Peptide solution (10 μL, 40 μM) or diluted gel was deposited onto freshly cleaved mica surface and air-dried. AFM characterizations were performed on a Veeco Dimension 5000 Scanning Probe Microscope with a Nanoscope V controller (Digital Instruments, Inc.). All samples were prepared on mica substrate and measured without treatment. Al-coated silicon AFM tips (NSC 15/AIBS, MikroMasch, Estonia) with a tip radius of 10 nm were used to probe the surface profiles of the films. Tapping-mode AFM imaging was used according to well-established procedures. All images were post-treated with NanoScope Analysis 1.5 Software.
Nanoscope 5 controller
Manufactured by Digital Instruments
Sourced in United States
The Nanoscope V controller is a specialized piece of laboratory equipment designed for use with scanning probe microscopes. It serves as the central control unit, providing the necessary power, signals, and data acquisition capabilities to operate the microscope. The Nanoscope V is responsible for managing the scanning and feedback mechanisms that enable high-resolution imaging and analysis of samples at the nanoscale level.
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Lab products found in correlation
Nanoscope iiia controller, by Digital Instruments (3 mentions)
Omcl ac160ts, by Olympus (3 mentions)
Spm probe, by MikroMasch (3 mentions)
Nsc15 aibs, by MikroMasch (2 mentions)
Multimode scanning probe microscope, by Digital Instruments (1 mentions)
Dimension 3100 scanning probe microscope, by Digital Instruments (1 mentions)
Hq nsc19 al bs tip, by MikroMasch (1 mentions)
Multimode afm, by Veeco (1 mentions)
Nanowizard 3, by Bruker (1 mentions)
Mica surface, by Agar Scientific (1 mentions)
Eclipse ti, by Nikon (1 mentions)
Dimension icon afm, by Bruker (1 mentions)
Rtespa 300, by Bruker (1 mentions)
Dimension 3100 spm, by Digital Instruments (1 mentions)
Multimode spm, by Digital Instruments (1 mentions)
15 protocols using nanoscope 5 controller
1
Nanoscale Peptide Surface Characterization
2
Tapping Mode AFM Imaging of Nanoscale Samples
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For AFM inspection, 40-μl sample aliquots were centrifuged at 1700 × g for 5 min using an Eppendorf 5417R centrifuge. The pellet was suspended in an equal volume of water, and a 10-μl aliquot was deposited on freshly cleaved mica and dried under mild vacuum. Tapping mode AFM images were acquired in air using a Dimension 3100 Scanning Probe Microscope equipped with a “G” scanning head (maximum scan size 100 μm) and driven by a Nanoscope IIIa controller, and a Multimode Scanning Probe Microscope equipped with “E” scanning head (maximum scan size 10 μm), driven by a Nanoscope V controller (Digital Instruments, Bruker). Single beam uncoated silicon cantilevers (type OMCL-AC160TS, Olympus) were used. The drive frequency varied between 280 and 330 kHz, the scan rate was between 0.4 and 0.7 Hz. Height and width of imaged objects were measured from the corresponding cross-section profiles in topographic AFM images. Widths at half-height were measured to correct tip size effects (20 (link)) and standard errors are reported. The object volume V was calculated from the equation,
where h is the imaged object height and a is its half-corrected width (20 (link)).
where h is the imaged object height and a is its half-corrected width (20 (link)).
3
Atomic Force Microscopy of EpolC1576
4
AFM Characterization of Peptide Films
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Peptide solution (10 μl, 40 μM) or diluted gel was deposited onto freshly cleaved mica surface and air dried. AFM characterizations were performed on a Veeco Dimension 5,000 Scanning Probe Microscope with a Nanoscope V controller (Digital Instruments, Inc.). All the samples were prepared on mica substrate and measured without treatment. Al-coated silicon AFM tips (NSC 15/AIBS, MikroMasch, Estonia) with a tip radius of 10 nm were used to probe the surface profiles of the films. Tapping-mode AFM imaging was used according to well-established procedures. All the images were post-treated with NanoScope Analysis 1.5 Software.
5
Atomic Force Microscopy of Purified Inclusion Bodies
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Purified IBs were resuspended in water at a protein concentration of 2 mg/mL and diluted 10 or 100 times. A 10 µL aliquot was deposited on freshly cleaved mica and dried under mild vacuum. Digestion with PK was performed by incubating 40 µL of undiluted IBs with 3.2 µL of a 10 mg/mL PK stock solution for 60 min at 37°C. Digested samples were then diluted 100 times and a 10 µL aliquot was deposited on freshly cleaved mica and dried under mild vacuum. Tapping mode atomic force microscopy (AFM) images were acquired in air using a Dimension 3000 SPM, equipped with a “G” scanning head (maximum scan size of 100 µm) and driven by a Nanoscope IIIa controller, and a Multimode SPM equipped with a “E” scanning head (maximum scan size of 10 µm) and driven by a Nanoscope V controller (Digital Instruments, Veeco). Single-beam uncoated silicon cantilevers (type OMCL-AC160TS, Olympus) were used. The drive frequency was between 260 and 330 kHz; the scan rate was 0.4–0.8 Hz.
