Implementation of 1-and 2-input logic gates and composite circuits via 3-input 1-output DNA algorithmic assembly

Abstract We describe the assembly of 3-input 1-output DNA algorithmic logic gates capable of generating algorithmic lattices through tile-based self-assembly. By designing 31-rule logic gates, we demonstrate that all 1-input 1-output (11-rule) and 2-input 1-output (21-rule) logic functions can be effectively implemented using only a subset of 3-input 1-output logic patterns. Specific rules such as R015, R051, and R085—applied within the framework of the 31-rule gate—were used to represent R1 in the 11-rule and R03, R05 in the 21-rule, with various reading directions (downward, horizontal, and upward). Double-crossover (DX) DNA tiles are used as rule and connector units, and successful assembly is confirmed through atomic force microscopy (AFM). We also demonstrate a complex digital logic circuit composed of both 11-rule and 21-rule gates using a single 3-input 1-output rule (R243), which faithfully replicates the circuit logic through a programmable DNA lattice. This study provides a modular and scalable approach to DNA-based logic computation and highlights the versatility of programmable molecular assemblies for future applications in nanoelectronics.