Biomolecular Detection Device
20220397573 · 2022-12-15
Inventors
- Yves Lukas Blickenstorfer (Zurich, CH)
- Christof Fattinger (Basel, CH)
- Andreas Frutiger (Zurich, CH)
- Andreas Michael Reichmuth (Zurich, CH)
- Janos Voeroes (Zurich, CH)
Cpc classification
G01N33/543
PHYSICS
G01N33/54373
PHYSICS
International classification
Abstract
Disclosed herein is a biomolecular detection device (1) for analyzing a cell, vesicle or a cellular or vesicular component, comprising an evanescent illuminator with an optical coupling unit configured for generating an evanescent field from coherent light (L) with a predefined wavelength on a first surface of the evanescent illuminator. The first surface of evanescent illuminator comprises a template nanopattern (5), containing a coherent arrangement of a plurality of predetermined lines along which membrane recognition elements for a binder structure (82) of a transmembrane protein (81), preferably a laterally diffusible transmembrane protein, of the cell, vesicle or the cellular or vesicular component (8) are arranged. The membrane recognition elements (53) are configured to bind the binder structure (82) of the transmembrane protein (81) for forming a transmembrane nanopattern within the cell, vesicle or the cellular or vesicular component (8) based on the template nanopattern (5) of the evanescent illuminator, such that light of the evanescent field is scattered by the cell, vesicle or the cellular or vesicular component (8) bound to the membrane recognition elements (53). The predetermined lines are arranged such that light scattered by the cell, vesicle or cellular or vesicular components (8) bound to the membrane recognition elements (53) constructively interferes at a predefined detection site (7) with a difference in optical path length that is an integer multiple of the predefined wavelength of the coherent light (L).
Claims
1. A biomolecular detection device for analyzing a cell, vesicle, or a cellular or vesicular component, comprising an evanescent illuminator with an optical coupling unit configured for generating an evanescent field from coherent light (L) with a predefined wavelength on a first surface of the evanescent illuminator, the first surface of the evanescent illuminator comprising a template nanopattern, containing a coherent arrangement of a plurality of predetermined lines along which membrane recognition elements for a binder structure of a transmembrane protein of the cell, vesicle, or the cellular or vesicular component are arranged, wherein the membrane recognition elements are configured to bind the binder structure of the transmembrane protein for forming a transmembrane nanopattern within the cell, vesicle, or the cellular or vesicular component based on the template nanopattern of the evanescent illuminator, such that light of the evanescent field is scattered by the cell, vesicle, or the cellular or vesicular component bound to the membrane recognition elements, and wherein the predetermined lines are arranged such that light scattered by the cell, vesicle or cellular or vesicular components bound to the membrane recognition elements constructively interferes at a predefined detection site with a difference in optical path length that is an integer multiple of the predefined wavelength of the coherent light (L).
2. The biomolecular detection device according to claim 1, wherein the evanescent illuminator comprises a carrier with a planar waveguide arranged on a surface of the carrier and an optical coupler as the optical coupling unit for coupling coherent light (L) of a predefined wavelength into the waveguide such that the coherent light propagates through the planar waveguide with an evanescent field of the coherent light (L) propagating along a first surface of the planar waveguide and wherein the first surface of the planar waveguide comprising the template nanopattern.
3. The biomolecular detection device according to claim 1, wherein the evanescent illuminator is a total internal reflection system configured for providing a beam of coherent light (L) at the predetermined wavelength and at a predetermined angle onto the first surface of the evanescent illuminator by means of the optical coupling unit, optionally by a prism.
4. The biomolecular detection device according to claim 1, wherein the membrane recognition elements are antibodies being specific to at least the binder structure of the transmembrane protein, or wherein the membrane recognition elements contain an electrophile moiety for establishing a covalent bond with the binder structure of the transmembrane protein.
5. The biomolecular detection device according to claim 1, wherein the plurality of predetermined lines comprises curved lines with a curvature configured such that light of the evanescent field scattered by the cell, vesicle, or the cellular or vesicular component bound to the membrane recognition elements interferes at the predefined detection site.
6. The biomolecular detection device according to claim 1, wherein the first surface of the evanescent illuminator comprises a cell adhesive.
