On Optimizing DNA Sequence Design for DNA Logic AND Circuit

Abstract

DNA logic circuit is a popular research topic in biological computing. Initially, simple DNA logic gates were introduced. Later on, models of DNA logic circuits were proposed and simple circuits were successfully demonstrated. This paves way for the invention of DNA computers. However, constructing efficient logic gates from DNA materials is a very complex task because of the properties of DNA, which consists only of 4 different types of nucleotides and the chemical bonding possibilities between different pairs of DNA nucleotides. Constructing logic gates would yield unwanted secondary structures of logic gates because there are a lot of possibilities for other DNA structures to be created from using only four types of nucleotides due to different bonding alignment patterns.This research aims to develop a method which selects the most suitable DNA sequence to be used to construct DNA logic AND gate. This work is a proof of concept that DNA logic gate could be designed more efficiently. Our method is to generate all possible sequences (considering all alignment positions) and select the sequences that yield highest possibility of constructing such a structure. The selected sequences were then applied with the primer design rules in order to filter undesired sequences according to the biological requirements. We performed experiments in silico and the experimental results showed that 75% of the outputs from the application could form our expected structure with highest probability. This significantly helps us save cost from running experiments in vitro.