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S5 took place by deposition of the aminoalkyl SAM from the gas phase (Scheme 2.4). Theremaining PMMA was stripped and the complementary areas were passivated with 2-[Methoxy(polyethyleneoxy)propyl] trimethoxysilane (referred as PEG silane) in distilled toluenefor 2 hours, Scheme 2.6. The substrates were later copiously rinsed with toluene followed withethanol and dried with a stream of N2.Then the -CD SAM was assembled as described inthe previous section. Protein immobilization on patterned surfacesWe deposited a drop of adamantyl modified protein aggregates (25 µl, 0.4µM) in an aqueous buffered solution (20 mM HEPES, pH 8.0, 0.03 wt % -DDM (n-dodecyl- -D-maltoside), 1mM AdHEG) onto the substrate which was previously treated with AdHEG( 25 µl, 1 mM) for 10 minutes. A 20 minute incubation of the protein solution was donein a humid environment. The sample was then rinsed with buffer. The concentration ofprotein was optimized in a dilution experiment. The protein concentration in the dropvolume was chosen to be sufficient to cover the active area below the hemispherical drop. Atomic force characterizationA custom-built stand-alone AFM combined with a confocal fluorescent (spectral)microscope was used for morphological and optical characterization.7For AFM imaging standard silicon nitride cantilevers with a length of 85 µm, force constant of 0.5 N/m, and operating frequencies of 25–35 kHz (in liquid) (ThermoMicroscopes, Sunnyvale, CA)were used. AFM images were obtained using tapping mode in liquid (10 mM TRIS-HCl,150mM KCl). Images contained 256x256 or 512x512 pixels and were recorded at a linescanning frequency of 2–4 Hz. Topographical images were quantitatively analyzed usingthe Scanning Probe Image Processor (SPIP) software (Image Metrology ApS, Lyngby,