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Fortunati S, Vasini I, Giannetto M, Mattarozzi M, Porchetta A, Bertucci A, Careri M. Controlling Dynamic DNA Reactions at the Surface of Single-Walled Carbon Nanotube Electrodes to Design Hybridization Platforms with a Specific Amperometric Readout. Anal Chem 2022; 94:5075-5083. [PMID: 35303407 PMCID: PMC8968946 DOI: 10.1021/acs.analchem.1c05294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
Carbon nanotube (CNT)-based
electrodes are cheap, highly performing,
and robust platforms for the fabrication of electrochemical sensors.
Engineering programmable DNA nanotechnologies on the CNT surface can
support the construction of new electrochemical DNA sensors providing
an amperometric output in response to biomolecular recognition. This
is a significant challenge, since it requires gaining control of specific
hybridization processes and functional DNA systems at the interface,
while limiting DNA physisorption on the electrode surface, which contributes
to nonspecific signal. In this study, we provide design rules to program
dynamic DNA structures at the surface of single-walled carbon nanotubes
electrodes, showing that specific DNA interactions can be monitored
through measurement of the current signal provided by redox-tagged
DNA strands. We propose the use of pyrene as a backfilling agent to
reduce nonspecific adsorption of reporter DNA strands and demonstrate
the controlled formation of DNA duplexes on the electrode surface,
which we then apply in the design and conduction of programmable DNA
strand displacement reactions. Expanding on this aspect, we report
the development of novel amperometric hybridization platforms based
on artificial DNA structures templated by the small molecule melamine.
These platforms enable dynamic strand exchange reactions orthogonal
to conventional toehold-mediated strand displacement and may support
new strategies in electrochemical sensing of biomolecular targets,
combining the physicochemical properties of nanostructured carbon-based
materials with programmable nucleic acid hybridization.
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Affiliation(s)
- Simone Fortunati
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Ilaria Vasini
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Marco Giannetto
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Monica Mattarozzi
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Alessandro Porchetta
- Department of Chemical Sciences, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Alessandro Bertucci
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Maria Careri
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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2
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Price CAH, Pastor-Perez L, Reina TR, Liu J. Yolk-Shell structured NiCo@SiO2 nanoreactor for CO2 upgrading via reverse water-gas shift reaction. Catal Today 2022. [DOI: 10.1016/j.cattod.2020.09.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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3
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Bag S, Rauwolf S, Schwaminger SP, Wenzel W, Berensmeier S. DNA Binding to the Silica: Cooperative Adsorption in Action. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5902-5908. [PMID: 33951395 DOI: 10.1021/acs.langmuir.1c00381] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The adsorption and desorption of nucleic acid to a solid surface is ubiquitous in various research areas like pharmaceutics, nanotechnology, molecular biology, and molecular electronics. In spite of this widespread importance, it is still not well understood how the negatively charged deoxyribonucleic acid (DNA) binds to the negatively charged silica surface in an aqueous solution. In this article, we study the adsorption of DNA to the silica surface using both modeling and experiments and shed light on the complicated binding (DNA to silica) process. The binding agent mediated DNA adsorption was elegantly captured by cooperative Langmuir model. Bulk-depletion experiments were performed to conclude the necessity of a positively charged binding agent for efficient DNA binding, which complements the findings from the model. A profound understanding of DNA binding will help to tune various processes for efficient nucleic acid extraction and purification. However, this work goes beyond the DNA binding and can shed light on other binding agent mediated surface-surface, surface-molecule, molecule-molecule interaction.
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Affiliation(s)
- Saientan Bag
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz-1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Rauwolf
- Bioseparation Engineering Group, Department of Mechanical Engineering, Technical University of Munich (TUM), Munich 85748, Germany
| | - Sebastian P Schwaminger
- Bioseparation Engineering Group, Department of Mechanical Engineering, Technical University of Munich (TUM), Munich 85748, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz-1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Sonja Berensmeier
- Bioseparation Engineering Group, Department of Mechanical Engineering, Technical University of Munich (TUM), Munich 85748, Germany
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4
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Spontaneous Grafting of OH-Terminated Molecules on Si−H Surfaces via Si–O–C Covalent Bonding. SURFACES 2021. [DOI: 10.3390/surfaces4010010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The surface functionalization of oxide-free hydrogen-terminated silicon (Si−H) enables predictably tuning its electronic properties, by incorporating tailored functionality for applications such as photovoltaics, biosensing and molecular electronics devices. Most of the available chemical functionalization approaches require an external radical initiator, such as UV light, heat or chemical reagents. Here, we report forming organic monolayers on Si–H surfaces using molecules comprising terminal alcohol (–OH) groups. Self-assembled monolayer (SAM) formation is spontaneous, requires no external stimuli–and yields Si–O–C covalently bound monolayers. The SAMs were characterized by X-ray photoelectron spectroscopy (XPS) to determine the chemical bonding, by X-ray reflectometry (XRR) to determine the monolayers thicknesses on the surface and by atomic force microscopy (AFM) to probe surface topography and surface roughness. The redox activity and the electrochemical properties of the SAMs were studied using cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The availability and the ease of incorporating OH groups in organic molecules, makes this spontaneous grafting as a reliable method to attach molecules to Si surfaces in applications ranging from sensing to molecular electronics where incorporating radical initiator setups is not accessible.
