A Novel Constraint for Thermodynamically Designing DNA Sequences
A Novel Constraint for Thermodynamically Designing DNA Sequences
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DOI：
10.1371/journal.pone.0072180
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发表时间：
2013-08
期刊：
影响因子：
3.7
通讯作者：
Qiang Zhang;Bin Wang;Xiaopeng Wei;Changjun Zhou
中科院分区：
文献类型：
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作者：
Qiang Zhang;Bin Wang;Xiaopeng Wei;Changjun Zhou
生物技术和生物分子的进步已经为DNA引入了新的用途，例如DNA计算，存储和加密。对于这些应用，DNA序列设计需要最大的期望（和最小的不期望）杂交，其是来自2条单链DNA的单个新DNA链的产物。在这里，我们提出了一种新的约束设计DNA序列的热力学性质的基础上。DNA设计的现有约束是基于汉明距离的，这是一种不解决DNA序列的热力学性质的约束。使用一种独特的，改进的遗传算法，我们设计的DNA序列集，满足不同的距离约束，并采用基于最小自由能（MFE）的自由能隙来衡量DNA序列的基础上设置的热力学性质。当比较的最佳约束的汉明距离，我们的方法产生了更好的热力学品质。然后，我们使用我们改进的遗传算法，以获得下界的DNA序列集。在这里，我们讨论了新的约束参数对自由能隙的影响。
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.