A novel constraint for thermodynamically designing DNA sequences

PloS One
Qiang ZhangChangjun Zhou

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.

References

Jun 14, 2003·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Robert Penchovsky, Jörg Ackermann
Jan 13, 2005·Journal of Molecular Biology·Mirela AndronescuAnne Condon
Sep 8, 2005·Nucleic Acids Research·Dan TulpanLloyd M Smith
Nov 15, 2005·Nucleic Acids Research·Michael R ShortreedLloyd M Smith
Mar 31, 2007·IEEE Transactions on Nanobioscience·John A RoseAkira Suyama
Feb 26, 2010·BMC Bioinformatics·Dan TulpanSerge Léger
Sep 16, 2010·IEEE Transactions on Nanobioscience·Qiang ZhangChangjun Zhou
May 23, 2012·PloS One·Leonid V Bystrykh

Citations

Mar 14, 2017·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Bin WangZiqi Wei
Mar 11, 2017·Computational Intelligence and Neuroscience·Bin WangXuedong Zheng
Aug 1, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Bin WangChangjun Zhou

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