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Tip-radius-induced artifacts in AFM images of protamine-complexed DNA fibers
M J Allen1, N V Hud, M Balooch
1Biomedical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA 94550.
Abstract:
Isolated DNA fibers complexed with protamine (the chromosomal protein that packages DNA in mammalian sperm) have been produced by partially decondensing the highly compacted mouse sperm chromatin particle on a glass coverslip. These DNA fibers were then scanned with the atomic force microscope (AFM). While the smallest of the fibers appear in AFM images as ribbon-like structures 250-350 A wide and 10-25 A high, experiments indicate that these images are the result of a convolution of the imaging-tip's shape with the object's actual shape. In such convolutions the height of the object is affected only by the compressibility of the object, while the width is affected in addition by the sharpness of the tip. Images of polyamidoamine particles also appear to show this artifact. We have also deduced the tip's radius of curvature from images of sharp steps and attempt to demonstrate the artifacts associated with a relatively large imaging tip.
Insights
Atomic force microscopy (AFM) reveals artifacts in imaging DNA-protamine complexes. The imaging tip
Area of Science:
- Molecular Biology
- Biophysics
- Nanotechnology
Background:
- Mammalian sperm DNA is highly compacted by protamine, forming a dense chromatin particle.
- Understanding the structure of decondensed sperm chromatin is crucial for reproductive biology.
- Atomic Force Microscopy (AFM) is a powerful tool for visualizing nanoscale structures.
Purpose of the Study:
- To investigate the structure of isolated DNA fibers complexed with protamine from mouse sperm.
- To analyze AFM imaging artifacts when visualizing these decondensed DNA-protamine fibers.
- To characterize the influence of AFM tip shape on image dimensions.
Main Methods:
- Partially decondensing mouse sperm chromatin to isolate DNA-protamine fibers.
- Imaging the isolated fibers using Atomic Force Microscopy (AFM).
- Analyzing AFM image characteristics (width, height) and comparing them with known properties.
- Imaging polyamidoamine particles and sharp steps to identify imaging artifacts.
Main Results:
- AFM images of DNA-protamine fibers showed ribbon-like structures (250-350 Å wide, 10-25 Å high).
- These dimensions are artifacts resulting from the convolution of the AFM tip's shape with the actual fiber shape.
- The observed height is influenced by sample compressibility, while width is affected by tip sharpness.
- Similar artifacts were observed with polyamidoamine particles, and tip radius was deduced.
Conclusions:
- AFM imaging of decondensed DNA-protamine fibers is subject to tip-convolution artifacts.
- The apparent width and height in AFM images do not directly represent the true dimensions of the fibers.
- Understanding these artifacts is essential for accurate interpretation of AFM data in nanoscale imaging.