Images were acquired with a NanoScope MultiMode VIII AFM microscope (Bruker Nano Surfaces, Santa Barbara, CA, USA) operating in soft tapping mode, or ScanAsyst® mode, using cantilevers with 2 nm nominal tip radius. Areas of 4×4 μm2 were scanned at a rate of 0.5 Hz with a resolution of 2048×2048 pixels. After filtering the images to remove scan line offsets, tilt, and bow, DNA/protein molecules were measured with NanoScope Analysis or the NeuronJ plugin [55 (link)] of ImageJ [56 ]. The length measurement function was used to obtain the contour length of DNA length and establish the position of particle binding; lengths were then normalized by setting them all to 1510 bp for the 186 CI binding fragment, or 1737 bp for the lambda CI binding fragment. The Particle Analysis function of the NanoScope Analysis software was used to measure the diameter, height and volume of bound protein molecules.
Nanoscope multimode 8 afm microscope
Manufactured by Bruker
Sourced in United States
The NanoScope MultiMode VIII AFM microscope is a high-resolution atomic force microscope designed for advanced surface analysis. It provides quantitative nanoscale imaging and measurement capabilities for a wide range of materials and samples.
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2 protocols using nanoscope multimode 8 afm microscope
1
Nanoscale Analysis of DNA-Protein Interactions
2
Atomic Force Microscopy Imaging of DNA-Protein Complexes
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Images were acquired with a NanoScope MultiMode VIII AFM microscope (Bruker Nano Surfaces, Santa Barbara, CA, USA) operating in Peak Force Tapping Mode using ScanAsyst‐Air cantilevers with 2 nm nominal tip radius. Areas of 5 × 5 μm2 were scanned at a rate of 0.27 Hz with a resolution of 2560 × 2560 pixels. After filtering the images to remove scan line offsets and tilt/bow, DNA molecules were interactively traced with the NeuronJ35 plug‐in of ImageJ.36 For both the looped and unlooped molecules, segments between end points and proteins, or between two proteins, were measured to determine the positions of all proteins along the DNA. Figure 3 and Supporting Information Fig. S2 show the ensemble of lac repressor positions for both looped and unlooped was tightly grouped at the near and far operator sites. The observed loops were between these two positions. The position of protein along each DNA molecule was normalized by the measured DNA length of the molecule set equal to 1524 bp.
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