| Accession | GMS-140-1
URL copied to the clipboard |
| Title | Real-time formation of PRM-DNA condensation on mica |
| Submit date | 2025-05-08 15:37:29 |
| Last update date | 2025-05-08 17:32:24 |
| Contact | Richard WONG rwong AT staff.kanazawa-u.ac.jp Kanazawa University |
| Sharing | |
| Total file size | 2.29 MB |
| Keywords | DNA HS-AFM Protamine Nanoscale Synthetic DNA |
| Experiment type | HS-AFM |
| Summary | The scanning area, 800 nm × 800 nm, was taken with 180 × 180 pixels at 2 sec per frame. Cropped scanning area, 400 nm × 400 nm (scale bar: 80 nm). |
| Citation(s) | Nucleic Acids Research, Volume 53, Issue 6, 11 April 2025, gkaf152, https://doi.org/10.1093/nar/gkaf152 |
| Organism | OTHERs |
| Cell (Tissue) | not applicable |
| Protocol | High-speed AFM (HS-AFM) imaging was performed using a custom-built tapping mode setup, following established protocols. For scanning, we employed small cantilevers (BL-AC10-DS-A2 from Olympus, Tokyo, Japan; USC-F1.2-k0.15 and USC-F1.5-k0.6 from NanoWorld, Neuchâtel, Switzerland) with spring constants of 0.1, 0.15, or 0.6 N/m and corresponding resonance frequencies of 1.2 or 1.5 MHz. To enhance imaging resolution, amorphous carbon was deposited onto the cantilever tips using electron-beam deposition (EBD) via a field emission scanning electron microscope (ELS-7500, Elionix Inc., Tokyo, Japan). A 670 nm laser beam was focused on the EBD-modified tip through a 20× objective lens (CFI S Plan Fluor ELWD, Nikon, Tokyo, Japan), and cantilever deflection was monitored using a position-sensitive two-segment PIN photodiode. |
| Data processing | All HS-AFM images were processed and analyzed using ImageJ software. To correct background trends, a first-order polynomial fit was applied along both the x- and y-axes. Image clarity was then enhanced using the “Gaussian Blur” plugin, which applies a Gaussian smoothing filter. Cross-sectional height measurements were also performed within ImageJ to quantify spatial features. The resulting image sequences were exported as AVI-format videos and subsequently organized, edited, and compiled using the Adobe Creative Cloud suite. |
| [923] NARMov3.mp4
PRM-induced DNA looping video/mp4 2.29 MB MD5: 613b3f9e7d3ec8fb3b1302c5eaffe8a5 |
