The Scanning Tunneling Microscope is a useful tool for analyzing the surface structure of small and large molecules. In this experiment, DNA molecules placed on a highly ordered pyrolytic graphite substrate were successfully imaged using a Burleigh Instructional STM. Upon cross section analysis of the images, structures were obtained whose dimensions for width, length, and major/minor groove separations were similar to accepted values for DNA. The two methods for tip construction seemed to provide tips that yielded similar resolution. Therefore, the mechanical construction method, because of its ease, was preferred. Finally, a 3 ul sample of 100 ng/l DNA solution provided enough DNA on the substrate so that extensive searches were unnecessary.
Perhaps the largest source of error and greatest cause of poor resolution on the atomic scale came from the tip. Multiple atom tips often distort images on the surface due to multiple surface/tip tunneling. In fact, a tip that is tunneling in several locations can produce a double image. Another tip distortion noticed was side tunneling. This would occur as the tip approached a large molecule such as DNA on the substrate. The effect would give images whose width was anywhere from 25-55 angstroms and edges were not clearly defined. This phenomenon was often observed. Other reasons for lack of resolution could have included thermal drift caused by the kinetic energy of a large molecule resting on a substrate and lack of adsorption of the DNA to the substrate.6
Future experimenters might work to better refine the etching process for tip construction. Also, to avoid thermal drift and other environmental factors samples could be cooled and imaged in a vacuum. Finally, more time would result in the ability to image more molecules of DNA on the substrate
The future of imaging DNA with the STM is probably limited by the ability to make finer and finer tips. Although several studies have successfully imaged DNA and nucleotides with the STM, other methods of Scanning Probe Microscopy have been used to image DNA to even higher resolutions. Perhaps some time in the near future scientists will be able to sequence DNA using nothing but an STM. However, until technology catches up with the dreams of eager undergraduates, such goals will have to wait.