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5
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Gonçales VR, Lian J, Gautam S, Tilley RD, Gooding JJ. Functionalized Silicon Electrodes in Electrochemistry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:135-158. [PMID: 32289237 DOI: 10.1146/annurev-anchem-091619-092506] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Avoiding the growth of SiOx has been an enduring task for the use of silicon as an electrode material in dynamic electrochemistry. This is because electrochemical assays become unstable when the SiOx levels change during measurements. Moreover, the silicon electrode can be completely passivated for electron transfer if a thick layer of insulating SiOx grows on the surface. As such, the field of silicon electrochemistry was mainly developed by electron-transfer studies in nonaqueous electrolytes and by applications employing SiOx-passivated silicon-electrodes where no DC currents are required to cross the electrode/electrolyte interface. A solution to this challenge began by functionalizing Si-H electrodes with monolayers based on Si-O-Si linkages. These monolayers have proven very efficient to avoid SiOx formation but are not stable for a long-term operation in aqueous electrolytes due to hydrolysis. It was only with the development of self-assembled monolayers based on Si-C linkages that a reliable protection against SiOx formation was achieved, particularly with monolayers based on α,ω-dialkynes. This review discusses in detail how this surface chemistry achieves such protection, the electron-transfer behavior of these monolayer-modified silicon surfaces, and the new opportunities for electrochemical applications in aqueous solution.
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Affiliation(s)
- Vinicius R Gonçales
- School of Chemistry, Australia Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, NSW 2052, Australia; ,
| | - Jiaxin Lian
- School of Chemistry, Australia Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, NSW 2052, Australia; ,
| | - Shreedhar Gautam
- School of Chemistry, Australia Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, NSW 2052, Australia; ,
| | - Richard D Tilley
- School of Chemistry, Australia Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, NSW 2052, Australia; ,
| | - J Justin Gooding
- School of Chemistry, Australia Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, NSW 2052, Australia; ,
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6
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Petralia S, Forte G, Zimbone M, Conoci S. The cooperative interaction of triplex forming oligonucleotides on DNA-triplex formation at electrode surface: Molecular dynamics studies and experimental evidences. Colloids Surf B Biointerfaces 2019; 187:110648. [PMID: 31767411 DOI: 10.1016/j.colsurfb.2019.110648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/28/2019] [Accepted: 11/13/2019] [Indexed: 12/27/2022]
Abstract
An extensive study on cooperative interaction of Triplex Forming Oligonucleotides (TFOs) with a double strand DNA, to form a triplex-DNA structure at electrode surface, is here reported. The cooperative effect on triplex structure formation was assumed by the higher binding enthalpy value, calculated for the interaction between the duplex DNA structure and the TFO1 and TFO2 probes (-67.3 KJ/mol), respect the sum of the single duplex-TFO1 and duplex-TFO2 interactions (-47.0 kJ/mol). The formation of triplex-DNA structure was proven by kinetic modelling study performed using the Luzar and Chandler model. The results indicate that after 500 ns from interaction, H-bonds between the base pairs in the double strand DNA are weaken while new H-bonds between the TFOs and duplex DNA are formed. Molecular dynamic (MD) simulations indicate that the TFOs sequence distance (138 bps) and the amount of TA*T triplet units are the keystones for the effectiveness of the cooperative effect, reaching for the selected target a minimum of energy value of -19452.6 kJ/mol. The MD data were experimentally corroborated by electrochemical measurements, detecting a HBV-clone genome at TFOs modified electrode surface. The interaction was electrochemical transduced by an intercalative Osmium based compound. The Langmuir isotherm model reports for the forming triplex DNA an association constant value of about 2.9 × 1016M-1, this high value could be attributed to the synergic contribution of the TFOs cooperative effect and to the rigid circular duplex structure. Finally, AFM and SEM investigations suggest the formation of a triplex-DNA structure at electrode surface, consisting in circles of about 1.5 um in diameter with asymmetric stranded thickness. This finding data paving the way to future development of advanced miniaturized DNA computing and biosensors.
