Nanoscope 5 multi mode scanning probe microscope

Manufactured by Veeco

The Nanoscope V Multi-Mode scanning probe microscope is a laboratory instrument designed for high-resolution imaging and analysis of surface topography. It uses a sharp probe to scan the sample surface, providing detailed information about the sample's physical and chemical properties at the nanoscale level. The core function of the Nanoscope V is to enable researchers and scientists to investigate the surface characteristics of a wide range of materials and samples with high precision and accuracy.

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Lab products found in correlation

Matlab image processing toolbox, by MathWorks (3 mentions) Matlab, by MathWorks (2 mentions) Mica substrate, by Ted Pella (1 mentions) Image processing toolbox, by MathWorks (1 mentions) Jem 2100 tem, by JEOL (1 mentions)

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Nanoscope V

6 protocols using nanoscope 5 multi mode scanning probe microscope

AFM Probing of Huntingtin Aggregates

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Ex situ atomic force microscopy (AFM) was used to investigate the morphology of htt aggregates formed in the presence or absence of lipid vesicles. Htt-exon1(46Q) (20 μM) was incubated with and without 400 μM lipid vesicles (to result in a 20:1 lipid:protein ratio) at 37 °C for a period of 8 h. After 1, 3, 5, and 8 h of incubation, a 2 μL aliquot of each condition was deposited on freshly cleaved mica for 1 min. Then, the mica was rinsed with 18 MΩ water and dried with a gentle stream of clean air. Samples were imaged using a Nanoscope V Multi-Mode scanning probe microscope (VEECO) equipped with a closed-loop vertical engage J-scanner. Silicon-oxide cantilevers with nominal spring constant of 40 N/m and a resonance frequency of 300 kHz were used. Scan rates were set to 1.99 Hz with cantilever drive frequencies at 10% off resonance. All images were analyzed using the Matlab image processing toolbox (MathWorks) as previously described [5 (link),43 (link)].

Beasley M., Groover S., Valentine S, & Legleiter J. (2020). Lipid headgroups alter huntingtin aggregation on membranes. Biochimica et biophysica acta. Biomembranes, 1863(1), 183497.

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Atomic Force Microscopy of Cyclic Peptides

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The cyclic peptide CHP1404
and the scrambled-sequence control (also head-to-tail cyclized) were
synthesized by a commercial service (LifeTein, LLC., Hillsborough,
New Jersey, USA). In situ AFM experiments were performed on freshly
cleaved highly oriented pyrolytic graphite (HOPG) with a Nanoscope
V MultiMode scanning probe microscope (Veeco, Santa Barbara, CA) equipped
with a closed-loop “vertical engage” J-scanner and a
sealable tapping fluid cell. Images were acquired using rectangular-shaped
silicon nitride cantilevers (Vista Probes, Phoenix, AZ) with spring
constants of ≈0.1 N/m. Scan rates were set at 1–2 Hz
with cantilever drive frequencies ranging from ≈7 to 9 kHz.
The free amplitude of the cantilever was ≈20 nm, and the tapping
amplitude was set at 75% of free amplitude. Peptide samples were prepared
in 18 MΩ water, bath sonicated for 15 min, and directly injected
into the fluid cell. After experimenting with different peptide concentrations,
the peptide concentration used to produce the images in Figure 12 was 0.6 mg/mL
(0.37 mmol/L).

Legleiter J., Thakkar R., Velásquez-Silva A., Miranda-Carvajal I., Whitaker S., Tomich J, & Comer J. (2022). Design of Peptides that Fold and Self-Assemble on Graphite. Journal of Chemical Information and Modeling, 62(17), 4066-4082.

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Atomic Force Microscopy of Purified Proteins

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The purified GST protein and co-incubated peptides were maintained at 37°C in Eppendorf tubes and 1400 rpm for the duration of the experiment in an orbital mixer. At 24 h after cleavage of GST with factor Xa protease, a 5.0 μL aliquot of each protein incubation was spotted onto a freshly cleaved mica substrate (Ted Pella Inc., Redding, CA), for 30 seconds, washed with 200μl of ultra-pure water to remove salt and dried gently with a stream of clean air. The mica was placed on metal pucks and stored in a covered petri dish until imaging.
AFM imaging Experiments were performed with a Nanoscope V Multi-Mode scanning probe microscope (Veeco, Santa Barbara,CA) equipped with a closed loop vertical engage J-scanner. All images were acquired with diving board shaped silicon-oxide cantilevers with a nominal spring constant of 40 N/m and resonance frequency of about ~300 kHz. Scan rates were set at 1–2 Hz with cantilever drive frequencies 10% below resonance. All images were analyzed using Matlab with the image processing toolbox (MathWorks, Natick, MA) as previously described.^{18 (link)}

