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  • 1.
    Afrasiabi, Roodabeh
    et al.
    KTH, School of Information and Communication Technology (ICT).
    Jokilaakso, Nima
    KTH, School of Biotechnology (BIO).
    Localized Functionalization and Integration with Microfluidics for Multiplexed Biomolecule Detection using Silicon Nanoribbon-FET SensorsManuscript (preprint) (Other academic)
    Abstract [en]

    Biological processes causing different medical conditions are seldom characterized by the simple presence or absence of a single biomarker molecule and it can be expected that biosensors with options for multiplexed detection of a panel of analytes will be required for the development of bed-side diagnostic/prognostic tools for personalized healthcare. One sensor technology with potential to be used for label-free detection of biomolecules is based on Silicon Nanoribbon Field-Effect Transistors (SiNR FET). In this study, the possibilities for multiplexed detection of biomolecules have been explored by the integration of a SiNR FET device with a microfluidic system, in combination with localized immobilization of receptor molecules using a microdispensing instrument. SiNR FET devices were fabricated using CMOS technology and integrated with a microfluidic delivery system composed of channels defined in an SU-8 layer, covered with a PDMS lid. Switching between buffer solutions of different pH was used to demonstrate that the microfluidic system could be used for controlled sample delivery. The shift in conductance of the sensing wire upon change of pH showed that the SiNR FET devices were functional. Protocols for surface functionalization and biomolecule immobilization were evaluated using model systems based on synthetic complementary DNA oligonucleotides and the protein A-derived Z domain and its interaction with immunoglobulin G. The study demonstrates that localized immobilization of biomolecules on silicon nanoribbons can be achieved, opening up for multiplexed detection of analytes and improved possibilities for referencing.

  • 2.
    Afrasiabi, Roodabeh
    et al.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Jokilaakso, Nima
    KTH, School of Biotechnology (BIO), Protein Technology.
    Schmidt, Torsten
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Björk, P.
    Eriksson Karlström, Amelie
    KTH, School of Biotechnology (BIO), Protein Technology.
    Linnros, Jan
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Effect of microwave-assisted silanization on sensing properties of silicon nanoribbon FETs2015In: Sensors and actuators. B, Chemical, ISSN 0925-4005, E-ISSN 1873-3077, Vol. 209, p. 586-595Article in journal (Refereed)
    Abstract [en]

    An important concern with using silicon nanoribbon field-effect transistors (SiNR FET) for ion-sensing is the pH-response of the gate oxide surface. Depending on the application of the FET sensor, this response has to be chemically manipulated. Thus in silicon oxide-gated pH-sensors with integrated sensor and reference FETS, a surface with high pH-sensitivity, compared to the bare gate oxide, is required in the sensor FETs (SEFET), whereas in the reference FETs (REFET) the surface has to be relatively pH-insensitive. In order to control the sensitivity and chemistry of the oxide surface of the nanoribbons, a silanization reagent with a functional group is often self-assembled on the SiNR surface. Choice of a silanization reaction that results in a self-assembled layer on a silicon oxide surface has been studied extensively over the past decades. However, the effect of various self-assembled layers such as monolayers or mixed layers on the electrical response of SiNR FETs in aqueous solution needs to be exploited further, especially for future integrated SEFET/REFET systems. In this work, we have performed a comprehensive study on 3-aminopropyltriethoxysilane (APTES) silanization of silicon oxide surfaces using microwave (MW) heating as a new biocompatible route to conventional methods. A set of complementary surface characterization techniques (ellipsometry, AFM and ATR-FTIR) was used to analyze the properties of the APTES layer deposited on the silicon surface. We have found that a uniform monolayer can be achieved within 10 min by heating the silanization solution to 75 degrees C using MW heating. Furthermore, electrical measurements suggest that little change in device performance is observed after exposure to MW irradiation. Real-time pH measurements indicate that a uniform APTES monolayer not only reduces the pH sensitivity of SiNR FET by passivating the surface silanol groups, but also makes the device less sensitive to cation concentration in the background electrolyte. Our silanization route proves promising for future chemical surface modification of on-chip REFETs.

