Images and

Results

Once the tip, sample, and STM were prepared various images of DNA molecules were collected. The images were then filtered with a Fast-Fourier-Transform, LowPass filter, and Band Stop filter. Measurements for molecular width, and major/minor groove separations were obtained.

This is an 150 x150 angstrom image of the naked HOPG surface taken in constant height mode with the STM. Notice the regular array of carbon atoms. Also note the change in color from left to right. This color change denotes a gradual downward slope from left to right. In a previous experiment other images of the HOPG surface were obtained at various magnifications.
Here is a 3750 x 3750 angstrom image of a glob of DNA dried on the HOPG substrate. Measuring the structure on the left-hand side of the glob reveals a length of about 1500 angstroms. The 450bp DNA used in this experiment has an approximate length of 1530 angstroms. 8 At first one might be tempted to believe that the three streaks running diagonally across the image are DNA molecules. However, these streaks represent a boundary between two layers in the graphite surface and are much too long to be the DNA dried on the surface.

Such images as the one pictured above could been seen over the surface of the HOPG substrate. The frequency of these "globs" depended on the concentration of DNA dried on the surface. This particular substrate that produced the image above had 3 ul of 100 ng/l DNA in an aqueous solution. Below is an 150 x 150 angstrom image of a section of a DNA molecule captured on the HOPG substrate.

This image was captured using a bias voltage of 0.3 mV and a reference current of 1.2 nA. Some atomic structure in the DNA molecule (left) can be seen and the graphite substrate is visible on either side. The image was captured within ten minutes of the complete evaporation of the water on the substrate.

Below is a filtered and analyzed image of the DNA molecule pictured above.

This analysis represents a determination of the molecular width of the DNA molecule. Notice, first, the right-hand twist of the helix. Second, notice the relative uniformity in width of the molecule. Previous studies have determined the width to be 23.0 angstroms. 9 The average value of the data below yields a molecular width of 24.7 angstroms.


This particular analysis represents the surface features down the central axis of the DNA molecule. Notice the regular repeat of peaks in the graph. These peaks probably represent major and minor grooves along the molecule. One turn in the DNA helix represent the combination of a major and minor groove. In this experiment the average separation between a turn along the molecule was determined to be 33.3 angstroms. The accepted value for one turn is approximately 34 angstroms. 10 Furthermore, the separation of the major and minor grooves was found to be about 22.55 and 10.75 angstroms, respectively.


The next series of images is another DNA molecule imaged on the surface of the HOPG substrate. The first image represents a 750 x 750 angstrom area. The actual image is on the left the filtered image is on the right.

Notice that the structure continues out side of the image thus it is at least 750 angstroms in length. The next image represent the same structure only zoomed in by a factor of five. A quick cross sectional analysis reveals a sudden jump in the surface and a return to the substrate level.



This image was captured with a bias voltage of 0.35 mV and a reference current of 2.0 nA. The unfiltered image reveals some atomic detail but fails to yield any molecular substructure.

The filtered 3d image of the DNA molecule clearly reveals some aspects of its substructure. Notice the right-hand helix and the repeating major/minor grooves.



This is the 150 x 150 angstrom, 2d, unfiltered DNA image. A cross sectional analysis reveals a repeating substructure with a length of about 33 angstroms. Some structure within this length, as well.



This is the 150 x 150 angstrom, 2d, filtered, DNA molecule. Again, the substructure is quite evident. Cross section analysis graphically reveals the repeating turns in the molecule. The average turn length from the data yields about 29 angstroms.

The following data shows the spacing of the minor groove. The average minor groove spacing is about 8.3 angstroms.