Electronic structures of DNA molecules and their alignment control on Si(1Â 0Â 0) substrates with one-dimensional lattices

We have carried out molecular-orbital calculations of the four bases of DNA, adenine (A), thymine (T), guanine (G), and cytosine (C), and the dimer dApA formed from a deoxyadenosine by using a phosphate and terminating at the sites of 5′ and 3′. The calculated results for A, T, G, and C are compared with the UPS spectra obtained by using a He II lamp with irradiation at 40.8 eV, and the experimental spectra are found to be generally reproduced by the calculations. We have also examined the alignment of 1.5-μm-length ring-shaped pBR322DNA composed of 4361 bp on Si(1 0 0) substrates with one-dimensional lattices. It is found that pBR322DNA can be observed only in the bottom parts of the one-dimensional lattice, while no appreciable DNA can be observed on the top parts of the lattice. These results suggest that DNA alignment can be controlled by one-dimensional lattices on Si(1 0 0) substrates through capillary action.