DNA Computing and Molecular Programming

Fluorophores have been employed extensively in DNA nanotechnology, principally in donor-acceptor combinations, enabling Föster resonant energy transfer (FRET) to be used for applications, such as monitoring hybridization reactions and monitoring DNA nanomachine functions. FRET is an energy non-conserving process in which a bundle of energy, referred to as a Frenkel exciton, is transferred from the donor fluorophore to the acceptor. The characteristic length scale at which FRET sets in is called the Föster radius and is typically about 5 nm. If the donor and accepter are brought to within less than 2 nm of each other, the energy transfer can occur in an energy conserving manner referred to as coherent FRET. A Frenkel exciton, undergoing coherent FRET exchange among a cluster of chromophores, spreads out over the cluster in a wave-like manner, referred to as a quantum walk. Frenkel excitons also exhibit particle-like aspects and are best viewed as fully quantum mechanical entities. One manifestation of particle-like behavior is that, when two excitons encounter each other, they can experience a two-body interaction that gives rise to quantum mechanical phase shifts. In order for this to happen the chromophores must possess a permanent electric dipole moment and this requires the chromophores to be asymmetric. These two properties of Frenkel excitons – their wave-like behavior and their two-body interaction – are sufficient to enable universal quantum computation. I will describe how these two features can be exploited to implement a complete set of quantum gates for universal quantum computation. Quantum computing, regardless of its embodiment, is a race against decoherence, the process by which the wave-like behavior is destroyed. Chromophores, residing in buffer and attached to DNA, are in an environment highly susceptable to this process. It remains to be seen whether the decoherence rate can be reduced enough to enable Frenkel excitons to perform universal quantum computation by undergoing a many-body quantum walk over a network of chromophores attached to a DNA scaffold. From One, Many: Programmably Reconfigurable, Multiscale Materials Built with DNA