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Affiliation(s)
| | - Giuseppe Forte
- Department of Drug Science, University of Catania, via S. Sofia 64, 95123, Catania, Italy
| | | | - Sabrina Conoci
- Department of Chemical Science, University of Messina, Via Stagno d'Alcontres, 98166, Messina, Italy
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7
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Charge-Dependent Regulation in DNA Adsorption on 2D Clay Minerals. Sci Rep 2019; 9:6808. [PMID: 31048707 PMCID: PMC6497631 DOI: 10.1038/s41598-019-41093-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/27/2019] [Indexed: 01/22/2023] Open
Abstract
DNA purification is essential for the detection of human clinical specimens. A non-destructive, controllable, and low reagent consuming DNA extraction method is described. Negatively charged DNA is absorbed onto a negatively charged montmorillonite to achieve non-destructive DNA extraction based on cation bridge construction and electric double layer formation. Different valence cation modified montmorillonite forms were used to validate the charge-dependent nature of DNA adsorption on montmorillonite. Electric double layer thickness thinning/thickening with the high/lower valence cations exists, and the minerals tended to be sedimentation-stable due to the Van der Waals attraction/electrostatic repulsion. Li-modified montmorillonite with the lowest charge states showed the best DNA adsorption efficiency of 8–10 ng/μg. Charge-dependent regulating research provides a new perspective for controllable DNA extraction and a deep analysis of interface engineering mechanisms.
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8
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Zarei L, Tavallaie R, Choudhury MH, Parker SG, Bakthavathsalam P, Ciampi S, Gonçales VR, Gooding JJ. DNA-Hybridization Detection on Si(100) Surfaces Using Light-Activated Electrochemistry: A Comparative Study between Bovine Serum Albumin and Hexaethylene Glycol as Antifouling Layers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14817-14824. [PMID: 30185042 DOI: 10.1021/acs.langmuir.8b02222] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Light can be used to spatially resolve electrochemical measurements on a semiconductor electrode. This phenomenon has been explored to detect DNA hybridization with light-addressable potentiometric sensors and, more recently, with light-addressable amperometric sensors based on organic-monolayer-protected Si(100). Here, a contribution to the field is presented by comparing sensing performances when bovine serum albumin (BSA) and hexaethylene glycol (OEG6) are employed as antifouling layers that resist nonspecific adsorption to the DNA-modified interface on Si(100) devices. What is observed is that both sensors based on BSA or OEG6 initially allow electrochemical distinction among complementary, noncomplementary, and mismatched DNA targets. However, only surfaces based on OEG6 can sustain electroactivity over time. Our results suggest that this relates to accelerated SiO x formation occasioned by BSA proteins adsorbing on monolayer-protected Si(100) surfaces. Therefore, DNA biosensors were analytically explored on low-doped Si(100) electrodes modified on the molecular level with OEG6 as an antifouling layer. First, light-activated electrochemical responses were recorded over a range of complementary DNA target concentrations. A linear semilog relation was obtained from 1.0 × 10-11 to 1.0 × 10-6 mol L-1 with a correlation coefficient of 0.942. Then, measurements with three independent surfaces indicated a relative standard deviation of 4.5%. Finally, selectivity tests were successfully performed in complex samples consisting of a cocktail mixture of four different DNA sequences. Together, these results indicate that reliable and stable light-activated amperometric DNA sensors can be achieved on Si(100) by employing OEG6 as an antifouling layer.
