Fluorescence Resonance Energy Transfer (FRET) is a mechanism which describes the photonic energy transfer between two light-sensitive molecules (chromophores). A donor chromophore, initially in its electronic excited state, may transfer energy in the form of undetectable virtual photons to an acceptor chromophore. FRET has been widely used to study the structure and dynamic of biomolecules. Specifically, by using dyes conjugated on a DNA strand, FRET can be applied to molecular sensors in which fluorescence signals change as a result of altered distance between donor and acceptor chromophores due to hybridization or enzymatic reactions. In addition, the DNA strand can act as a photonic wire along which the photonic energy is transferred. However, because fluorescence is highly influenced by environmental conditions and surrounding molecules, the energy transfer from a donor dye conjugated on a DNA strand is easily quenched by the dye-DNA and dye-dye interaction, often lowering FRET efficiency to the acceptor dye. Furthermore, when multiple chromophore/fluorescent donors and acceptor groups/entities are arranged on 2D and 3D DNA structures, contact and other quenching mechanisms can occur which greatly reduce the long range FRET efficiency. This rapid loss of long distance FRET efficiency greatly reduces the viability of DNA based photonic wires and antennas and negates any useful or practical applications. Therefore quenching should be resolved in order to apply the molecular FRET system to the device fabrication with efficient energy transfer.