Towards Reliable Simulation of Bounded Fan-in Boolean Circuits using Molecular Beacon

A fundamental concept in computer science is that of the universal Turing machine which is an abstract definition of a general purpose computer. It has also been shown that any computer which is able to simulate Boolean circuits of any complexity is such a general purpose computer. However, few studies have devoted to DNA computer of this kind. Molecular beacon is a hairpin-formed oligonucleotide probe, which can report the presence of target sequence in solution with higher specificity compared with linear probe. It is particularly useful when single base discrimination is desired in the process of hybridization underlying DNA computing. In this paper, molecular beacon is utilized to simulate logical AND and OR gates. Then we present simulating an instance of bounded fan-in Boolean circuit comprising of these gates in time proportional to the depth of the circuit. The purpose of this paper is to explore the possibility of reliably simulating Boolean circuits using molecular beacon