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Affiliation(s)
- Leila Zarei
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology , The University of New South Wales , Sydney , New South Wales 2052 , Australia
| | - Roya Tavallaie
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology , The University of New South Wales , Sydney , New South Wales 2052 , Australia
| | - Moinul H Choudhury
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology , The University of New South Wales , Sydney , New South Wales 2052 , Australia
| | - Stephen G Parker
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology , The University of New South Wales , Sydney , New South Wales 2052 , Australia
| | - Padmavathy Bakthavathsalam
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology , The University of New South Wales , Sydney , New South Wales 2052 , Australia
| | - Simone Ciampi
- Department of Chemistry , Curtin University , Bentley , Western Australia 6102 , Australia
| | - Vinicius R Gonçales
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology , The University of New South Wales , Sydney , New South Wales 2052 , Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology , The University of New South Wales , Sydney , New South Wales 2052 , Australia
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9
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Li Y, Artés JM, Demir B, Gokce S, Mohammad HM, Alangari M, Anantram MP, Oren EE, Hihath J. Detection and identification of genetic material via single-molecule conductance. NATURE NANOTECHNOLOGY 2018; 13:1167-1173. [PMID: 30397286 DOI: 10.1038/s41565-018-0285-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 09/20/2018] [Indexed: 05/05/2023]
Abstract
The ongoing discoveries of RNA modalities (for example, non-coding, micro and enhancer) have resulted in an increased desire for detecting, sequencing and identifying RNA segments for applications in food safety, water and environmental protection, plant and animal pathology, clinical diagnosis and research, and bio-security. Here, we demonstrate that single-molecule conductance techniques can be used to extract biologically relevant information from short RNA oligonucleotides, that these measurements are sensitive to attomolar target concentrations, that they are capable of being multiplexed, and that they can detect targets of interest in the presence of other, possibly interfering, RNA sequences. We also demonstrate that the charge transport properties of RNA:DNA hybrids are sensitive to single-nucleotide polymorphisms, thus enabling differentiation between specific serotypes of Escherichia coli. Using a combination of spectroscopic and computational approaches, we determine that the conductance sensitivity primarily arises from the effects that the mutations have on the conformational structure of the molecules, rather than from the direct chemical substitutions. We believe that this approach can be further developed to make an electrically based sensor for diagnostic purposes.
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Affiliation(s)
- Yuanhui Li
- Electrical and Computer Engineering Department, University of California Davis, Davis, CA, USA
| | - Juan M Artés
- Electrical and Computer Engineering Department, University of California Davis, Davis, CA, USA
- Biophysics and Photosynthesis, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Chemistry Department, University of Massachusetts Lowell, Lowell, MA, USA
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - Sumeyye Gokce
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - Hashem M Mohammad
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA
| | - Mashari Alangari
- Electrical and Computer Engineering Department, University of California Davis, Davis, CA, USA
| | - M P Anantram
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA.
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey.
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey.
| | - Joshua Hihath
- Electrical and Computer Engineering Department, University of California Davis, Davis, CA, USA.
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10
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Veerbeek J, Steen R, Vijselaar W, Rurup WF, Korom S, Rozzi A, Corradini R, Segerink L, Huskens J. Selective Functionalization with PNA of Silicon Nanowires on Silicon Oxide Substrates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:11395-11404. [PMID: 30179484 PMCID: PMC6158678 DOI: 10.1021/acs.langmuir.8b02401] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/29/2018] [Indexed: 06/02/2023]
Abstract
Silicon nanowire chips can function as sensors for cancer DNA detection, whereby selective functionalization of the Si sensing areas over the surrounding silicon oxide would prevent loss of analyte and thus increase the sensitivity. The thermal hydrosilylation of unsaturated carbon-carbon bonds onto H-terminated Si has been studied here to selectively functionalize the Si nanowires with a monolayer of 1,8-nonadiyne. The silicon oxide areas, however, appeared to be functionalized as well. The selectivity toward the Si-H regions was increased by introducing an extra HF treatment after the 1,8-nonadiyne monolayer formation. This step (partly) removed the monolayer from the silicon oxide regions, whereas the Si-C bonds at the Si areas remained intact. The alkyne headgroups of immobilized 1,8-nonadiyne were functionalized with PNA probes by coupling azido-PNA and thiol-PNA by click chemistry and thiol-yne chemistry, respectively. Although both functionalization routes were successful, hybridization could only be detected on the samples with thiol-PNA. No fluorescence was observed when introducing dye-labeled noncomplementary DNA, which indicates specific DNA hybridization. These results open up the possibilities for creating Si nanowire-based DNA sensors with improved selectivity and sensitivity.