Arndt J.R., Chaibva M., Beasley M., Karanji A.K., Kondalaji S.G., Khakinejad M., Sarver O., Legleiter J, & Valentine S.J. (2019). Nucleation inhibition of Huntingtin protein (htt) by polyproline PPII helices: a potential interaction with the N-terminal α-helical region of htt. Biochemistry, 59(4), 436-449.

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Imaging Amyloid-β Oligomers by AFM and TEM

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For atomic force microcopy imaging, preformed Aβ-iO were deposited on freshly cleaved mica (Ted Pella Inc., Redding, CA) and allowed to sit for 30 s. The mica substrate was then washed with 200 μL of ultrapure water and dried with a gentle stream of nitrogen. Samples were imaged in tapping mode via ex situ AFM using a Nanoscope V MultiMode scanning probe microscope (Veeco, Santa Barbara, CA). AFM images were analyzed with Matlab equipped with the image processing toolbox (Mathworks, Natick, MA). For negative stain electron microscopy, 6 μl of preformed Aβ*56 oligomers were applied to ultra-thin copper 400 mesh carbon grids (Electron Microscopy Sciences) and imaged on a JEOL JEM-2100 TEM.

Thibaudeau T.A., Anderson R.T, & Smith D.M. (2018). A common mechanism of proteasome impairment by neurodegenerative disease-associated oligomers. Nature Communications, 9, 1097.

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Imaging Huntingtin Protein Aggregation

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Purified htt–exon1(46Q) (10 μM) was incubated with and without lipid vesicles (100 μM for a 10:1 lipid:protein ratio) at 37°C with constant orbital agitation. At the desired time points, 2 μL of each sample was deposited on freshly cleaved mica. One minute after deposition, the mica was rinsed with 200 μL of 18 MΩ water and dried with a gentle stream of clean air. Samples were imaged using a Nanoscope V Multi‐Mode scanning probe microscope (VEECO) equipped with a closed loop vertical engage J‐scanner. Silicon‐cantilevers with a nominal spring constant of 40 N/m and a resonance frequency of 300 kHz were used. All images were collected with a scan rate of 1.99 Hz and cantilever drive frequencies at 10%–20% of resonance. Images were analyzed using the Matlab image processing toolbox (MathWorks) as previously described (Burke & Legleiter, 2013 (link)).

Stonebraker A.R., Beasley M., Massinople S., Wunder M., Li P., Valentine S.J, & Legleiter J. (2023). Cholesterol impacts the formation of huntingtin/lipid complexes and subsequent aggregation. Protein Science : A Publication of the Protein Society, 32(5), e4642.

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Imaging Aggregation Inhibitor Effects on Huntingtin

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Incubations of htt-exon1(46Q) (20 μM) in the presence and absence of small molecule aggregation inhibitors (100 μM) were maintained at 37 °C and 1400 rpm using an orbital mixer. Control incubations of small molecule aggregation inhibitors (100 μM) alone were also used. In addition, incubations performed with lipid vesicles were performed at a lipid:peptide ratio of 20:1. At various time points, 2 μL aliquots of each condition were deposited on freshly cleaved mica (Ted Pella Inc., Redding, CA) for 1 min, washed with 200 μL of ultrapure water, and dried using a gentle stream of clean air. Images were collected using a Nanoscope V Multi-Mode scanning probe microscope (VEECO) equipped with a closed loop vertical engage J-scanner. Silicon oxide cantilevers with a nominal spring constant of 40 N/m and a resonance frequency of 300 kHz were used. Scan rates were set between 1 and 2 Hz with cantilever drive frequencies at 10% of resonance. All images were then analyzed using the MATLAB image processing toolbox (MathWorks) as previously described.(59 (link),60 )

Beasley M., Stonebraker A.R., Hasan I., Kapp K.L., Liang B.J., Agarwal G., Groover S., Sedeghi F, & Legleiter J. (2019). Lipid membranes influence the ability of small molecules to inhibit huntingtin fibrillization. Biochemistry, 58(43), 4361-4373.

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