Improving Initial Pool Generation of Direct-Proportional Length-Based DNA Computing by Parallel Overlap Assembly

Abstract

A direct-proportional length-based DNA computing approach for weighted graph problems has been proposed where the cost of each path is encoded by the length of oligonucleotides in a proportional way. During the initial pool generation, the hybridization/ligation phase is carried out where all the combinations are generated in the solution. However, this encoding suffers from biological behavior of hybridization since longer oligonucleotides are more likely to hybridize as oppose to the shorter ones. Recently, parallel overlap assembly (POA) has been recognized as an efficient initial pool generation of DNA computing for weighted graph problems. If POA is employed during the initial pool generation of direct-proportional length-based DNA computing, we expected that the biological influence contributed by various lengths of the oligonucleotides could be minimized as much as possible. Thus, in this paper we found 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.