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Affiliation(s)
- Janneke Veerbeek
- Molecular NanoFabrication group, MESA+ Institute for Nanotechnology, and BIOS Lab on a
Chip group, MESA+ Institute for Nanotechnology, TechMed Centre and
Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Raymond Steen
- Molecular NanoFabrication group, MESA+ Institute for Nanotechnology, and BIOS Lab on a
Chip group, MESA+ Institute for Nanotechnology, TechMed Centre and
Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Wouter Vijselaar
- Molecular NanoFabrication group, MESA+ Institute for Nanotechnology, and BIOS Lab on a
Chip group, MESA+ Institute for Nanotechnology, TechMed Centre and
Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - W. Frederik Rurup
- Molecular NanoFabrication group, MESA+ Institute for Nanotechnology, and BIOS Lab on a
Chip group, MESA+ Institute for Nanotechnology, TechMed Centre and
Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Saša Korom
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Andrea Rozzi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Roberto Corradini
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Loes Segerink
- Molecular NanoFabrication group, MESA+ Institute for Nanotechnology, and BIOS Lab on a
Chip group, MESA+ Institute for Nanotechnology, TechMed Centre and
Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Jurriaan Huskens
- Molecular NanoFabrication group, MESA+ Institute for Nanotechnology, and BIOS Lab on a
Chip group, MESA+ Institute for Nanotechnology, TechMed Centre and
Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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11
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Park JS, Kim HJ, Lee JH, Park JH, Kim J, Hwang KS, Lee BC. Amyloid Beta Detection by Faradaic Electrochemical Impedance Spectroscopy Using Interdigitated Microelectrodes. SENSORS (BASEL, SWITZERLAND) 2018; 18:E426. [PMID: 29389878 PMCID: PMC5855898 DOI: 10.3390/s18020426] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/13/2018] [Accepted: 01/24/2018] [Indexed: 01/06/2023]
Abstract
Faradaic electrochemical impedance spectroscopy (f-EIS) in the presence of redox reagent, e.g., [Fe(CN)₆]3-/4-, is widely used in biosensors owing to its high sensitivity. However, in sensors detecting amyloid beta (Aβ), the redox reagent can cause the aggregation of Aβ, which is a disturbance factor in accurate detection. Here, we propose an interdigitated microelectrode (IME) based f-EIS technique that can alleviate the aggregation of Aβ and achieve high sensitivity by buffer control. The proposed method was verified by analyzing three different EIS-based sensors: non-faradaic EIS (nf-EIS), f-EIS, and the proposed f-EIS with buffer control. We analyzed the equivalent circuits of nf-EIS and f-EIS sensors. The dominant factors of sensitivity were analyzed, and the impedance change rates via Aβ reaction was compared. We measured the sensitivity of the IME sensors based on nf-EIS, f-EIS, and the proposed f-EIS. The results demonstrate that the proposed EIS-based IME sensor can detect Aβ with a sensitivity of 7.40-fold and 10.93-fold higher than the nf-EIS and the f-EIS sensors, respectively.
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Affiliation(s)
- Jin Soo Park
- Center for BioMicrosystems, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea.
- Department of Electrical Engineering, Korea University, Seoul 02841, Korea.
| | - Hye Jin Kim
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea.
- Department of Electrical Engineering, Korea University, Seoul 02841, Korea.
| | - Ji-Hoon Lee
- Center for BioMicrosystems, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea.
| | - Jung Ho Park
- Department of Electrical Engineering, Korea University, Seoul 02841, Korea.
| | - Jinsik Kim
- Department of Medical Biotechnology, College of Life Science and Biotechnology, Dongguk University, Seoul 10326, Korea.
| | - Kyo Seon Hwang
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea.
| | - Byung Chul Lee
- Center for BioMicrosystems, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea.
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12
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Aragonès AC, Darwish N, Ciampi S, Sanz F, Gooding JJ, Díez-Pérez I. Single-molecule electrical contacts on silicon electrodes under ambient conditions. Nat Commun 2017; 8:15056. [PMID: 28406169 PMCID: PMC5399279 DOI: 10.1038/ncomms15056] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 02/23/2017] [Indexed: 12/19/2022] Open
Abstract
The ultimate goal in molecular electronics is to use individual molecules as the active electronic component of a real-world sturdy device. For this concept to become reality, it will require the field of single-molecule electronics to shift towards the semiconducting platform of the current microelectronics industry. Here, we report silicon-based single-molecule contacts that are mechanically and electrically stable under ambient conditions. The single-molecule contacts are prepared on silicon electrodes using the scanning tunnelling microscopy break-junction approach using a top metallic probe. The molecular wires show remarkable current–voltage reproducibility, as compared to an open silicon/nano-gap/metal junction, with current rectification ratios exceeding 4,000 when a low-doped silicon is used. The extension of the single-molecule junction approach to a silicon substrate contributes to the next level of miniaturization of electronic components and it is
anticipated it will pave the way to a new class of robust single-molecule circuits. The next level of miniaturization of electronic circuits calls for a connection between current single-molecule and traditional semiconductor processing technologies. Here, the authors show a method to prepare metal/molecule/silicon diodes that present high current rectification ratios exceeding 4,000.