  • 3.
    Afrasiabi, Roodabeh
    et al.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Jokilaakso, Nima
    KTH, School of Biotechnology (BIO), Protein Technology.
    Schmidt, Torsten
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Eriksson Karlström, Amelie
    KTH, School of Biotechnology (BIO), Protein Technology.
    Linnros, Jan
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Microwave-assisted silanization of SiNW-FET: characterization and effect on sensing propertiesManuscript (preprint) (Other academic)
  • 4. Chen, Si
    et al.
    Jokilaakso, Nima
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Björk, Per
    Eriksson Karlström, Amelie
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Zhang, Shi-Li
    A two-terminal silicon nanoribbon field-effect pH sensor2010In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 97, no 26, p. 264102-Article in journal (Refereed)
    Abstract [en]

    This paper reports on a two-terminal silicon nanoribbon (SiNR) field-effect pH sensor operated in electrolyte. Observed experimentally and confirmed by modeling, the sensor is activated by self-gating with a gate bias set by the potential difference of the two terminals. The effect of this gate bias on the SiNR conductance is modulated by the potential drop over the electrical double layer (EDL) established on the SiNR surface, similarly to the threshold voltage modulation by EDL in a three-terminal SiNR field-effect transistor with an independent gate electrode. The potential drop over EDL is determined by the pH value of the electrolyte.

  • 5. Chen, Si
    et al.
    Nyholm, Leif
    Jokilaakso, Nima
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Karlström, Amelie Eriksson
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Linnros, Jan
    KTH, School of Information and Communication Technology (ICT), Material Physics.
    Smith, Ulf
    Zhang, Shi-Li
    Current Instability for Silicon Nanowire Field-Effect Sensors Operating in Electrolyte with Platinum Gate Electrodes2011In: Electrochemical and solid-state letters, ISSN 1099-0062, E-ISSN 1944-8775, Vol. 14, no 7, p. J34-J37Article in journal (Refereed)
    Abstract [en]

    Current instability is observed for silicon nanowire field-effect transistors operating in electrolytes with Pt gate electrodes. A comparative study involving an Ag/AgCl-reference gate electrode reveals that the effect results from a drift in the potential at the Pt-electrode/electrolyte interface. In a phosphate buffer saline of pH 7.4, the stabilization of the potential of the Pt electrode was found to require approximately 1000 s. A concurrent potential drift, with a comparable time constant, occurring at the electrolyte/oxidized-nanowire interface rendered a complex device current response which complicated the interpretation of the results.

  • 6. Honarvar, Hadis
    et al.
    Jokilaakso, Nima
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Andersson, Karl
    Malmberg, Jennie
    Rosik, Daniel
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Orlova, Anna
    Eriksson Karlström, Amelie
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Tolmachev, Vladimir
    Järver, Peter
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Evaluation of backbone-cyclized HER2-binding 2-helix Affibody molecule for In Vivo molecular imaging2013In: Nuclear Medicine and Biology, ISSN 0969-8051, E-ISSN 1872-9614, Vol. 40, no 3, p. 378-386Article in journal (Refereed)
    Abstract [en]

