Design, Assembly and Operations of a Series of Photochemically Controlled DNA Logic Devices

Description

This is a chemistry proposal focusing on the design, assembly and operation of photon-responsive DNA-based systems which imitate function of signal communication. Due to the limitation of top-down approach to fabricate smaller silicon chips for conventional computers, bottom-up approach becomes a promising alternative means to construct nanoscale molecular devices which can be operated by external stimuli (input) and generate some signals (outputs). We propose to build a simple and universal DNA-based platform consisting of two photolabile molecules, namely (2,7-bis-{4-nitro-8-[3-(2- propyl)-styryl]}-9,9-bis-[1-(3,6-dioxaheptyl)]-fluorene and 1-(2-nitrophenyl)-ethyl molecules, FRET fluorophore pairs and G-rich sequences as construction elements. Two different wavelengths of light (e.g. ultraviolet at 320 nm, and near infrared-red at 800 nm) are used as the two inputs to trigger photocleavage of photolabile molecules. The resulting FRET fluorescence changes accompanied by the dissociation/association of cleavable DNA oligonucleotides and the formation/deformation of G-quadruplex are used as output of 1 or 0. By adjusting the position of photocleavable molecules and number of nucleotides between them, a series of Boolean logic gates (YES, NOT, AND, OR, NAND, NOR gates) at molecular level is created. Combinational logic gates such as INHIBIT gate can also be fabricated by interconnecting basic logic elements including OR and NOT gates. The novelty is to use lights as inputs to trigger the logic operation of DNA devices. This would create a new paradigm of inputs that allows for temporal and spatial control with high specificity and overcoming the drawback of chemical inputs including waste accumulation and delivery kinetics. As light wave can be instantaneously converted into electrical outputs and vice versa, the use of photochemical inputs can shorten the gap between silicon-based computing circuity and DNA computation. This interrelation is significant for further thriving on the interface of electronic devices and DNA-based logic gates. As compared to other logic gates, this system gives real-time response while the final readout gate can be easily reset to its original state. This potentially enables devices to be used repeatedly. Although they may not yet able to rival semiconductor-based computing devices, they still emulate the digital logic circuits and serves as alternative computational media to certain extent. A successful outcome of this proposed work could lead to a step towards employing photon-responsive DNA devices as versatile tools in DNA computing, display device, optical communication and data storage. This technique brings forward with its capability to locally and spatially control logic gates at a resolution in the nm range.