1
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Bellassai N, D’Agata R, Marti A, Rozzi A, Volpi S, Allegretti M, Corradini R, Giacomini P, Huskens J, Spoto G. Detection of Tumor DNA in Human Plasma with a Functional PLL-Based Surface Layer and Plasmonic Biosensing. ACS Sens 2021; 6:2307-2319. [PMID: 34032412 PMCID: PMC8294610 DOI: 10.1021/acssensors.1c00360] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/13/2021] [Indexed: 12/20/2022]
Abstract
Standard protocols for the analysis of circulating tumor DNA (ctDNA) include the isolation of DNA from the patient's plasma and its amplification and analysis in buffered solutions. The application of such protocols is hampered by several factors, including the complexity and time-constrained preanalytical procedures, risks for sample contamination, extended analysis time, and assay costs. A recently introduced nanoparticle-enhanced surface plasmon resonance imaging-based assay has been shown to simplify procedures for the direct detection of tumor DNA in the patient's plasma, greatly simplifying the cumbersome preanalytical phase. To further simplify the protocol, a new dual-functional low-fouling poly-l-lysine (PLL)-based surface layer has been introduced that is described herein. The new PLL-based layer includes a densely immobilized CEEEEE oligopeptide to create a charge-balanced system preventing the nonspecific adsorption of plasma components on the sensor surface. The layer also comprises sparsely attached peptide nucleic acid probes complementary to the sequence of circulating DNA, e.g., the analyte that has to be captured in the plasma from cancer patients. We thoroughly investigated the contribution of each component of the dual-functional polymer to the antifouling properties of the surface layer. The low-fouling property of the new surface layer allowed us to detect wild-type and KRAS p.G12D-mutated DNA in human plasma at the attomolar level (∼2.5 aM) and KRAS p.G13D-mutated tumor DNA in liquid biopsy from a cancer patient with almost no preanalytical treatment of the patient's plasma, no need to isolate DNA from plasma, and without PCR amplification of the target sequence.
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Affiliation(s)
- Noemi Bellassai
- Department
of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95122 Catania, Italy
| | - Roberta D’Agata
- Department
of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95122 Catania, Italy
- INBB,
Istituto Nazionale di Biostrutture e Biosistemi, Viale delle Medaglie d’Oro, 305, 00136 Roma, Italy
| | - Almudena Marti
- Department
of Molecules & Materials, MESA+ Institute for Nanotechnology,
Faculty of Science & Technology, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Andrea Rozzi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 17/A, 43124 Parma, Italy
| | - Stefano Volpi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 17/A, 43124 Parma, Italy
| | - Matteo Allegretti
- Oncogenomics
and Epigenetics, IRCCS Regina Elena National
Cancer Institute, Via
Elio Chianesi, 53, 00144 Rome, Italy
| | - Roberto Corradini
- INBB,
Istituto Nazionale di Biostrutture e Biosistemi, Viale delle Medaglie d’Oro, 305, 00136 Roma, Italy
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 17/A, 43124 Parma, Italy
| | - Patrizio Giacomini
- Oncogenomics
and Epigenetics, IRCCS Regina Elena National
Cancer Institute, Via
Elio Chianesi, 53, 00144 Rome, Italy
| | - Jurriaan Huskens
- Department
of Molecules & Materials, MESA+ Institute for Nanotechnology,
Faculty of Science & Technology, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Giuseppe Spoto
- Department
of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95122 Catania, Italy
- INBB,
Istituto Nazionale di Biostrutture e Biosistemi, Viale delle Medaglie d’Oro, 305, 00136 Roma, Italy
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2
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Wang L, Schubert US, Hoeppener S. Surface chemical reactions on self-assembled silane based monolayers. Chem Soc Rev 2021; 50:6507-6540. [PMID: 34100051 DOI: 10.1039/d0cs01220c] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In this review, we aim to update our review "Chemical modification of self-assembled silane-based monolayers by surface reactions" which was published in 2010 and has developed into an important guiding tool for researchers working on the modification of solid substrate surface properties by chemical modification of silane-based self-assembled monolayers. Due to the rapid development of this field of research in the last decade, the utilization of chemical functionalities in self-assembled monolayers has been significantly improved and some new processes were introduced in chemical surface reactions for tailoring the properties of solid substrates. Thus, it is time to update the developments in the surface functionalization of silane-based molecules. Hence, after a short introduction on self-assembled monolayers, this review focuses on a series of chemical reactions, i.e., nucleophilic substitution, click chemistry, supramolecular modification, photochemical reaction, and other reactions, which have been applied for the modification of hydroxyl-terminated substrates, like silicon and glass, which have been reported during the last 10 years.
