All AFM imaging was carried out at room temperature with the samples hydrated in imaging buffer. Data were recorded using a Dimension FastScan Bio AFM (Bruker, Santa Barbara, USA), using force–distance-curve based imaging (PeakForce Tapping mode). Force–distance curves were recorded over 10–40 nm (PeakForce Tapping amplitude of 5–20 nm), at a frequency of 8 kHz. FastScan D (Bruker) cantilevers were used for all imaging (resonance frequency of ∼110 kHz, nominal spring constant ∼0.25 Nm–1). Images were processed using first-order line-by-line flattening, median line-by-line flattening and zeroth order plane fitting to remove the sample tilt and background using Gwyddion.
Dimension fastscan bio afm
Manufactured by Bruker
Sourced in United States
The Dimension FastScan Bio AFM is an atomic force microscope designed for high-speed, high-resolution imaging of biological samples. It provides rapid scanning capabilities and advanced imaging modes to enable real-time observation of dynamic biological processes.
Automatically generated - may contain errors
Lab products found in correlation
Fastscan d, by Bruker (3 mentions)
Nanoscope analysis v1, by Bruker (2 mentions)
G250 2 mica sheets, by Agar Scientific (2 mentions)
Matlab, by MathWorks (1 mentions)
Fastscan d cantilever, by Bruker (1 mentions)
1d image analysis software, by Kodak (1 mentions)
Nanoscope analysis software, by Bruker (1 mentions)
11 protocols using dimension fastscan bio afm
1
AFM Imaging of Hydrated Samples
2
Nuclear Pore Complex Dynamics Analyzed by AFM
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
All
AFM measurements were performed at
room temperature in import buffer (20 mM Hepes, 110 mM CH3COOK, 5 mM Mg(H3COO)2, 0.5 mM EGTA, pH 7.4).
Kymographs were obtained using a Dimension FastScan Bio AFM (Bruker),
using tapping mode AFM. FastScan D (Bruker) cantilevers were used
for all experiments, and the applied force was minimized (optimized)
as described for the NuPODs. Images of the nuclear envelope were recorded
to ascertain if the AFM tip probed the cytoplasmic or nucleoplasmic
face of the nuclear envelope.17 (link) A 300 ×
300 nm image at 304 samples/line of a single NPC was recorded; this
ensured capture of background nuclear envelope as well as the NPC.
When the position along the slow-scan axis was at the center of the
NPC (seeFigure 1 A,B,
AFM images, white-dashed lines), the slow scan-axis movement was disabled.
A kymograph was then produced with height in the fast-scan axis and
time in the slow-scan axis. The line rate was set to 5, 10, or 20
Hz, and the gains were optimized to best track the contours of the
sample.
AFM measurements were performed at
room temperature in import buffer (20 mM Hepes, 110 mM CH3COOK, 5 mM Mg(H3COO)2, 0.5 mM EGTA, pH 7.4).
Kymographs were obtained using a Dimension FastScan Bio AFM (Bruker),
using tapping mode AFM. FastScan D (Bruker) cantilevers were used
for all experiments, and the applied force was minimized (optimized)
as described for the NuPODs. Images of the nuclear envelope were recorded
to ascertain if the AFM tip probed the cytoplasmic or nucleoplasmic
face of the nuclear envelope.17 (link) A 300 ×
300 nm image at 304 samples/line of a single NPC was recorded; this
ensured capture of background nuclear envelope as well as the NPC.
When the position along the slow-scan axis was at the center of the
NPC (see
AFM images, white-dashed lines), the slow scan-axis movement was disabled.
A kymograph was then produced with height in the fast-scan axis and
time in the slow-scan axis. The line rate was set to 5, 10, or 20
Hz, and the gains were optimized to best track the contours of the
sample.
3
Atomic Force Microscopy of GaN Surface
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Atomic force microscopy (AFM) imaging was performed using a Bruker Dimension FastScan Bio AFM equipped with ScanAsyst mode. The functionalized GaN surface was scanned using line scan rates of 1–2 Hz and 512 samples per line. Measurements were done in the tapping mode in air. AFM images of several areas of the GaN surface were recorded for reproducibility. Images were analyzed by Gwyddion 2.5, and then a Gaussian function was fitted into the height profile to estimate the height and its standard error for each feature.
4
Measuring Cell Modulus with AFM
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Cell modulus measurements were performed as in ref. 4 . Briefly, force-displacement curves for intact MSC nuclei were acquired using a Bruker Dimension FastScan Bio AFM. MLCT-SPH-5um -DC-A probes were used to decrease variables in calculating moduli. MSCs were located using the AFM’s optical microscope and engaged on using a minimal force set point (1–3 nN) to ensure contact while minimizing applied force and resultant deformation prior to testing. Ramps were performed over the approximate center of each nucleus for all samples. After engaging on a selected nucleus to ensure probe/nucleus contact as described above, force curve ramping was performed at a rate of 2 µm/s over 2 µm total travel (1 µm approach, 1 µm retract). 5 replicate force-displacement curves with an indentation depth of at least ~500 nm were acquired and saved for each nucleus tested, with at least 3 s of rest between ramps. Cell modulus was determined using Hertz model and analyzed using Atomic J57 (link).
5
Mechanical Properties of Isolated Nuclei
6
Visualizing Protein Complexes by AFM
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Atomic force microscopy was measured with a Bruker Dimension FastScan Bio AFM equipped with the ScanAsyst mode. The respective 1P3T-HSA and Me1P3T-HSA solution (20 µL, 600 nM) was deposited onto freshly cleaved mica surface and left for 5 min at room temperature to allow the protein complexes to adsorb. After an addition of additional 20 µL of MilliQ Water into the sample, the sample was scanned at the rate between 1 and 3 Hz. Several images in different areas were taken to ensure reproducibility of the results. All images were analyzed using the NanoScope Analysis 1.50 and Gwyddion 2.38 software.
