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Nanoscope iiia controller

Manufactured by Bruker
Sourced in Germany, United States

The Nanoscope IIIa controller is a versatile instrument designed for scanning probe microscopy applications. It provides the necessary control and data acquisition capabilities to operate atomic force microscopes (AFMs) and other scanning probe techniques. The Nanoscope IIIa controller is a core component of Bruker's scanning probe microscopy systems, enabling high-resolution imaging and analysis of a wide range of materials and surfaces.

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17 protocols using nanoscope iiia controller

1

Atomic Force Microscopy Imaging Protocol

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Atomic force microscopy (AFM) images were obtained using a Bioscope AFM (Bruker, Inc.) with NanoScope III A controller. Silicon cantilevers (MikroMasch, Inc., NSC15/Si3N4/AIBS/50) were used as probes for the tapping mode measurements. AFM images were taken with 256 × 256 pixel resolution over areas of 1–10,000 μm2 at scan rates of 0.25–1.0 Hz.
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2

Amyloid-β Aggregation Inhibition

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Compounds 2, 5, 11, and 12 were
dissolved in DMSO at concentrations ranging from 2.0 mg/mL to 3.3
mg/mL. Aβ42 (Bachem) was dissolved in TFA to obtain
a 1 mg/mL stock solution. In each experiment, appropriate peptide
aliquots were deposited in glass vials and dried under a gentle nitrogen
stream. Aggregation was initiated by hydrating the peptide with PBS
premixed with the compound under study. The final compound and peptide
concentrations were 100 μM and 50 μM, respectively. In
the control samples, PBS was premixed with DMSO volumes equivalent
to those present in the compound aliquots employed for the experiments.
Aggregation was performed at room temperature.
For AFM inspection,
sample aliquots of 20 μL were deposited on a freshly cleaved
mica surface and incubated for 7 min. Samples were then gently rinsed
with Milli-Q water and dried overnight under mild vacuum. Tapping
mode AFM images were acquired in air using a Dimension 3100 SPM (Bruker,
Karlsruhe, Germany) equipped with “G” scanning head
(maximum scan size 100 μm) and driven by a Nanoscope IIIa controller
(Bruker). Single-beam uncoated silicon cantilevers (type TESPA_V2,
Bruker) were used. The drive frequency was 300–320 kHz, and
the scan rate was 0.5 Hz.
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3

Nanoparticle Morphological Analysis by AFM

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The morphological analysis of nanoparticles was performed on a Bruker Dimension 3100 atomic force microscope (AFM), equipped with a Nanoscope IIIa controller (Bruker, Karlsruhe, Germany). Before the analysis, 5 µL of NPs suspension (0.25 mg/mL) was transferred onto a clean glass slide and air dried. Images of NPs were then obtained in intermittent contact mode (Tapping Mode) with n-type silicon cantilevers (HQ:NSC14/Al BS, nominal tip radius <10 nm, typical resonance frequency of about 160 kHz, nominal spring constant of 5 N/m; manufactured by µmash, Sofia, Bulgaria) 2% below resonance frequency at a root mean square (RMS) amplitude of around 2 Volts. Further data analysis was carried out using NanoScope Analysis version 1.5 (Bruker, Billerica, MA, USA).
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4

Characterization of Polycation/miRNA Complexes

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1H NMR spectra were measured on a Bruker ARX 400 MHz spectrometer using DMSO-d6 (for TA-Br), CDCl3 (for TA-PGMA) and D2O (for TP, TP-E, and TP-ColIV) as the solvents with tetramethylsilane (Me4Si) as an internal standard. Thermogravimetric analysis measurement of TA-Br-Gd was performed on a Thermal Gravimetric Analyzer (TG 209, NETZSCH). GPC measurement of TA-PGMA was performed on a Waters GPC system with DMSO as the eluent. The concentrations of Gd3+ in TP and TP-Gd were investigated using inductively coupled plasma mass spectrometry (ICP-MS, Thermo Scientific iCAP 6000 series). The fluorescence intensities of rhodamine B modified ColIV and TP-ColIV-RhB were characterized using a fluorescence spectrophotometer (Hitachi F-7000). Dynamic light scattering (DLS) measurements of polycation/miRNA complexes were performed with a Zetasizer Nano ZS equipped with a laser of wavelength 633 nm at a 173° scattering angle (Malvern Instruments, Southborough, MA). Atomic force microscopy (AFM) studies were carried out with the Dimension Icon model with a Nanoscope IIIa controller (Bruker, Santa Barbara, CA), where samples were imaged using the ScanAsyst mode. Gel electrophoresis was implemented in a Sub-Cell system (Bio-Rad Laboratories), and then a UV transilluminator and BioDco-It imaging system (UVP Inc.) was employed to record miRNA bands.
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5

Tapping Mode Atomic Force Microscopy

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Experiments were performed using a multimode AFM equipped with a NanoScope IIIA controller (Bruker) operating in tapping mode; the NanoScope 5.30r2 software version was used. Si cantilevers (Bruker) were used with a force constant of 2.8 N/m and a resonance frequency of 75 kHz. The phase signal was set to 0 at a frequency 5 to 10% lower than the resonance one. Drive amplitude was 600 mV, and the amplitude set point Asp was 1.8 V. The ratio between the amplitude set point and the free amplitude (Asp/A0) was kept equal to 0.8.
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6