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Affiliation(s)
- Albert C Aragonès
- Department of Materials Science and Physical Chemistry &Institute of Theoretical and Computational Chemistry (IQTC), University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.,Institute for Bioengineering of Catalonia (IBEC), Baldiri Reixac 15-21, 08028 Barcelona, Spain.,Centro Investigación Biomédica en Red (CIBER-BBN), Campus Río Ebro-Edificio I+D, Poeta Mariano Esquillor s/n, 50018 Zaragoza, Spain
| | - Nadim Darwish
- Department of Chemistry, Faculty of Science &Engineering, Curtin University, Nanochemistry Research Institute, Perth, Western Australia 6102, Australia
| | - Simone Ciampi
- Department of Chemistry, Faculty of Science &Engineering, Curtin University, Nanochemistry Research Institute, Perth, Western Australia 6102, Australia
| | - Fausto Sanz
- Department of Materials Science and Physical Chemistry &Institute of Theoretical and Computational Chemistry (IQTC), University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.,Institute for Bioengineering of Catalonia (IBEC), Baldiri Reixac 15-21, 08028 Barcelona, Spain.,Centro Investigación Biomédica en Red (CIBER-BBN), Campus Río Ebro-Edificio I+D, Poeta Mariano Esquillor s/n, 50018 Zaragoza, Spain
| | - J Justin Gooding
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Ismael Díez-Pérez
- Department of Materials Science and Physical Chemistry &Institute of Theoretical and Computational Chemistry (IQTC), University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.,Institute for Bioengineering of Catalonia (IBEC), Baldiri Reixac 15-21, 08028 Barcelona, Spain.,Centro Investigación Biomédica en Red (CIBER-BBN), Campus Río Ebro-Edificio I+D, Poeta Mariano Esquillor s/n, 50018 Zaragoza, Spain
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13
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Wu F, Zhang DW, Wang J, Watkinson M, Krause S. Copper Contamination of Self-Assembled Organic Monolayer Modified Silicon Surfaces Following a "Click" Reaction Characterized with LAPS and SPIM. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:3170-3177. [PMID: 28285531 DOI: 10.1021/acs.langmuir.6b03831] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A copper(I)-catalyzed azide alkyne cycloaddition (CuAAC) reaction combined with microcontact printing was used successfully to pattern alkyne-terminated self-assembled organic monolayer-modified silicon surfaces. Despite the absence of a copper peak in X-ray photoelectron spectra, copper contamination was found and visualized using light-addressable potentiometric sensors (LAPS) and scanning photo-induced impedance microscopy (SPIM) after the "click"-modified silicon surfaces were rinsed with hydrochloric acid (HCl) solution, which was frequently used to remove copper residues in the past. Even cleaning with an ethylenediaminetetraacetic acid (EDTA) solution did not remove the copper residue completely. Different strategies for avoiding copper contamination, including the use of bulky chelators for the copper(I) catalyst and rinsing with different reagents, were tested. Only cleaning of the silicon surfaces with an EDTA solution containing trifluoroacetic acid (TFA) after the click modification proved to be an effective method as confirmed by LAPS and SPIM results, which showed the expected potential shift due to the surface charge introduced by functional groups in the monolayer and allowed, for the first time, imaging the impedance of an organic monolayer.
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Affiliation(s)
| | - De-Wen Zhang
- Institute of Materials, China Academy of Engineering Physics , Jiangyou 621908, Sichuan, P.R. China
| | - Jian Wang
- Institute of Medical Engineering, School of Basic Medical Science, Xi'an Jiaotong University Health Science Center , Xi'an 710061, P.R. China
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14
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Miranda-Castro R, Sánchez-Salcedo R, Suárez-Álvarez B, de-Los-Santos-Álvarez N, Miranda-Ordieres AJ, Jesús Lobo-Castañón M. Thioaromatic DNA monolayers for target-amplification-free electrochemical sensing of environmental pathogenic bacteria. Biosens Bioelectron 2017; 92:162-170. [PMID: 28213329 DOI: 10.1016/j.bios.2017.02.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/26/2017] [Accepted: 02/10/2017] [Indexed: 10/20/2022]
Abstract
Genosensing technology has mostly based on mixed self-assembled monolayers (SAMs) of thiol-modified oligonucleotides and alkanethiols on gold surfaces. However, the typical backfilling approach, which incorporates the alkanethiol in a second step, gives rise to a heterogeneous distribution of oligonucleotide probes on the surface, negatively affecting to both hybridization efficiency and surface stability. Despite aromatic thiols present a remarkably different behavior from alkanethiols, with higher rigidity and stronger intermolecular interactions, they have been scarcely explored for the fabrication of DNA sensing platforms. We have investigated different approaches involving SAMs of aromatic thiols, namely p-mercaptobenzoic acid (p-MBA) and p-aminothiophenol (p-ATP), to yield DNA sensing layers for sequence-specific detection of target oligonucleotides. The studied monolayers were evaluated by DNA surface coverage and further information was obtained by determining their functionality in a sandwich hybridization assay with enzymatic amplification of the electrochemical read-out. The insertion of thiol-oligonucleotides into p-ATP monolayers previously oxidized, and the covalent binding of amino-oligonucleotides to pure p-MBA monolayers give rise to increased storage stability and better analytical performance. The quantification of RNA from Legionella pneumophila cellular lysates was successfully performed, illustrating the usefulness of these sensing architectures for detecting pathogenic bacteria.