7
Multi-Sample AFM for Biofluids Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The system is based on a Dimension FastScan-Bio AFM (Bruker, Santa Barbara, CA, USA). The tip is mounted on a z-scanner that can be used in fluid. The stage of the FastScan-Bio AFM has been modified to host a sample holder able to hold a sample in each of its 12 wells (3 × 4). This Multi-Well plate can be removed and replaced with accuracy such that the vertical position is known to within a few hundred nanometers. The modified stage with the Multi-Well plate is shown in Fig 1A . Each of the wells can hold a small round coverslip with a diameter of 8 mm, in fluid (Menzel-Gläser, Braunschweig, DE). The coverslip is secured with a bio-compatible spring and a spring clamp, as shown in Fig 1B .
8
Atomic Force Microscopy of NuPODs
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
All
AFM measurements were performed at
room temperature in liquid. Images were obtained using a Dimension
FastScan Bio AFM (Bruker) operated in Tapping mode. FastScan D (Bruker)
cantilevers were used for all imaging with a resonance frequency of
∼110 kHz, measured spring constant of ∼0.15 N m–1, and quality factor of ∼2 in water. The force
applied to the sample was minimized by setting the highest possible
amplitude set-point voltage, which was typically above 85% of free
oscillation close to the sample surface. Single line scanning experiments
provided an enhanced time resolution while minimizing disturbance
to the NuPODs. For these experiments, a single NuPOD was centered
and the frame size decreased to 120 nm before disabling the slow-scan
axis over the center of the pore. Where possible, data were collected
at 5, 10, and 20 Hz for each pore imaged.
AFM measurements were performed at
room temperature in liquid. Images were obtained using a Dimension
FastScan Bio AFM (Bruker) operated in Tapping mode. FastScan D (Bruker)
cantilevers were used for all imaging with a resonance frequency of
∼110 kHz, measured spring constant of ∼0.15 N m–1, and quality factor of ∼2 in water. The force
applied to the sample was minimized by setting the highest possible
amplitude set-point voltage, which was typically above 85% of free
oscillation close to the sample surface. Single line scanning experiments
provided an enhanced time resolution while minimizing disturbance
to the NuPODs. For these experiments, a single NuPOD was centered
and the frame size decreased to 120 nm before disabling the slow-scan
axis over the center of the pore. Where possible, data were collected
at 5, 10, and 20 Hz for each pore imaged.
9
Visualizing DNA Scaffolds with AFM
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA was visualised by PAGE on polyacrylamide gels (15%, 19:1 acyrlamide/bis-acrylamide). Samples were loaded with Blue/Orange loading dye, run at 80 V for 360 minutes and stained with SYBR Gold Nucleic Acid Gel Stain. Imaging was carried out using Kodak 1D image analysis software.
Densitometry was undertaken using ImageJ. The total intensity in each lane was obtained and the relative intensity of each band as a percentage of the total lane intensity was calculated.
For analysing DNA scaffolds containing 0 and 20 base mismatches using AFM, 50 μl of DNA (8–10 ng in total) in 10 mM Tris-EDTA pH 8 buffer was allowed to adsorb on a freshly cleaved mica surface, pre-treated with 10 mM NiCl2 for 20 minutes in a high humidity chamber. A further 100 μl of 10 mM Tris-EDTA pH 8 buffer was afterwards added. The resulting sample was imaged with a Dimension FastScan Bio AFM (Bruker, USA) in peak force tapping mode, in liquid, with a Fastscan-D cantilever (Bruker, USA) at an amplitude set point of 250 mV and 57.68 mV drive amplitude. All the captured AFM images were analysed with the Nanoscope Analysis software from Bruker.
Densitometry was undertaken using ImageJ. The total intensity in each lane was obtained and the relative intensity of each band as a percentage of the total lane intensity was calculated.
For analysing DNA scaffolds containing 0 and 20 base mismatches using AFM, 50 μl of DNA (8–10 ng in total) in 10 mM Tris-EDTA pH 8 buffer was allowed to adsorb on a freshly cleaved mica surface, pre-treated with 10 mM NiCl2 for 20 minutes in a high humidity chamber. A further 100 μl of 10 mM Tris-EDTA pH 8 buffer was afterwards added. The resulting sample was imaged with a Dimension FastScan Bio AFM (Bruker, USA) in peak force tapping mode, in liquid, with a Fastscan-D cantilever (Bruker, USA) at an amplitude set point of 250 mV and 57.68 mV drive amplitude. All the captured AFM images were analysed with the Nanoscope Analysis software from Bruker.
10
Niosome Morphology Assessed by AFM
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Morphological examination of both niosome formulations was performed by atomic force microscopy (AFM). Each formulation (5 -10µL) was deposited onto freshly cleaved mica surfaces (G250-2 Mica sheets 1" x 1" x 0.006"; Agar Scientific Ltd., Essex, UK), and left in to air dry for 1 h before AFM imaging. The images were obtained by scanning the mica surface in air under ambient conditions using a Dimension FastScan BioAFM (Bruker, CA, USA) operated on Peak Force QNM mode. The AFM measurements were obtained using ScanAsyst-air probes. AFM images were collected by random spot surface sampling (at least three areas). The analyses were performed using the Nanoscope Analysis v1.4 (Bruker, USA).
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!