Since the early 90’s the pursuit of DNA-based computers has evolved from non-deterministic polynomial problems to Boolean and arithmetical operations. Along with the development of DNA origami and discoveries such as deoxyribozymes and aptamers, multiple DNA-computer blueprints have arisen. Nevertheless, challenges remain in the integration of multiple operators to build large scale circuitry. Optimization of a structure that connects logic gates and can be integrated in more complex molecular circuits is required. In this study we developed a DNA platform mimicking a nanochip wafer to promote easy scalability for complex operations. DNA four-way junction (4WJ) has been reported as the core structure of Boolean logic gates. It was hypothesized that the attachment of multiple layers of 4WJ crossover strands to a DNA scaffold would bring in proximity for these metastable structures to communicate and interact in a domino-like effect triggered by the hybridization of a short DNA oligonucleotide, called (input). To determine the effective length of the communication chain, 5 layers of crossover strands were assembled by Watson-Crick base pairing to a DNA scaffold structure and a molecular beacon probe was setup as reporter (output) of the relay. Results supported the hypothesis, showing an effective relay when more than one layer is assembled to the scaffold versus when free in solution. The relay’s S/B decayed exponentially with the number of concatenated layers. Furthermore, the integration and intercommunication of a total of 10 layers of 4WJ crossover strands was investigated and results will be presented.

Intercommunication of DNA crossover layers bound to DNA scaffold

ACS Spring 2022

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