Design of photonic crystals fabricated from DNA lattices

The fabrication of photonic band gap materials requires the ability to manipulate materials of contrasting dielectric properties on the nanoscale level. These crystals can be engineered either with the "top down" approach utilized in lithographic and etching techniques [1] or the "bottom up" approach of self-assembly utilized in colloidal suspensions[2]. Both methods deal with controlling the geometry of traditional semiconductor materials. The Watson-Crick base pairing of DNA presents an alternative medium that can be employed in the self-assembly of photonic crystals.[3] Through careful control of the molecule's nucleic acid sequence, DNA can form stable branched junctions.[4] The sequence of single strands of DNA is choosen to maximize Watson-Crick base pairing, avoid sequence symmetries and eliminate branch point migrations. The FORTRAN code SEQUIN AIDS in the design of branched junctions based on these sequence requirements.[5] These junctions have been used as building blocks for molecular crystals[6], nanoscale devices|7, 8| and DNA computers[9j. Based on the design of a single DNA bundle consisting of antiparallel double helices created by Mathieu, Mao and Seeman[10], a two-dimensional trigonal lattice can be designed (see Fig 1). The band structure for this crystal was calculated by approximating the lattice as cylindrical rods of water (radius of r = 3√3 - lnm) cut into a material with the same dielectric constant as DNA [ε_DNA - 16.0) [11] with a lattice constant of a=6√3nm. Since a gap is expected to occur in a wavelength region comparable to the lattice constant, a dielectric constant for water in the far UV was used (ε_H2_O = 2.0) [12]. Using the MIT Photonic-Bands (MPB) package[13], a band gap for TE polarization between 0.00822 microns and 0.01228 microns was calculated, (see Fig. 2) . Since moving the gap region to longer wavelengths requires a larger lattice constant, a superstructure for this crystal is being investigated. In addition, the attachment of high dielectric ceramics to the DNA scaffolding at periodic intervals would allow for greater dielectric contrast.