Abstract
Biotechnological and biomolecular advances have introduced novel uses for DNA such as DNA computing, storage, and encryption. For these applications, DNA sequence design requires maximal desired (and minimal undesired) hybridizations, which are the product of a single new DNA strand from 2 single DNA strands. Here, we propose a novel constraint to design DNA sequences based on thermodynamic properties. Existing constraints for DNA design are based on the Hamming distance, a constraint that does not address the thermodynamic properties of the DNA sequence. Using a unique, improved genetic algorithm, we designed DNA sequence sets which satisfy different distance constraints and employ a free energy gap based on a minimum free energy (MFE) to gauge DNA sequences based on set thermodynamic properties. When compared to the best constraints of the Hamming distance, our method yielded better thermodynamic qualities. We then used our improved genetic algorithm to obtain lower-bound DNA sequence sets. Here, we discuss the effects of novel constraint parameters on the free energy gap.
Highlights
More than half a century has passed since the double helix configuration of DNA was identified [1]
The hybridization reaction between 2 DNA sequences is important for advanced DNA applications because its efficiency and accuracy directly influence application reliability; false hybridization is an unavoidable artifact of combining DNA strands due to biotechnical limitations
False hybridizations occur as false positives and false negatives [3,4]
Summary
More than half a century has passed since the double helix configuration of DNA was identified [1]. Such knowledge about DNA contributes to virtually every area of science, including the use of DNA as a computational tool [2]. A false positive hybridization is a new duplex formed by mismatched single DNA sequences, due to a lack of single-strand similarities. Designing DNA sequences which satisfy some constraints could reduce false positives and improve hybridization uncertainty and inaccuracy between probes and their complementary targets. Accurate DNA production reduces false hybridizations and improves accuracy. The goal of DNA sequence design is to find the maximal number of designs that satisfy single or combinatorial constraints as well as the smallest design that satisfies these constraints
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