title: A novel constraint for thermodynamically designing DNA sequences.
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.
authors.affiliation: Key Laboratory of Advanced Design and Intelligent Computing (Dalian University), Ministry of Education, Dalian, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhang
authors.forename: Bin
authors.initials: B
authors.lastname: Wang
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Wei
authors.forename: Changjun
authors.initials: C
authors.lastname: Zhou
mesh_terms: D000465:Algorithms; D001482:Base Composition; D001483:Base Sequence; D015342:DNA Probes / Q000235:genetics*; D008957:Models, Genetic; D012984:Software; D013816:Thermodynamics
chemical_list: D015342:DNA Probes