    Introduction: Affibody molecules, small scaffold proteins, have demonstrated an appreciable potential as imaging probes. Affibody molecules are composed of three alpha-helices. Helices 1 and 2 are involved in molecular recognition, while helix 3 provides stability. The size of Affibody molecules can be reduced by omitting the third alpha-helix and cross-linking the two remaining, providing a smaller molecule with better extravasation and quicker clearance of unbound tracer. The goal of this study was to develop a novel 2-helix Affibody molecule based on backbone cyclization by native chemical ligation (NCL). Methods: The HER2-targeting NCL-cyclized Affibody molecule Z(HER2:342min) has been designed, synthesized and site-specifically conjugated with a DOTA chelator. DOTA-Z(HER2:342min) was labeled with In-111 and (68) Ga. The binding affinity of DOTA-Z(HER2:342min) was evaluated in vitro. The targeting properties of In-111- and (68) Ga-DOTA-Z(HER2:342min) were evaluated in mice bearing SKOV-3 xenografts and compared with the properties of In-111- and (68) Ga-labeled PEP09239, a DOTA-conjugated 2-helix Affibody analogue cyclized by a homocysteine disulfide bridge. Results: The dissociation constant (K-D) for DOTA-Z(HER2:342min) binding to HER2 was 18 nM according to SPR measurements. DOTA-Z(HER2:342min) was labeled with In-111 and (68) Ga. Both conjugates demonstrated bi-phasic binding kinetics to HER2-expressing cells, with K-D1 in low nanbmolar range. Both variants demonstrated specific uptake in HER2-expressing xenografts. Tumor-to-blood ratios at 2 h p.i. were 6.1 +/- 1.3 for In-111-DOTA-Z(HER2:342min) and 4.6 +/- 0.7 for (68) Ga-DOTA-Z(HER2:342min). However, the uptake of DOTA-Z(HER2:342min) in lung, liver and spleen was appreciably higher than the uptake of PEP09239-based counterparts. Conclusions: Native chemical ligation enables production of a backbone-cyclized HER2-binding 2-helix Affibody molecule (Z(HER2:342min)) with low nanomolar target affinity and specific tumor uptake.

  • 7.
    Jokilaakso, Nima
    KTH, School of Biotechnology (BIO), Protein Technology.
    A Biotechnology Perspective on Silicon Nanowire FETs for Biosensor Applications2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The study of silicon nanowire-FET-based electronic biosensor applications is an emerging scientific field. These biosensors have the benefit of being theoretically extremely sensitive and reports of down to femtomolar (fM) levels of biomolecule detection have been reported. This thesis is written from a biotechnological perspective on the development of a silicon nanowire-FET biosensor. The thesis project was oriented towards developing a novel affinity-based silicon nanowire-FET biosensor based on small (2-3 nm) protein affinity-binders denoted Affibody molecules. The hypothesis was that a smaller biological detector element would reduce the effect of Debye screening of the charged biomarker. This hypothesis was neither proved nor disproved, and a substantial amount of time and effort was spent on improving the function of the different biosensor components. In paper I, a study on the effect of the redox state and pH at solvent-to-surface interfaces of the reference gate electrodes was done by using solutions with alternating pH and varying ratios of the Fe(CN)63-/ Fe(CN)64- redox pair. These experiments showed that the selection of reference gate electrode has major implications on the signal readout in terms of false response and current instability. While a current drop due to potential change on the surface of a platinum reference electrode was observed, no such thing was observed using a silver/silver chloride reference gate electrode. The conclusion is that it is critical for performance to use a reference gate electrode that has a stable electrode potential such as silver/silver chloride. In paper II, a discovery was made when intending to use nanowire joule heating to lyse HT-29 and MCF-7 cells. Using fringing electric fields irreversible electroporation of a cell on top of a nanowire was achieved at 600-1200 mVpeak-to-peak at 10 MHz for 2 ms. The process was monitored using a 3,3´-dihexyloxacarbocyanine iodide (DiOC6(3)) and Propidium Iodide (PI) live-dead dye kit. The nanowire-mediated electroporation method releases the cell content without the risk of heat denaturation and it is ultra-localized. To address the concern on how to control and monitor organosilane monolayer formation in the surface functionalization of silicon nanowires, a microwave-assisted method was evaluated in paper III. Using ellipsometry, AFM, ATR-FTIR and fluorescence scanning it was shown that less than 10 minutes of incubation in 1% (v/v) APTES in toluene at 75⁰C is needed for formation of a 0.7 nm monolayer. In paper IV, surface functionalization was further explored by using microdispensing of solutions of capture probes for localized functionalization of individual devices for a multiplexed silicon nanowire-FET biosensor application. Besides showing by fluorescent scanning that oligonucleotide or protein spots of ~ 100 μm diameters could be deposited on individual silicon nanowires, the functionalization chemistry was validated by using the same protocol for immobilization of the Z domain from Staphylococcus aureus Protein A (SpA) on silicon dioxide-coated SPR sensor chips, followed by real-time detection of the binding of immunoglobulin G. The immunoglobulins as affinity-binders have a drawback due to large size and the importance of having the binding event near the device in silicon nanowire-FET biosensor due to the effect of Debye screening. In paper V, in an effort to further minimize the size of affinity-binders of potential value as capture probes in silicon nanowire-FET applications, a backbone-cyclized, minimized 2-helix affibody-molecule (ZHER2:342min) was designed and produced by Solid Phase Peptide Synthesis(SPPS). The 2-helix affibody-molecule was evaluated for in vivo molecular imaging of HER2-expressing tumours, which was demonstrated in mice carrying SKOV-3 xenografts.