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Affiliation(s)
- Rebeca Miranda-Castro
- Departamento de Química Física y Analítica, Universidad de Oviedo, 33006 Oviedo, Spain
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15
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Hinman SS, Cheng Q. Bioinspired Assemblies and Plasmonic Interfaces for Electrochemical Biosensing. J Electroanal Chem (Lausanne) 2016; 781:136-146. [PMID: 28163664 PMCID: PMC5283611 DOI: 10.1016/j.jelechem.2016.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Electrochemical biosensing represents a collection of techniques that may be utilized for capture and detection of biomolecules in both simple and complex media. While the instrumentation and technological aspects play important roles in detection capabilities, the interfacial design aspects are of equal importance, and often, those inspired by nature produce the best results. This review highlights recent material designs, recognition schemes, and method developments as they relate to targeted electrochemical analysis for biological systems. This includes the design of electrodes functionalized with peptides, proteins, nucleic acids, and lipid membranes, along with nanoparticle mediated signal amplification mechanisms. The topic of hyphenated surface plasmon resonance assays is also discussed, as this technique may be performed concurrently with complementary and/or confirmatory measurements. Together, smart materials and experimental designs will continue to pave the way for complete biomolecular analyses of complex and technically challenging systems.
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Affiliation(s)
- Samuel S. Hinman
- Environmental Toxicology, University of California – Riverside, Riverside, CA 92521, USA
| | - Quan Cheng
- Environmental Toxicology, University of California – Riverside, Riverside, CA 92521, USA
- Department of Chemistry, University of California – Riverside, Riverside, CA 92521, USA
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16
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Gebala M, La Mantia F, Michaels PE, Ciampi S, Gupta B, Parker SG, Tavallaie R, Gooding JJ. Electric Field Modulation of Silicon upon Tethering of Highly Charged Nucleic Acids. Capacitive Studies on DNA‐modified Silicon (111). ELECTROANAL 2016. [DOI: 10.1002/elan.201600285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Magdalena Gebala
- Analytische Chemie – Elektroanalytik & Sensorik, Ruhr-Universität Bochum Universitätsstr.150 D-44780 Bochum Germany
- Department of Biochemistry Stanford University Stanford CA 94305 USA
| | - Fabio La Mantia
- Energiespeicher- und Energiewandlersysteme Universität Bremen Wiener Str. 12 D-28359 Bremen Germany
| | - Pauline Eugene Michaels
- School of Chemistry and the Australian Centre for NanoMedicine The University of New South Wales Sydney NSW 2052 Australia
| | - Simone Ciampi
- School of Chemistry and the Australian Centre for NanoMedicine The University of New South Wales Sydney NSW 2052 Australia
| | - Bakul Gupta
- School of Chemistry and the Australian Centre for NanoMedicine The University of New South Wales Sydney NSW 2052 Australia
| | - Stephen G. Parker
- School of Chemistry and the Australian Centre for NanoMedicine The University of New South Wales Sydney NSW 2052 Australia
| | - Roya Tavallaie
- School of Chemistry and the Australian Centre for NanoMedicine The University of New South Wales Sydney NSW 2052 Australia
| | - J. Justin Gooding
- School of Chemistry and the Australian Centre for NanoMedicine The University of New South Wales Sydney NSW 2052 Australia
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17
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Choudhury MH, Ciampi S, Yang Y, Tavallaie R, Zhu Y, Zarei L, Gonçales VR, Gooding JJ. Connecting electrodes with light: one wire, many electrodes. Chem Sci 2015; 6:6769-6776. [PMID: 28757968 PMCID: PMC5508692 DOI: 10.1039/c5sc03011k] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 08/28/2015] [Indexed: 11/21/2022] Open
Abstract
The requirement of a wire to each electrode is central to the design of any electronic device but can also be a major restriction. For example it entails space restrictions and rigid device architecture in multi-electrode devices. The finite space that is taken up by the array of electrical terminals and conductive pads also severely limits the achievable density of electrodes in the device. Here it is shown that a travelling light pointer can be used to form transient electrical connections anywhere on a monolithic semiconductor electrode that is fitted with a single peripheral electrical terminal. This is achieved using hydrogen terminated silicon electrodes that are modified with well-defined organic monolayers. It is shown that electrochemical information can be either read from or written onto these surfaces. Using this concept it is possible to form devices that are equivalent to a conventional electrode array but that do not require a predetermined architecture, and where each element of the array is temporally "connected" using light stimulus; a step change in capability for electrochemistry.
