Design tools for the fabrication of a photonic crystal based on DNA junctions

SEQUIN is a sequence design program used to create stable immobile DNA junctions. Several modifications to this program have been introduced that allow for the design of molecules containing multiple cross-overs on a single strand (ie. PX molecule) and molecules containing sticky-ends. There is also an inclusion of single mismatch pairing thermodynamics in the energy calculations and the addition of a graphical interface based on a two-dimensional grid with run time allocatable parameters. Using this program, a 2D photonic crystal can be designed. The structure of the crystal was modeled as cylindrical rods of water cut into a solid material with a dielectric constant equal to that of bulk DNA. The band gap for several variations of this crystal were calculated, all of which exist in the far UV to soft X-ray region. Current investigations include the possiblility of tiling together a superstructure for this 2D crystal in order to create a band gap at longer wavelengths.