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Affiliation(s)
- Limin Wang
- Laboratory of Organic Chemistry and Macromolecular Chemistry (IOMC), Friedrich Schiller University, Humboldtstr. 10, 07743 Jena, Germany
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3
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Abstract
Bioelectronics explores the use of electronic devices for applications in signal transduction at their interfaces with biological systems. The miniaturization of the bioelectronic systems has enabled seamless integration at these interfaces and is providing new scientific and technological opportunities. In particular, nanowire-based devices can yield smaller sized and unique geometry detectors that are difficult to access with standard techniques, and thereby can provide advantages in sensitivity with reduced invasiveness. In this review, we focus on nanowire-enabled bioelectronics. First, we provide an overview of synthetic studies for designed growth of semiconductor nanowires of which structure and composition are controlled to enable key elements for bioelectronic devices. Second, we review nanowire field-effect transistor sensors for highly sensitive detection of biomolecules, their applications in diagnosis and drug discovery, and methods for sensitivity enhancement. We then turn to recent progress in nanowire-enabled studies of electrogenic cells, including cardiomyocytes and neurons. Representative advances in electrical recording using nanowire electronic devices for single cell measurements, cell network mapping, and three-dimensional recordings of synthetic and natural tissues, and in vivo brain mapping are highlighted. Finally, we overview the key challenges and opportunities of nanowires for fundamental research and translational applications.
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Affiliation(s)
- Anqi Zhang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jae-Hyun Lee
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Center for Nanomedicine, Institute for Basic Science (IBS), Advanced Science Institute, Yonsei University, Seoul, 03722, Korea
| | - Charles M Lieber
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
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4
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Zheng Z, Zhang H, Zhai T, Xia F. Overcome Debye Length Limitations for Biomolecule Sensing Based on Field Effective Transistors
†. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202000584] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Zhi Zheng
- Engineering Research Center of Nano‐Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences Wuhan Hubei 430074 China
| | - Hongyuan Zhang
- Engineering Research Center of Nano‐Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences Wuhan Hubei 430074 China
| | - Tianyou Zhai
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology Wuhan Hubei 430074 China
| | - Fan Xia
- Engineering Research Center of Nano‐Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences Wuhan Hubei 430074 China
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5
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Pan W, Han Z, Chang Y, Duan X. Three-dimensional biosensor surface based on novel thorns-like polyelectrolytes. Biosens Bioelectron 2020; 167:112504. [DOI: 10.1016/j.bios.2020.112504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 11/29/2022]
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6
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Mensah K, Cissé I, Pierret A, Rosticher M, Palomo J, Morfin P, Plaçais B, Bockelmann U. DNA Hybridization Measured with Graphene Transistor Arrays. Adv Healthc Mater 2020; 9:e2000260. [PMID: 32602657 DOI: 10.1002/adhm.202000260] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/04/2020] [Indexed: 12/20/2022]
Abstract
Arrays of field-effect transistors are fabricated from chemical vapor deposition grown graphene (GFETs) and label-free detection of DNA hybridization performed down to femtomolar concentrations. A process is developed for large-area graphene sheets, which includes a thin Al2 O3 layer, protecting the graphene from contamination during photolithographic patterning and a SiOx capping for biocompatibility. It enables fabrication of high-quality transistor arrays, exhibiting stable close-to-zero Dirac point voltages under ambient conditions. Passivation of the as-fabricated chip with a layer composed of two different oxides avoids direct electrochemical contact between the DNA solutions and the graphene layer during hybridization detection. DNA probe molecules are electrostatically immobilized via poly-l-lysine coating of the chip surface. Adsorption of this positively charged polymer induces a positive shift of the Dirac point and subsequent immobilization of negatively charged DNA probes induces a negative shift. Spatially resolved hybridization of DNA sequences is performed on the GFET arrays. End-point as well as real-time in situ measurements of hybridization are achieved. A detection limit of 10 fm is observed for hybridization of 20-nucleotide DNA targets. Typical voltage signals are around 100 mV and spurious drifts below 1 mV per hour.