  • 8.
    Jokilaakso, Nima
    et al.
    KTH, School of Biotechnology (BIO), Protein Technology.
    Afrasiabi, Roodabeh
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Larsson, Andréas
    KTH, School of Biotechnology (BIO), Protein Technology.
    Björk, Per
    ACREO Swedish ICT.
    Schönberg, Tommy
    ACREO Swedish ICT.
    Linnros, Jan
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Eriksson Karlström, Amelie
    KTH, School of Biotechnology (BIO), Protein Technology.
    Spot-on functionalization of SiO2 for multiplexed silicon nanowire-FET biosensorsManuscript (preprint) (Other academic)
  • 9.
    Jokilaakso, Nima
    et al.
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Salm, Eric
    Chen, Aaron
    Millet, Larry
    Guevara, Carlos Duarte
    Dorvel, Brian
    Reddy, Bobby, Jr.
    Eriksson Karlström, Amelie
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Chen, Yu
    Ji, Hongmiao
    Sooryakumar, Ratnasingham
    Bashir, Rashid
    Ultra-localized single cell electroporation using silicon nanowires2013In: Lab on a Chip, ISSN 1473-0197, E-ISSN 1473-0189, Vol. 13, no 3, p. 336-339Article in journal (Refereed)
    Abstract [en]

    Analysis of cell-to-cell variation can further the understanding of intracellular processes and the role of individual cell function within a larger cell population. The ability to precisely lyse single cells can be used to release cellular components to resolve cellular heterogeneity that might be obscured when whole populations are examined. We report a method to position and lyse individual cells on silicon nanowire and nanoribbon biological field effect transistors. In this study, HT-29 cancer cells were positioned on top of transistors by manipulating magnetic beads using external magnetic fields. Ultra-rapid cell lysis was subsequently performed by applying 600-900 mV(pp) at 10 MHz for as little as 2 ms across the transistor channel and the bulk substrate. We show that the fringing electric field at the device surface disrupts the cell membrane, leading to lysis from irreversible electroporation. This methodology allows rapid and simple single cell lysis and analysis with potential applications in medical diagnostics, proteome analysis and developmental biology studies.

  • 10. Salm, E.
    et al.
    Duarte, C.
    Jokilaakso, Nima
    KTH, School of Biotechnology (BIO), Molecular Biotechnology (closed 20130101).
    Bashir, R.
    Integrated 'lab-on-a-transistor': With droplets-in-air for parallel nanoliter reactions2012In: Proceedings of the 16th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2012, Chemical and Biological Microsystems Society , 2012, p. 1945-1947Conference paper (Refereed)
    Abstract [en]

    We aim to take 'lab-on-chip' technology further by introducing the concept of a 'lab-on-transistor'. In this methodology, laboratory operations, such as heating, cell lysis, and detection, are performed on a single transistor instead of on an entire microchip. To demonstrate this concept, we developed a heating technique that allows transistors to act as electrically addressable, individual heating units. We have coupled the transistor heaters with placement of sub-nanoliter droplets to create individual heated reaction volumes. Under this configuration transistors become highly localized heater/sensors capable of high-speed thermocycling (>25°C/s) of <1nL reactions with potential for electrical detection of biological analytes.

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