AFM Metrology and Analysis of Stainless Steel, Plasmid DNA, Nano-structure on Plexiglass
Introduction
Three samples were prepared and submitted for AFM analysis. They are: 1) stainless steel surface, 2) plasmid DNA on as-received
and NaOH-treated glass substrates, and 3) a nanostructure on a plexiglass. A Nano-R2™ AFM system was used in this measurement
and analysis. This work is to show the capability of Pacific Nanotechnology’s Nano-R2™ AFM to image and analyze nanosized structures.
Example results are shown and discussed below.
Experiment
All sample measurement was carried out in air using the Close-Contact (or “Tapping”) Mode of Nano-R2™ AFM equipped with a light
lever scanner. The Close-Contact Mode was found the most suitable for these samples. Commercially available silicon probes with a
normalized radius of < 10 nm were used in all data acquisition.
The Nano-R2™ system was calibrated in the X, Y, and Z axes before measurement. We utilized the standard samples to calibrate Zheight
channel, and resulting system accuracy was ± 1 %. The resonant frequency and phase angle were automatically tested prior
to measurement. Data were processed using the NanoRule+™ software. Different scanning rates, resolutions angles and GPID of the
feedback system were used to achieve optimal results. Grain analysis was done using the Grain Analysis function of the NanoRule+™.
Results and Discussion
Stainless Steel Surface
This sample was measured during a demo on November 6, 2006. A few more scans were taken to confirm the acquired results. Figure
1A (10 × 10 μm) shows the typical topography of the stainless steel surface. Figure 1B (3 × 3 μm) is a close-look at the sample
using the Zoom-In function of the systems. Figure 1C is a 3D view of the same structure as Figure 1B. Line Analysis and Roughness
measurement were performed as shown in Figure 2. Example results are discussed below.
Figure 1: Typical topography of the stainless steel surface. (A) A 10 × 10 μm scan; (B) A 3 × 3 μm scan; (C) 3D view of the same structure as (B). The Zscale
is 120.18 nm for (B-C).
Figure 2A: Dimension Analysis for the stainless steel. The pair 1 (red) shows that
the particle 1 is 25.36 nm high; The pair 2 (green) represents that the particle 2
is 43 nm in diameter (FWHM, full width at half maximum); The well-known tip
broadening effect makes particle diameter look greater than height.
The Line Analysis in the NanoRule+™ is capable of giving virtually any pixel-to-pixel dimension. Figure 2A shows an example dimension
measurement of the stainless steel surface. The pair 1 (red) indicates that the particle 1 is 25.36 nm high above the surface; pair 2
(blue) represents that the particle 2 is 43 nm in diameter (FWHM, full width at half maximum). The height of the particle 2 was measured
as ~11 nm (not shown). This discrepancy results from the well-known tip broadening effect. The stainless steel is a smooth surface with
some grooves and nano or micro-sized particles.
Figure 2B: Roughness Measurement
The roughness of the smooth part (green square in Figure 2B) is about 5.59 nm RMS. The roughness of the whole area is 14.3 nm
RMS due to the grooves and particles.
Plasmid DNA
Figure 3: Plasmid DNA on as-received glass. (A) Topography; (B) Phase Image.
Figure 4: Magnified view of DNA on as-received glass. (A) 1.51 × 1.51 μm; (B) 1 × 1 μm; (C) 3D view of 800 × 800 nm.
Plasmid DNA molecules with different lengths were found on the as-received glass substrate. The sample maximum height ranges from
4-9 nm, determined by the particle-like structures (arrows) indicated in Figure 4A-B. The crystallographic width of a double-stranded
B-DNA molecule is about 2 nm, however, AFM height is ~0.6 nm because an AFM probe puts pressure on single DNA molecules.
As a result, the smaller height and greater width are observed in most cases. The highest features in Figure 4 could be coiled DNA knots which stood above the surface,
resulting in 4-9 nm maximum height. Figure 8 shows two reference DNA micrographs
on a freshly-cleaved mica surface. Because of low concentration, annealing, and
through rinse during preparation, molecules settle down with less coiled-knots. As a
result, the maximum height in Figure 8 is 1.47 nm and 0.83 nm. Figure 5 is plasmid
DNA on NaOH-treated glass. We did not observe apparent differences from the DNA
on as-received glass substrate. |
Figure 5: Plasmid DNA on NaOH-treated
glass,
similar to on as-received glass.
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