Nanoscope software

Sso10a-DNA complexes were formed by incubating 100 ng of nicked pRD24 with varying amounts of Sso10a proteins in 10 μl AFM buffer [40 mM Hepes (pH 7.5) and 25 mM NaCl] for 10 min at room temperature (~23 °C). After incubation, this mixture was diluted 10-fold in 1 mM MgCl₂ and directly deposited onto freshly cleaved mica. After 40 s, the mica disc was rinsed with HPLC water and dried with nitrogen gas. The AFM images were collected on a NanoScopeIII AFM (Digital Instruments, Santa Barbara, CA) using micro cantilevers (Olympus MCL-AC240TS-W2, resonance frequency 70 kHz, spring constant 2 N/m). Images were obtained using tapping mode in air at 2 Hz and flattened using Nanoscope software (Veeco Instruments).

An AFM microscope with a scanning SPM probe of the NanoScope MultiMode type (Veeco Metrology, Inc., Santa Barbara, CA, USA) was used to obtain surface images of the obtained materials. Nanoscope software (Veeco Metrology, Inc. Santa Barbara, CA, USA) was applied to establish the roughness parameters, such as the root mean square (R_q) and arithmetical mean deviation of the assessed profile (R_a).

Peptide solutions were characterized using a Nano-Scope IIIa scanning probe work station equipped with a MultiMode head using a vertical engage E-series piezoceramic scanner (Veeco, Santa Barbara, CA). AFM probes were single-crystal silicon microcantilevers with 300-kHz resonant frequency and 42 Newton/meter spring constant model OMCL-AC160TS-W2 (Olympus). A 10μl of 0.1M NaOH was spotted onto mica, rinsed with 2 drops of deionized H₂O, then a 10-μl sample solution of PrP_106-126 or PrP-FL (From a 20μM stock solution) were spotted on freshly cleaved mica, incubated at room temperature for 3 minutes, rinsed with 20μl of filtered (Whatman Anotop 10) MilliQ water (Millipore), and blown dry with tetrafluoroethane (CleanTex MicroDuster III). Image data were acquired at scan rates between 1 and 2 Hz with drive amplitude and contact force kept to a minimum. Data were processed to remove vertical offset between scan lines by applying zero order flattening polynomials using Nanoscope software (Version 5.31r1,Veeco).

AFM imaging was performed in atomic force microscopy tapping mode with a Veeco multimode scanning probe microscope (Bruker, USA). The images were scanned using silicon cantilevers (NCH-VS1-W, Nanoworld, Switzerland) with a resonance frequency of 320 kHz and a force constant of 42 N·m⁻¹. All images were processed using Nanoscope software package (V7.30r1sr3, Veeco).
The roughness layer thickness RLT^AFM is evaluated from the topography images measured by AFM, compare Figure 2. The roughness layer is the region of the cellulose film where both, material and ambient medium (water or air) are found, i.e., the region containing the boundary between cellulose film and surrounding. The thickness of this region depends on the roughness of the film. We have defined the roughness layer as the z-directional layer containing 95% of the surface roughness. For calculation, the histogram of the topography distribution is evaluated. From each edge of the histogram, 2.5% of the topography values are clipped off, the topography range comprising the remaining 95% of height values is defined as the roughness layer thickness. We are not using 100% of the values because the topography distribution is close to normally distributed which means there are always some far outliers which would bloat the roughness layer beyond the true surface interaction range.

Surface morphology and roughness of the films on Si, glass, Cu, Ni and Al were determined on a Veeco Multimode Quadrax MM scanning probe microscope (Bruker, Billerica, MA, USA) using Si cantilevers (NCH-VS1-W from NanoWorld AG, Neuchatel, Switzerland) with a resonance frequency of 320 kHz and a force constant of 42 N·m⁻¹. On the polymer substrates, the films were analyzed using a FastScanBio AFM using a FastScan-A cantilever (both from Bruker NANO) with typical resonance frequencies and force constants around 1.4 MHz and 18 N·m⁻¹, respectively. All samples were analyzed in tapping mode in an ambient atmosphere at room temperature at the lowest possible force load and scan rates were adapted to obtain reliable surface data. Root mean square (RMS; R_q) roughness calculation and image processing was performed with the Nanoscope software (V7.30r1sr3, Veeco, Plainview, NY, USA).

The surface pictures of the PLA-based films were obtained by means of an AFM microscope with a scanning probe of the NanoScope MultiMode type (Veeco Metrology, Inc., Santa Barbara, CA, USA). Analyses were performed in the tapping mode, in air, at room temperature. Using a scan area of 5 × 5 µm and Nanoscope software (Veeco Metrology, Inc. Santa Barbara, CA, USA), the roughness parameters such as the root mean square (R_q) and arithmetical mean deviation of the assessed profile (R_a) were calculated.