A new approach for Boolean matrix multiplication with DNA computing

This paper presents a new approach to solve Boolean matrix multiplication using a bio-inspired evolutionary method with DNA computing. While there are many papers proposing the use of DNA for actual computation, very few of these theories are realized in laboratory experiments and those which are successfully implemented are mostly based on protocols introduced in Adleman-Lipton architecture. The use of restriction enzymes in Adleman-Lipton protocols is a limiting factor for the number of synthesizable unique sequences in DNA computing. Synthesized primers are needed to initially generate possible solutions, increasing the complexity and becoming a hurdle for DNA computing to be used for larger computations despite its massive parallel processing characteristics. The hybridization-ligation method used as initial pool generation also has its drawbacks in terms of generation speed and material consumption. In this paper, we introduce a method to implement Boolean matrix multiplication with DNA computing which is less time consuming and less complexities in its designs by eliminating the use of restriction enzymes and by using parallel overlap assembly (POA) method as initial pool generation replacing hybridization-ligation method.