Fig 1 lists the elemental compositions (not including hydrogen) and ratios of key elements for the four nucleotides. Furthermore, the purines (A and G) possess more nitrogen than their complements (T and C) because of their imidazole ring. It is noted that nitrogen is present in the nucleobases and absent in the phosphate-sugar backbone. We have utilized specimens with oligomers containing only one of the four single bases (Adenine (A), Cytosine (C), Guanine (G), or Thymine (T)). Here we present detailed measurements analyzing the possibility to utilize AES and XPS signals to detect nucleotide-specific contrast. In a second study we noted that preliminary results on a single set of samples suggested the possibility that two well-established spectroscopic techniques, X-ray Photoelectron Spectroscopy (XPS) and Auger electron spectroscopy (AES), may be applicable to enable DNA imaging. In a prior study we focused on establishing nucleotide-specific variations of low energy electron reflectivity.
Furthermore, an imaging method could enable long read lengths, which reduce the computational complexity and uncertainty associated with stitching the segments to assemble the full sequence. Amplification is not needed, which eliminates another source of error in sequencing. The elimination of labels not only simplifies the preparation of the DNA strand, but it eliminates the errors associated with attaching the labels and correlating the nucleotides to their labels. If sufficient contrast can be achieved then, in principle, sub-nanometer DNA sequence images may be achievable without the need for heavy atom labeling. The absence of radiation damage associated with low impact energies motivates our goal to establish the feasibility of nucleotide-specific contrast mechanisms that may enable the sequencing of DNA by electron imaging techniques. For example, experimental work carried out by Fink’s group has demonstrated that DNA withstands a radiation dose of 10 8 electrons/nm 2 accumulated over more than one hour with impact energies from 60 to 230 eV. Scattering electron beams with significantly lower energies has been shown to prevent radiation damage to biological molecules. Furthermore, the complications associated with reliably labeling the bases lead to significant read errors. The radiation damage limits the electron dose and thereby the throughput. The high impact energy, however, not only produces radiation damage, it necessitates the use of heavy atom labels to provide contrast in the image of the nucleotides. Transmission Electron Microscopy (TEM) has been explored for imaging long DNA segments by utilizing high electron energies (80–300 keV) to achieve sub-nanometer resolution. Furthermore, the complex repetitive nature of DNA makes it costly, time consuming, and in some cases impossible to accurately reassemble the complete sequence from short reads.
Important applications like de novo sequencing assembly, determination of point mutations, differentiation of closely related species, and targeted resequencing require low error rates. Another drawback is the relatively large raw read error rate. One major drawback is that these technologies typically identify only 10–100 bases out of the 3 billion base pairs in the human genome in a given sequence segment or read. Established sequencing technologies based on capillary array electrophoresis and cyclic array sequencing offer such analytical capability, and currently marketed 2nd generation sequencers are delivering information at a cost of less than $5,000/genome. Oxygen is a highly reactive element that promotes rapid combustion and is often used in industrial applications.Significant demand exists for the development of high throughput technologies capable of extremely low-cost, high quality DNA sequencing. Oxygen is colorless, odorless, and tasteless in its gaseous form, and condenses to pale blue liquid and solid forms. Accounting for one-fifth of the earth’s atmosphere, oxygen combines with most elements and is a component of thousands of organic compounds. Oxygen is critical for life on Earth, produced by plants during photosynthesis and necessary for aerobic respiration in animals. Oxygen, the "elixir of life", was discovered by Joseph Priestly and Carl Wilhem Scheele independently of each other in the 1770’s. Discoverer: Joseph Priestley/Carl Scheele