Implementing logical inference based on DNA assembly

Algorithms and information processing, fundamental to biological system, are an essential aspect of many elementary physical phenomena, such as molecular self-assembly. Self-assembly system has been proved to be capable of performing many logic operations by the early work. A significant challenge related to the design of molecular information processing systems is to develop a programmable architecture that controls the states of individual molecular events. Here, a novel systematic implementation of logical inference is presented based on DNA tile assembly system. Exploiting the intrinsic programmable capability of molecular interactions, firstly a seed tile configuration is constructed to encode the input information of a logical inference problem, including all facts, all inference rules and their equivalent rules. Then, three tile assembly subsystems are discussed to fulfil the main logical deduction steps. We describe mechanisms for finding the successful solutions among the many parallel assemblies. A whole tile assembly system is established on the base of a seed configuration and three subsystems. This prototype is the first programming language to implement deduction operations based on two-dimensional DNA assembly. It is demonstrated that algorithmic DNA tile assembly system can be treated as an important way to implement logic inference, which will shed light on aspects of applications in the field of artificial intelligence in the future.