6
DNA Nanostructure Imaging and Characterization
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The samples in Figure 4 a were imaged directly after glycerol purification. For the streptavidin labeling experiment (Figure 4 b), the appropriate digestion buffer was added after assembly to a final concentration of 1×, and the structures were digested with one of the two restriction endonucleases BstZ17I or ScaI-HF at a concentration of 1 U/μL at 37 °C for 2 h. The structures were then incubated with a 10× solution of streptavidin for 30 min and then glycerol purified.
For imaging, we added to a freshly cleaved mica surface, 30 μL of filtered 5× TAE/Mg2+ buffer, followed by 30 μL of a 10 mM solution of NiCl2 to increase the strength of the DNA–mica binding. After 5 min, we added 10–30 μL of the glycerol-purification fraction containing our desired product. AFM images were obtained using a Multimode 8 scanning probe microscope with a Digital Instruments Nanoscope V controller. Images were collected in aqueous phase using tapping mode, using the short and thin cantilevers in the SNL-10 silicon nitride cantilever chip. Within each of the two panels ofFigure 4 , the images were all generated using the same tip.
For imaging, we added to a freshly cleaved mica surface, 30 μL of filtered 5× TAE/Mg2+ buffer, followed by 30 μL of a 10 mM solution of NiCl2 to increase the strength of the DNA–mica binding. After 5 min, we added 10–30 μL of the glycerol-purification fraction containing our desired product. AFM images were obtained using a Multimode 8 scanning probe microscope with a Digital Instruments Nanoscope V controller. Images were collected in aqueous phase using tapping mode, using the short and thin cantilevers in the SNL-10 silicon nitride cantilever chip. Within each of the two panels of
7
Imaging Amyloid-β Fibrillization Kinetics
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Aliquots of Aβ40 samples with or without Hsp60, taken at the end of fibrillization kinetics, were deposited onto freshly cleaved mica surfaces (Agar Scientific, Assing, Italy) and incubated for up to 60 min at room temperature. Then, samples were rinsed with deionized water and dried under a low-pressure nitrogen flow. AFM measurements were performed using a Nanowizard III (JPK Instruments, Berlin, Germany) system mounted on an Eclipse Ti (Nikon, Japan) inverted optical microscope. Tapping mode AFM images were acquired in the air using a multimode scanning probe microscope driven by a nano-scope V controller (Digital Instruments, Bruker, Kennewick, WA, USA). Single-beam uncoated silicon cantilevers (type SPM Probe Mikromasch) were used. The drive frequency was between 260 and 325 kHz, and the scan rate was 0.25–0.7 Hz.
8
AFM Imaging of Exosome Samples
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Exosomes obtained by ultracentrifugation were resuspended in PBS and 50 μL aliquots were deposited on freshly cleaved mica, then washed and dried under mild vacuum. Tapping mode AFM images were acquired in air using a multimode scanning probe microscope driven by a nanoscope V controller (Digital Instruments, Bruker, Kennewick, WA, USA). Single-beam uncoated silicon cantilevers (type SPM Probe Mikromasch) were used. The drive frequency was between 260 and 325 kHz; the scan rate was 0.25–0.7 Hz.
9
Atomic Force Microscopy of Amyloid Fibrils
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A fibril suspension was deposited onto the freshly cleaved mica surface and incubated for 5 min at room temperature. The mica sheets were subsequently rinsed twice with Milli-Q water to remove the unbound substance. All imaging was performed under air conditions in tapping mode using antimony (n)-doped Si cantilevers with a constant force of 40 N/m (model RTESPA-300, Bruker, USA) at ~300 kHz on a Dimension Icon AFM with a Bruker Nanoscope V controller (Digital Instruments, Goleta, CA, USA). The images were recorded at a scan rate of 1 Hz. Fibril heights were measured by subtracting the average baseline from the highest peak, generating an accurate reading of the fibril diameters.
10
AFM Imaging of Purified Samples
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AFM images were obtained using an SPM MultiMode with Digital Instruments NanoScope V controller. Three microliters of purified samples (~3 nM DOJ) were deposited onto freshly cleaved mica (diameter, 9.5 mm; SPI Supplies) for imaging. After sample adsorption for approximately 2 min, 80 μl of 0.5× Tris-EDTA (10 mM MgCl2) and 2 μl of NiCl2 (100 mM) were then added onto the mica. The sample was imaged in ScanAsyst mode in fluid cell. The AFM tips used were on the short and thin cantilevers in the SNL-10 silicon nitride cantilever chip.
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