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S3 Protein labelingProtein aggregates in an aqueous buffered solution (20 mM HEPES, pH 8.0, 0.03 % -DDM (n-dodecyl- -D-maltoside)) were mixed at 1:20 molar equivalent with the AdI inDMSO. The total concentration of DSMO in the solution is < 1,3 % to prevent disruption of the complexes. The mixture was incubated overnight at +4°C under rotation at 2 rpm.Labeled protein was purified by desalting and was collected in the initial buffer. -CD layer formation onto non-patterned substratesSubstrates (microscope coverslips, Menzel-glaser # 1) were cleaned by immersion in piranha solution (3:1 concentrated H2SO4/ 33% aqueous H2O2) for 15 min, rinsed copiously with water and dried with N2. Warning: Piranha solution should be handledwith care.N-[3-(trimethoxysilyl)propyl]ethylenediamine] SAM formation wasperformed by gas-phase evaporation in a desiccator under vacuum overnight, rinsed withethanol and dried with N2. Transformation of the amine-terminated SAMs to isothiocyanate-terminated layers was accomplished by exposure to a 0.1 M solution of1,4-phenylenediisothiocyanate in toluene at 50 °C for 2 h under N2, followed by rinsing with toluene and drying with N2. -CD-terminated SAMs were obtained by reaction ofthe isothiocyanate-terminated monolayers with a 1mM solution of CD-heptamine in Millipore water (pH 8.5) at 50 °C for 2 h. The substrates were briefly sonicated inMillipore water, rinsed with Millipore water and gently dried in a stream of N2.Patterned surfaces CD-Fluoralkyl/PEG.
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S4 Chemically patterned amino-terminated/PEG surfaces were prepared as before.5Weused silicon ridges 40 nm with a period of 4 µm as hard stamp (similar to reference6). These dimensions are compatible with thesub-micrometer resolution of far field opticalmicroscopy used for optical characterization.Scheme 2. Representation of the different steps for the fabrication of the Chemically patterned surfaces ( -CD/PEG) by nanoimprint lithographyIn short, (Scheme 2), substrates (microscope coverslips, Menzel-glaser # 1) were cleaned byimmersion in piranha solution (3:1 concentrated H2SO4/ 33% aqueous H2O2) for 15 min, rinsedwith water and dried with N2.Warning: Piranha solution should be handled with care.Then they were coated with a 90 nm thick layer of PMMA (20 g/L) by spin coating. Stamp andsubstrate were put in contact; a pressure of 40 bars was applied at a temperature of 180 °C using ahydraulic press (Specac), separation was performed at 110 °C. After imprinting, the residual layerwas removed by physical etching during approximately 20 seconds in oxygen plasma (RIE-Elektrotech, 20 W, 10 mT, 10 sccm O2). In this step, the polymer-free areas lateral dimension isincreased in width, relative to that of the NIL stamp, since in the process the side walls ofthe polymer barrier are also slightly etched away.Subsequently, activation of the surface1. PMMA coating2. Hot embossing –removal of the stamp3. Residual layeretching6. Second silanation -passivation5. PMMA removal4. First silanation 7. Formation of the-CD SAMStampGlassPMMA