Experimental implementation of matrix multiplication by DNA computing

Abstract

In this chapter, a method to do binary multiplication with DNA molecules based on DNA computing is presented. The first proposal on matrix multiplication with DNA has been presented by John S. Oliver. However, here, the scheme of Boolean matrix multiplication, which has been proposed by Oliver, is improved, simplified, and realized in laboratory experiments. During the in vitro implementation, parallel overlap assembly is employed to construct every possible path in the directed graph in massively parallel fashion. A test of the reaction to identify the existence of a path is done by polymerase chain reaction. After that the product of polymerase chain reaction is subjected to polyacrylamide gel electrophoresis in order to visualize the result of the computation. By analyzing the existence of the bands of gel electrophoresis, it is able to read the output of the Boolean matrix multiplication. The experimental results prove the performance of a mathematical calculation based on DNA computing.