Atomic Force Microscopy Characterization of TDP-43 Aggregates

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Ct and FL TDP-43 were prepared and dialyzed as described above. After dialysis, a 20 μL aliquot of the whole sample (1.5 mg/mL) was deposited on freshly cleaved mica, incubated for 10 min, gently rinsed with MilliQ water and dried under mild vacuum. Diluted samples were also prepared by diluting 5 μL aliquots of the dialyzed sample (1.5 mg/mL) 100 and 1000 times. A 10 μL aliquot of each diluted sample was deposited and treated as described above. Tapping mode AFM images were acquired in air using a Dimension 3100 SPM (Bruker, Karlsruhe, Germany) equipped with “G” scanning head (maximum scan size 100 μm) and driven by a Nanoscope IIIa controller (Bruker), and a Multimode SPM (Bruker) equipped with “E” scanning head (maximum scan size 15 μm) and driven by a Nanoscope V controller (Bruker). Single beam uncoated silicon cantilevers (type OMCL-AC160TS, Olympus, Tokyo, Japan) were used. The drive frequency was 270-300 kHz and the scan rate was 0.3-0.7 Hz.
Aggregate heights and widths were measured from the cross section profiles of topographic AFM images. Sections were traced perpendicularly to the filament axis. The measured apparent widths were corrected for the tip-induced broadening in the image plane according to wmeasurement – wreal=22Rhh , where h is the measured object height and R is the AFM tip radius [32 (link)].
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7

Ferrlecit and Generic SFG Particle Characterization

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AFM was used to determine the size and particle morphology of Ferrlecit and generic SFG. Samples were diluted 1:20 using MilliQ water to reach a final concentration of 0.625 mg Fe per mL. 15 μL of the 1:20 solution was deposited onto a freshly cleaved mica disk (0.25 inch in diameter). After 30-s incubation, the mica surface was rinsed with water and dried by centrifugation. Each specimen was placed on the vacuum chuck of the Digital Instruments (Bruker Nano, Santa Barbara, CA, USA) NanoScope AFM system fitted with NanoScope IIIA Controller with Phase Extender Module and Dimension 3100 Large Sample AFM with type G Scanner. TappingMode™ was used to capture height and phase data types for 1 μm2 fields of view at a resolution of 512 × 512 pixels for images to be used for measurement. In three independent runs of specimen preparation and imaging for each lot, a total of 216 images were evaluated to analyze 2460 well-separated particles (950 for Ferrlecit lot #D2C283A, 534 for Ferrlecit lot #D2C593A, and 976 for generic SFG lot #132296.1) whose height could be readily measured.
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8

Atomic Force Microscopy of SAP Solutions

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SAP solutions were made at 1 mg/mL in sterile water, exposed to UV if indicated, and then diluted to 0.1 mg/ml in sterile water and placed in a sonicator bath for 30 min. Next, 50 μl of each solution was deposited onto freshly cleaved mica and allowed to adsorb to the surface for 5 min. Excess liquid was blotted from the mica using filter paper, and samples were stored at 4°C overnight to finish drying. Images were obtained using a Bruker multimode AFM with NanoScope IIIa controller. The AFM probe had a resonance frequency of 325 kHz and a force constant of 40 N/m (MikroMasch #HQ:NSC15/AL BS). Scanning was performed in tapping mode with a 2 Hz scan rate and 512 samples/line. AFM height images were corrected for low‐frequency noise and tilt by flattening them with NanoScope Analysis software v1.5 (Bruker).
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9

Multimode AFM Analysis of Earthworm

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An earthworm was taken from the artificial soil, rinsed, frozen using liquid nitrogen, and left in a lyophilizer for 24 hours. It was glued to a metal disc and analyzed using Multimode AFM with Nanoscope IIIa controller (Bruker) and vertical engagement (JV) 125 µm scanner in contact mode. Sharpened silicon-nitride tips were used (NP-S, Bruker, nom. freq. 16-28 kHz, nom. spring constant of 0.12 N/m). The force was kept at the lowest possible value in order to minimize the forces of interaction between the tip and the surface. The linear scanning rate was optimized between 1.5 and 2 Hz with a scan resolution of 512 samples per line.
Processing and analysis of images was carried out using NanoScope TM software (Bruker, version V614r1) . All images presented are raw data except for the first order two-dimensional flattening. Measurements were performed in air at room temperature and 50-60% relative humidity.
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10

Atomic Force Microscopy with Nanoscope IIIa

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We used the Nanoscope IIIa controller with extender module operated with version 6 software (Bruker AXS, Santa Barbara, California, USA). This controller was coupled to a Multimode AFM equipped with a low noise optical head, calibrated E- and J- piezoelectric scanners and PicoForce hardware (Bruker AXS). The imaging system is suspended on bungee cords with a vertical resonance of ∼0.5 Hz.
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