7. The biomolecular detection device according to claim 1, wherein at least one cell, vesicle, or cellular or vesicular component is bound via the binder structure of the transmembrane protein to the membrane recognition elements.
8. The biomolecular detection device according to claim 1, wherein the predetermined lines are separated from each other by areas devoid of membrane recognition elements and wherein the areas devoid of membrane recognition elements are configured to inverse an optical modulation, which is induced by the binding of a structural recognition element to the binder structure of the transmembrane protein, such that the signal obtained from binding of the structural recognition element to the binder structure of the transmembrane protein is provided in a different operating window of the biomolecular detection device, wherein the different operating window is at an intensity close to zero.
9. (canceled)
10. A method of detecting molecular interactions associated with cells, vesicles, or cellular or vesicular components, comprising: providing the biomolecular detection device according to claim 1; applying a cell or vesicle to the membrane recognition elements, wherein the cell or the vesicle comprises a membrane and at least one transmembrane protein with an extracellular or extravesicular binder structure, optionally where at least one transmembrane protein is laterally diffused along the membrane; aligning the al least one transmembrane protein of the cell or the vesicle according to the template nanopattern of the first surface of the evanescent illuminator, such that a transmembrane nanopattern is formed in the membrane of the cell or the vesicle, wherein the transmembrane pattern corresponds at least partially to the template nanopattern of the first surface of the evanescent illuminator; generating a beam of coherent light at a predefined beam generation location relative to the plurality of predetermined lines, the beam of coherent light having a predefined wavelength and being incident on the membrane recognition elements with the bound transmembrane protein in a manner that diffracted portions of the incident beam of coherent light constructively interfere at the predefined detection site relative to the plurality of predetermined lines with a difference in optical path length that is an integer multiple of the predefined wavelength of the coherent light to provide a signal representative of the membrane recognition elements with the transmembrane protein of a cell, vesicle, or cellular or vesicular component bound thereto at the predefined detection site; and measuring the signal representative for the membrane recognition elements with the transmembrane protein of a cell, vesicle, or cellular or vesicular component bound thereto.
11. The method according to claim 10, further comprising the step of comparing the measured signal representative of the membrane recognition elements with the transmembrane of a cell, vesicle, or cellular or vesicular component bound thereto, with an unbound signal representative of only the membrane recognition elements.
12. The method of claim 10, wherein a cell is applied to the membrane recognition elements and wherein before generating the beam of coherent light the cell is modified such that only parts of the cell membrane remain on the biomolecular detection device.
13. The method according to claim 10, wherein the binder structure of the transmembrane protein is specific to an antibody being arranged along the predefined lines of the evanescent illuminator of the biomolecular detection device.
14. The method according to claim 10, wherein a protein of interest of the biomolecular interaction comprises a high-mass moiety.
15. The method according to claim 10, wherein additionally, optionally simultaneously, a fluorescent and/or bioluminescent signal is recorded.
16. A method for generating a transmembrane nanopattern within a cell, vesicle, or cellular or vesicular component, the method comprising: providing the biomolecular detection device according to claim 1; applying a cell or a vesicle is applied to the membrane recognition elements, wherein the cell or the vesicle comprises a membrane and at least one transmembrane protein with an extracellular or extravascular binder structure; optionally laterally diffusing at least one transmembrane protein along the membrane; and binding the extracellular binding structure of the at least one transmembrane protein to any of the membrane recognition elements and aligning the at least one transmembrane protein according to the template nanopattern of the first surface of the evanescent illuminator, such that a transmembrane nanopattern is formed in the membrane of the cell or the vesicle, wherein the transmembrane pattern corresponds at least partially to the template nanopattern of the first surface of the evanescent illuminator.
17. The method according to claim 16, wherein the binder structure of the transmembrane protein is specific to an antibody being arranged along the predefined lines of the evanescent illuminator of the biomolecular detection device.
18. The method according to claim 12, wherein after aligning the transmembrane protein and forming of the transmembrane nanopattern, the cell is modified such that only parts of the cell membrane remain on the biomolecular detection device.
