridization supported successful DNA oligonucleotide probe microarray fabrication and specific capture bioactivity. Analogously printed arrays of thiolated streptavidin and non-thiolated streptavidin did not exhibit noticeable differences in either surface immobilization or analyte capture assay signals. Non-thiolated anti-human interleukin-1 beta printed on modified silicon nitride surfaces reactive to thiol chemistry exhibited comparable performance for capturing human interleukin-1 beta analyte to commercial amine-reactive microarraying polymer surfaces in sandwich immunoassays, indicating substantial non-specific antibody-surface capture responsible for analyte capture signal.
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Affiliation(s)
- Peng Wu
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872, USA
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Ray SG, Cohen H, Naaman R, Rabin Y. Where is the Sodium in Self-Assembled Monolayers of Single-Stranded DNA? J Am Chem Soc 2005; 127:17138-9. [PMID: 16332033 DOI: 10.1021/ja055201n] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Monolayers of single-stranded DNA (ssDNA) immobilized on surfaces form the basis of a number of important biotechnology applications, including DNA microarrays and biosensors. The organization of ssDNA as layer on a solid substrate allows one to investigate various properties of the DNA in a controlled manner and to use DNA for analytical applications as well as for exploring futuristic schemes for molecular electronics. It is commonly assumed that the adsorbed DNA layer contains some structural water and the cations. Here we show, based on XPS studies, that when monolayers of ssDNA are formed from sodium phosphate buffer and washed thoroughly, no Na+ signal is detected. A finite concentration of ions is observed when the DNA is made from a solution of Mg2+ ions, but it is still only a fifth of what it would be if all the phosphate ions were fully neutralized by the metal cations.
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Affiliation(s)
- Supratim Guha Ray
- Department of Chemical Physics and Chemical Research Support, Weizmann Institute, Rehovot 76100, Israel
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