Nanoscope iiia multimode afm

Manufactured by Bruker

Sourced in United States

The Nanoscope IIIa Multimode AFM is an atomic force microscope (AFM) produced by Bruker. It is designed to provide high-resolution imaging and analysis of surface topography at the nanoscale level. The instrument utilizes a cantilever-based sensing system to detect and measure the interactions between a sharp probe and the sample surface.

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Lab products found in correlation

Tespa v2, by Bruker (2 mentions) Nanoscope analysis v1, by Bruker (2 mentions) Rtesp afm probes, by Bruker (1 mentions) Pureyield plasmid miniprep kit, by Promega (1 mentions) Afm tips, by Bruker (1 mentions) Rtesp, by Bruker (1 mentions)

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Nanoscope IIIa MultiMode IIIa Multimode AFM

5 protocols using nanoscope iiia multimode afm

Tapping Mode AFM Imaging Protocol

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Images were collected in tapping mode with a Nanoscope IIIA Multimode AFM (Bruker, Billerica, MA, USA) using a TESPA-V2 n-doped silicon cantilever.

Lindqvist C., Moons E, & van Stam J. (2018). Fullerene Aggregation in Thin Films of Polymer Blends for Solar Cell Applications. Materials, 11(11), 2068.

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Atomic Force Microscopy of GPVI-Fibrinogen Interactions

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AFM images were taken using a surface of freshly cleaved mica that was treated with 50 μL of 2 mmol/L NiCl₂ for 5 minutes. Following treatment, the surface was rinsed with deionized water and dried with nitrogen gas. For imaging of GPVI/fibrinogen interactions, GPVI monomer or dimer was incubated with fibrinogen at a 1:1 molar ratio for at least 2 hours in HBS. The solution was diluted to a final concentration of 2.5 μg/mL (8 nmol/L, fibrinogen) in HBS, added to the pretreated mica surface for 10 s, diluted with 50× deionized water for 10 s, and dried under nitrogen gas. High-resolution imaging was done using a Nanoscope IIIa Multimode AFM (Bruker, Santa Barbara, CA) in tapping mode with a scan rate of 0.8 Hz. All measurements were done in air using silicon cantilevers (TESPA-V2, Bruker Santa Barbara, CA) with a typical radius of 7 nm. Three to 5 images were taken from each sample and samples were repeated at least 3×. Standard flattening of images was performed.
For expression and purification of recombinant GPVI and fibrinogen/αC fragments, purification of plasma fibrinogen/αC fragments, preparation and purification of X-, D-, E-fragment and D-dimer, FITC labeling of GPVI, SD (sodium dodecyl sulfate-dithiothreitol) test, and additional SPR experiments, see supplemental methods.

Xu R.G., Gauer J.S., Baker S.R., Slater A., Martin E.M., McPherson H.R., Duval C., Manfield I.W., Bonna A.M., Watson S.P, & Ariëns R.A. (2021). GPVI (Glycoprotein VI) Interaction With Fibrinogen Is Mediated by Avidity and the Fibrinogen αC-Region. Arteriosclerosis, Thrombosis, and Vascular Biology, 41(3), 1092-1104.

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Imaging GPVI/Fibrinogen Interactions by AFM

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AFM images were taken using a surface of freshly cleaved mica that was treated with 50 μl of 2 mM NiCl₂ for 5 min. Following treatment, the surface was rinsed with deionized water and dried with nitrogen gas. For imaging of GPVI/fibrinogen interactions, GPVI monomer or dimer was incubated with fibrinogen at a 1:1 molar ratio for at least 2 h in HBS. The solution was diluted to a final concentration of 2.5 μg/ml (8 nM, Fibrinogen) in HBS, added to the pre-treated mica surface for 10 s, diluted with 50X deionized water for 10 s, and dried under nitrogen gas. High resolution imaging was done using a Nanoscope IIIa Multimode AFM (Bruker, Santa Barbara, CA, USA) in tapping mode with a scan rate of 0.8 Hz. All measurements were done in air using silicon cantilevers (TESPA-V2, Bruker Santa Barbara, CA, USA) with a typical radius of 7 nm. 3-5 images were taken from each sample and samples were repeated at least three times. Standard flattening of images was performed.
For expression and purification of recombinant GPVI and fibrinogen/αC fragments, purification of plasma fibrinogen/αC fragments, preparation and purification of X-, D-, E-fragment and D-dimer, FITC labelling of GPVI, SD test and additional SPR experiments, see supplemental methods.

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AFM Visualization of Protein-DNA Complexes

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Circular supercoiled pUC18 plasmid was purified using a PureYield™ Plasmid Miniprep kit (Promega, Madison, WI, USA) following the provided protocol with two additional wash steps. Protein–DNA complexes were obtained by adding 4.5 ng purified pUC18 plasmid in Lrp binding buffer to varying concentrations of protein in a total volume of 15 μL, followed by a 20 min incubation at 37 °C. After incubation, the prepared samples were mixed with an equal volume of nickel absorption buffer (40 mM HEPES, 10 mM NiCl₂ (pH 6.74)). For each binding reaction, 10 μL was disposed onto a freshly cleaved mica disc and incubated for another 10 min to allow adsorption of the DNA on the mica. The mica surface was rinsed 5 times with water and gently dried with a stream of air. Atomic force microscopy (AFM) images were obtained using a Multimode Nanoscope IIIa AFM (Bruker, Billerica, MA, USA) operated in tapping mode in air. RTESP AFM probes (Bruker, Billerica, MA, USA) were ozone-cleaned just before use. Images were recorded at a scan rate of 1.5 Hz. Flattening of the images was performed by using NanoScope Analysis v1.5 software (Bruker, Billerica, MA, USA). 3-D images were shown with a pitch of 3°.

Lemmens L., Wang K., Ruykens E., Nguyen V.T., Lindås A.C., Willaert R., Couturier M, & Peeters E. (2022). DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in Sulfolobus acidocaldarius. Biomolecules, 12(4), 524.

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AFM Imaging of Protein-DNA Complexes

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For AFM imaging, protein-DNA binding mixtures containing 50 nM pUC18 plasmid DNA and 15 nM-30 nM SIRV2_Gp1 protein were prepared in adsorption buffer (40 mM HEPES pH 6.9, 10 mM NiCl₂) and deposited on freshly cleaved mica. After 5 min incubation, the mica surface was rinsed with deionized ultrapure water and blown dry with a gentle stream of nitrogen. Images were collected with a MultiMode (NanoScope IIIa) AFM (Bruker, Billerica, MA, USA) operated in tapping mode in air using RTESP (Bruker) AFM tips (cantilever length of 115–135 μm, width of 30–40 µm, a nominal spring constant of 20–80 N/m, and resonance frequencies in the range from 264 to 284 kHz). NanoScope Analysis v1.5 software (Bruker) was used to flatten the images, perform cross-section analyses of the complexes, and to make three-dimensional (3D) surface plots of selected complexes with a pitch of 3°.

Peeters E., Boon M., Rollie C., Willaert R.G., Voet M., White M.F., Prangishvili D., Lavigne R, & Quax T.E. (2017). DNA-Interacting Characteristics of the Archaeal Rudiviral Protein SIRV2_Gp1. Viruses, 9(7), 190.

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