Description
BRIEF DESCRIPTION OF THE FIGURES
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DESCRIPTION
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Example
Methods and Materials
[0154] Cell culture medium DMEM High Glucose (4.5 g/l) with L-Glutamine (BioConcept, Switzerland), Lipofectamine® 2000, Opti-MEM® I (1×) Versene 1:5000 (1×), hank's balanced salt solution (HBSS), Zeozin™ was purchased from Life Technologies Europe (Zug, Switzerland). HEPES was from GERBU Biotechnik GmbH (Heidelberg, Germany), Fetal Bovine Serum (FBS) was purchased from Sigma-Aldrich Chemie GmbH (Buchs SG, Switzerland). G418 was from InvivoGen (San Diego, USA), Tissue Culture Flasks from VWR International GmbH (Dietikon, Switzerland), Biofil® Tissue culture plate 24 wells were from Axon Lab AG (Baden-Dättwil, Switzerland). Corning Costar sterile black 96 well plates, clear bottom, TC treated, Poly-D-Lysine coated were from Vitaris AG (Baar, Switzerland), Custom coated CulturPlate-96, White Opaque 96-well Microplate, Sterile and Tissue Culture Treated and ViewPlate-96, White 96-well Microplate with Clear Bottom, Sterile and Tissue Culture Treated were from Perkin Elmer (Schwerzenbach, Switzerland). TPP 6-well tissue culture plates were from Faust Laborbedarf AG (Schaffhausen, Switzerland) Coelenterazine 400a, Deep Blue C (DBC) was purchased from Cayman Chemical (Ann Arbor, Mich., United States). The GRGDSPGSC-(DBCO) peptide was custom synthesized by LifeTein, LLC (Somerset, N.J., USA). BG-GLA-NHS was obtained from BioConcept Ltd. (Alschwil, Switzerland). Azido-PEG4-NHS was obtained from Jena Bioscience (Jena, Germany). The PAA-g-PEG-NH-PhSNPPOC copolymer, used as a biocompatible coating, was provided by SuSoS. Isoproterenol hydrochloride and formoterol hemifumarate was purchased from Tocris Bioscience (Bristol, UK). ICI 118,551 hydrochloride, Fluorescein-O′-acetic acid and all other chemicals were purchased from Sigma-Aldrich Chemie GmbH (Buchs SG, Switzerland). Thin-film optical waveguides with a 145 nm Ta.sub.2O.sub.5 layer were obtained from Zeptosens with the in and out coupling gratings covered with a 1 μm thick layer of SiO.sub.2 by IMT Masken and Teilungen AG (Greifensee, Switzerland).
Expression Constructs
[0155] Beta-Arrestin 2-mPlum: mPlum coding sequence was amplified by PCR (Phusion polymerase, Finnzymes) and transferred to a pcDNA3 expression vector containing the beta-arrestin2 coding sequence.
[0156] Beta-Arrestin 2-GFP: Beta-arrestin 2 coding sequence was amplified by PCR (Phusion polymerase, Finnzymes) and transferred to a pEGFP (Clonetech) expression vector.
Cell Lines and Cell Culture
[0157] A HEK293 cell line stably expressing the SNAP-beta2-adrenergic receptor (referred to as SNAP-β2AR) was purchased from Cisbio (Codolet, France). HEK293 stably overexpressing All HEK293 cells were cultured in DMEM supplemented with 10%-v/v fetal bovine serum and 600 μg/ml G418 with 5% CO2 at 37° C.
Preparation of Sensor Chips
[0158] Thin-film optical waveguides were treated with a similar protocol as reported previously (Nat. Nanotechnology 2017, DOI: 10.1038/NNANO.2017.168). In short, waveguides were washed with 0.1% aqueous Tween 20, followed by ultrasound assisted washing in MilliQ water, Isopropanol and Toluene. The chips were then soaked in warm Hellmanex III for 1 min, thoroughly rinsed with MilliQ water and cleaned with highly oxidizing Piranha solution (H.sub.2SO.sub.4/H.sub.2O.sub.2 7:3) for 30 min. After excessive washing with MilliQ water, the chips were centrifuge dried at 800 rcf for 2 min and activated by oxygen plasma. After plasma treatment, the chips were immediately immersed in the PAA-g-PEG-NH-PhSNPPOC graft copolymer coating solution (0.1 mg/ml in 1 mM HEPES pH 7.4) for 60 min. To fully passivate the layer, the chips were washed with MilliQ water and ethanol and immersed in a 25 mM solution of methyl chloroformate in anhydrous acetonitrile containing 2 equiv. of N,N-diisopropylethylamine for 5 min. The coated chips were washed with ethanol and MilliQ water, and blow dried by a nitrogen jet. Prepared sensor chips were stored in the dark at 4° C. until further use.