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Affiliation(s)
- Kokoura Mensah
- Laboratoire NanobiophysiqueESPCI ParisUniversité PSLCNRS Paris 75005 France
| | - Ismaïl Cissé
- Laboratoire NanobiophysiqueESPCI ParisUniversité PSLCNRS Paris 75005 France
| | - Aurélie Pierret
- Laboratoire de Physique de l'Ecole Normale SupérieureENSUniversité PSLCNRSSorbonne UniversitéUniversité Paris‐Diderot Paris 75005 France
| | - Michael Rosticher
- Laboratoire de Physique de l'Ecole Normale SupérieureENSUniversité PSLCNRSSorbonne UniversitéUniversité Paris‐Diderot Paris 75005 France
| | - José Palomo
- Laboratoire de Physique de l'Ecole Normale SupérieureENSUniversité PSLCNRSSorbonne UniversitéUniversité Paris‐Diderot Paris 75005 France
| | - Pascal Morfin
- Laboratoire de Physique de l'Ecole Normale SupérieureENSUniversité PSLCNRSSorbonne UniversitéUniversité Paris‐Diderot Paris 75005 France
| | - Bernard Plaçais
- Laboratoire de Physique de l'Ecole Normale SupérieureENSUniversité PSLCNRSSorbonne UniversitéUniversité Paris‐Diderot Paris 75005 France
| | - Ulrich Bockelmann
- Laboratoire NanobiophysiqueESPCI ParisUniversité PSLCNRS Paris 75005 France
- Institut Cochin 22 rue Méchain Paris 75014 France
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7
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Movilli J, Kolkman RW, Rozzi A, Corradini R, Segerink LI, Huskens J. Increasing the Sensitivity of Electrochemical DNA Detection by a Micropillar-Structured Biosensing Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4272-4279. [PMID: 32239946 PMCID: PMC7191753 DOI: 10.1021/acs.langmuir.0c00144] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/06/2020] [Indexed: 06/01/2023]
Abstract
The available active surface area and the density of probes immobilized on this surface are responsible for achieving high specificity and sensitivity in electrochemical biosensors that detect biologically relevant molecules, including DNA. Here, we report the design of gold-coated, silicon micropillar-structured electrodes functionalized with modified poly-l-lysine (PLL) as an adhesion layer to concomitantly assess the increase in sensitivity with the increase of the electrochemical area and control over the probe density. By systematically reducing the center-to-center distance between the pillars (pitch), denser micropillar arrays were formed at the electrode, resulting in a larger sensing area. Azido-modified peptide nucleic acid (PNA) probes were click-reacted onto the electrode interface, exploiting PLL with appended oligo(ethylene glycol) (OEG) and dibenzocyclooctyne (DBCO) moieties (PLL-OEG-DBCO) for antifouling and probe binding properties, respectively. The selective electrochemical sandwich assay formation, composed of consecutive hybridization steps of the target complementary DNA (cDNA) and reporter DNA modified with the electroactive ferrocene functionality (rDNA-Fc), was monitored by quartz crystal microbalance. The DNA detection performance of micropillared electrodes with different pitches was evaluated by quantifying the cyclic voltammetric response of the surface-confined rDNA-Fc. By decrease of the pitch of the pillar array, the area of the electrode was enhanced by up to a factor 10.6. A comparison of the electrochemical data with the geometrical area of the pillared electrodes confirmed the validity of the increased sensitivity of the DNA detection by the design of the micropillar array.
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Affiliation(s)
- Jacopo Movilli
- Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Ruben W Kolkman
- Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, Technical Medical Centre, Max Planck Institute for Complex Fluid Dynamics, University of Twente, 7522 NB Enschede, The Netherlands
| | - 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 I Segerink
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, Technical Medical Centre, Max Planck Institute for Complex Fluid Dynamics, University of Twente, 7522 NB Enschede, The Netherlands
| | - Jurriaan Huskens
- Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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8
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Movilli J, Di Iorio D, Rozzi A, Hiltunen J, Corradini R, Huskens J. "Plug-n-Play" Polymer Substrates: Surface Patterning with Reactive-Group-Appended Poly-l-lysine for Biomolecule Adhesion. ACS APPLIED POLYMER MATERIALS 2019; 1:3165-3173. [PMID: 32954353 PMCID: PMC7493307 DOI: 10.1021/acsapm.9b00814] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/01/2019] [Indexed: 06/11/2023]
Abstract
The immobilization of biomolecules onto polymeric surfaces employed in the fabrication of biomedical and biosensing devices is generally a challenging issue, as the absence of functional groups in such materials does not allow the use of common surface chemistries. Here we report the use of modified poly-l-lysine (PLL) as an effective method for the selective modification of polymeric materials with biomolecules. Cyclic olefin polymer (COP), Ormostamp, and polydimethylsiloxane (PDMS) surfaces were patterned with modified PLLs displaying either biotin or maleimide functional groups. Different patterning techniques were found to provide faithful microscale pattern formation, including micromolding in capillaries (MIMIC) and a hydrogel-based stamping device with micropores. The surface modification and pattern stability were tested with fluorescence microscopy, contact angle and X-ray photoelectron spectroscopy (XPS), showing an effective functionalization of substrates stable for over 20 days. By exploiting the strong biotin-streptavidin interaction or the thiol-maleimide coupling, DNA and PNA probes were displayed successfully on the surface of the materials, and these probes maintained the capability to specifically recognize complementary DNA sequences from solution. The printing of three different PNA-thiol probe molecules in a microarray fashion allowed selective DNA detection from a mixture of DNA analytes, demonstrating that the modified PLL methodology can potentially be used for multiplexed detection of DNA sequences.