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Affiliation(s)
- Moinul H Choudhury
- School of Chemistry , The University of New South Wales , Sydney , NSW 2052 , Australia .
| | - Simone Ciampi
- School of Chemistry , The University of New South Wales , Sydney , NSW 2052 , Australia .
| | - Ying Yang
- School of Chemistry , The University of New South Wales , Sydney , NSW 2052 , Australia .
| | - Roya Tavallaie
- School of Chemistry , The University of New South Wales , Sydney , NSW 2052 , Australia .
- Australian Centre for NanoMedicine , The University of New South Wales , Sydney , NSW 2052 , Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology , The University of New South Wales , Sydney , NSW 2052 , Australia
| | - Ying Zhu
- School of Chemistry , The University of New South Wales , Sydney , NSW 2052 , Australia .
| | - Leila Zarei
- School of Chemistry , The University of New South Wales , Sydney , NSW 2052 , Australia .
| | - Vinicius R Gonçales
- School of Chemistry , The University of New South Wales , Sydney , NSW 2052 , Australia .
| | - J Justin Gooding
- School of Chemistry , The University of New South Wales , Sydney , NSW 2052 , Australia .
- Australian Centre for NanoMedicine , The University of New South Wales , Sydney , NSW 2052 , Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology , The University of New South Wales , Sydney , NSW 2052 , Australia
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18
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Wang J, Wu F, Watkinson M, Zhu J, Krause S. "Click" Patterning of Self-Assembled Monolayers on Hydrogen-Terminated Silicon Surfaces and Their Characterization Using Light-Addressable Potentiometric Sensors. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:9646-9654. [PMID: 26274063 DOI: 10.1021/acs.langmuir.5b02069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Two potential strategies for chemically patterning alkyne-terminated self-assembled monolayers (SAMs) on oxide-free silicon or silicon-on-sapphire (SOS) substrates were investigated and compared. The patterned surfaces were validated using a light-addressable potentiometric sensor (LAPS) for the first time. The first strategy involved an integration of photolithography with "click" chemistry. Detailed surface characterization (i.e. water contact angle, ellipsometry, AFM, and XPS) and LAPS measurements showed that photoresist processing not only decreases the coverage of organic monolayers but also introduces chemically bonded contaminants on the surfaces, thus significantly reducing the quality of the SAMs and the utility of "click" surface modification. The formation of chemical contaminants in photolithography was also observed on carboxylic acid- and alkyl-terminated monolayers using LAPS. In contrast, a second approach combined microcontact printing (μCP) with "click" chemistry; that is azide (azido-oligo(ethylene glycol) (OEG)-NH2) inks were printed on alkyne-terminated SAMs on silicon or SOS through PDMS stamps. The surface characterization results for the sample printed with a flat featureless PDMS stamp demonstrated a nondestructive and efficient method of μCP to perform "click" reactions on alkyne-terminated, oxide-free silicon surfaces for the first time. For the sample printed with a featured PDMS stamp, LAPS imaging showed a good agreement with the pattern of the PDMS stamp, indicating the successful chemical patterning on non-oxidized silicon and SOS substrates and the capability of LAPS to image the molecular patterns with high sensitivity.
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Affiliation(s)
- Jian Wang
- School of Engineering and Materials Science and ‡School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, U.K
| | - Fan Wu
- School of Engineering and Materials Science and ‡School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, U.K
| | - Michael Watkinson
- School of Engineering and Materials Science and ‡School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, U.K
| | - Jingyuan Zhu
- School of Engineering and Materials Science and ‡School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, U.K
| | - Steffi Krause
- School of Engineering and Materials Science and ‡School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, U.K
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