Preparation of Template Nanopatterns
[0159] Template nanopatterns were prepared according to the standard reactive immersion lithography (RIL) process described (Nat. Nanotechnology 2017, DOI: 10.1038/NNANO.2017.168). Briefly, a copolymer-coated sensor chip was placed in a custom holder. The phasemask used to generate the nanopattern was aligned using an alignment help and the gap between the chip and phase mask was filled with a solution of 0.1%-v/v Hydroxyl amine in DMSO. The photolithographic exposure was conducted at 405 nm with a dose of 2000 mJ/cm.sup.2 in a custom-built setup. After illumination the chip was washed with isopropanol and MilliQ water and the activated ridges were functionalized with 1 mM amine reactive SNAP-tag substrate (BG-GLA-NHS), which is covalently bound by the SNAP-tag protein. In order to increase cell adhesion to the chip, remaining PhSNPPOC groups were removed by flood exposure. The free binding sites were then functionalized with the hetero biofunctional crosslinker azido-PEG4-NHS. Finally, the chip was incubated with an azide reactive aqueous solution of 0.5 mM GRGDSPGSC-(DBCO) overnight, washed with isopropanol and MilliQ water and dried with a jet of nitrogen.
Cell Measurements
[0160] SNAP-β.sub.2AR cells were grown to 60-80% confluency in T25 culture flasks, washed twice with warm phosphate-buffered saline (PBS), incubated with 1× Versene for 5 min and resuspended in cell culture medium. In order to decrease baseline signal contributions from non-functional cellular debris, the cells were centrifuged at 50 rpm for 1 min and resuspended in culture media two times sequentially. The cells were seeded to reach confluency on the waveguide in an incubation chamber containing 500 μl cell culture media. Cells were only seeded when viability exceeded 90%, as determined by a Countess automated cell counter (Invitrogen). Except for the real-time establishment of the transmembrane nanopattern, seeded cells were kept in a CO.sub.2 incubator at 37° C. for 2 h to allow cells adherence to the sensor chip (and covalent interaction of the SNAP-tag on the β.sub.2AR with the SNAP-tag substrate on the chip). The incubation chamber containing the cells was then washed twice with warm HBSS buffer (supplemented with 20 mM HEPES, pH 7.4) adjusted for DMSO and transferred to a modified F3000 ZeptoReader (Zeptosens) which was kept at 35° C. The biomolecular detection device was then allowed to temperature equilibrate inside the ZeptoReader for 5-10 min before performing the assay. For all assays, the signal was monitored for 7 min (baseline measurement) before careful substitution of the buffer with buffer containing the β.sub.2AR ligand and monitored for another 21 min thereafter. For the real-time establishment of the transmembrane nanopattern experiment, the measurement was performed in cell culture media supplemented with 20 mM HEPES, pH 7.4. Once the nanopattern was established, the culture media was carefully exchanged with HBSS buffer (supplemented with 20 mM HEPES, pH 7.4).
[0161] Typical instrument parameters for signal acquisition were as follows: one image every 10 s using the 635 nm laser with an integration time of 0.25-1 s depending on the intensity of the initial signal and a grey filter value of 0.001 in the illumination path of the ZeptoReader.
Data Analysis
[0162] For all assays, the square root of the raw signal was taken. The baseline was then fitted linearly and used to de-trend the signal. Data was then displayed as a fractional change compared to baseline.
[0163] For the BRET arrestin recruitment assay the concentration-response curves with area under the curve (AUC) vs. ligand concentrations were fitted using the nonlinear regression “log(inhibitor) vs. response (three parameters)” in Graph Pad Prism to calculate the pIC50 values.