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Affiliation(s)
- Jacopo Movilli
- Molecular
Nanofabrication Group, MESA+ Institute for Nanotechnology, Department
of Science and Technology, University of
Twente, P.O. Box 217, 7500
AE Enschede, The Netherlands
| | - Daniele Di Iorio
- Molecular
Nanofabrication Group, MESA+ Institute for Nanotechnology, Department
of Science and Technology, University of
Twente, P.O. Box 217, 7500
AE Enschede, The Netherlands
| | - Andrea Rozzi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Jussi Hiltunen
- VTT
Technical Research Center of Finland, 90570 Oulu, Finland
| | - Roberto Corradini
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Jurriaan Huskens
- Molecular
Nanofabrication Group, MESA+ Institute for Nanotechnology, Department
of Science and Technology, University of
Twente, P.O. Box 217, 7500
AE Enschede, The Netherlands
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9
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A new method for selective functionalization of silicon nanowire sensors and Bayesian inversion for its parameters. Biosens Bioelectron 2019; 142:111527. [DOI: 10.1016/j.bios.2019.111527] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/17/2019] [Accepted: 07/18/2019] [Indexed: 11/22/2022]
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10
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Movilli J, Rozzi A, Ricciardi R, Corradini R, Huskens J. Control of Probe Density at DNA Biosensor Surfaces Using Poly(l-lysine) with Appended Reactive Groups. Bioconjug Chem 2018; 29:4110-4118. [PMID: 30412384 PMCID: PMC6302315 DOI: 10.1021/acs.bioconjchem.8b00733] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Biosensors and materials
for biomedical applications generally
require chemical functionalization to bestow their surfaces with desired
properties, such as specific molecular recognition and antifouling
properties. The use of modified poly(l-lysine) (PLL) polymers
with appended oligo(ethylene glycol) (OEG) and thiol-reactive maleimide
(Mal) moieties (PLL-OEG-Mal) offers control over the presentation
of functional groups. These reactive groups can readily be conjugated
to, for example, probes for DNA detection. Here we demonstrate the
reliable conjugation of thiol-functionalized peptide nucleic acid
(PNA) probes onto predeposited layers of PLL-OEG-Mal and the control
over their surface density in the preceding synthetic step of the
PLL modification with Mal groups. By monitoring the quartz crystal
microbalance (QCM) frequency shifts of the binding of complementary
DNA versus the density of Mal moieties grafted to the PLL, a linear
relationship between probe density and PLL grafting density was found.
Cyclic voltammetry experiments using Methylene Blue-functionalized
DNA were performed to establish the absolute probe density values
at the biosensor surfaces. These data provided a density of 1.2 ×
1012 probes per cm2 per % of grafted Mal, thus
confirming the validity of the density control in the synthetic PLL
modification step without the need of further surface characterization.
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Affiliation(s)
- Jacopo Movilli
- Molecular NanoFabrication group, MESA+ Institute for Nanotechnology, Department of Science and Technology , University of Twente , P.O. Box 217, 7500 AE , Enschede , The Netherlands
| | - Andrea Rozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability , University of Parma , Parco Area delle Scienze 17/A , 43124 Parma , Italy
| | - Roberto Ricciardi
- Molecular NanoFabrication group, MESA+ Institute for Nanotechnology, Department of Science and Technology , University of Twente , P.O. Box 217, 7500 AE , Enschede , The Netherlands
| | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability , University of Parma , Parco Area delle Scienze 17/A , 43124 Parma , Italy
| | - Jurriaan Huskens
- Molecular NanoFabrication group, MESA+ Institute for Nanotechnology, Department of Science and Technology , University of Twente , P.O. Box 217, 7500 AE , Enschede , The Netherlands
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