Parallel overlap assembly for initial pool generation of direct-proportional length-based DNA

Abstract

In the previous work, in order to overcome the limitation of constant-proportional length-based DNA computing, an alternative approach, which is called directproportional length-based DNA computing for weighted graph problem has been proposed. Based on the proposed approach, the cost of each path is encoded proportionally to the length of oligonucleotides, or oligos for short. In other words, the longer oligos are employed to encode larger cost and vice versa. During the initial pool generation, the phase where all the combinations are generated in the solution, a method called hybridization/ligation is employed. However, the initial pool generation based on hybridization/ ligation suffers from the biochemical behavior of hybridization because the longer oligos are more likely to hybridize compared to the shorter oligos. In this paper, an efficient method for initial pool generation, which is parallel overlap assembly is studied, examined, and applied. It turns out that the hybridization/ligation method should be replaced with parallel overlap assembly, for a better and efficient initial pool generation of direct-proportional length-based DNA computing, and our argument is supported by implementing actual experiments.