论文标题
使用相似意义模型的热力学稳定的DNA代码设计
Thermodynamically Stable DNA Code Design using a Similarity Significance Model
论文作者
论文摘要
DNA代码设计旨在生成一组DNA序列（代码字），具有序列之间不希望的杂交及其反向组合（RC）对（RC）对（交叉杂交）的可能性最低。受到单个单链DNA（SSDNA）及其RC对构建的完美双螺旋的独特杂交亲和力（或稳定性）的启发，我们提出了一种新颖的相似性意义（SS）模型，以测量DNA序列之间的相似性。特别是，该提议的SS不是通过任何度量/方法直接测量两个序列的相似性，而是以一种评估在两个测量序列及其RC对的情况下，在理想的杂交中发生不良杂交的可能性更大。使用此SS模型，我们使用基于分类的算法构建了受几种组合约束的热力学稳定DNA代码。与现有方法相比，提出的方案导致具有较大代码大小和更宽的自由能差距（因此更好的跨杂交性能）的DNA代码。
DNA code design aims to generate a set of DNA sequences (codewords) with minimum likelihood of undesired hybridizations among sequences and their reverse-complement (RC) pairs (cross-hybridization). Inspired by the distinct hybridization affinities (or stabilities) of perfect double helix constructed by individual single-stranded DNA (ssDNA) and its RC pair, we propose a novel similarity significance (SS) model to measure the similarity between DNA sequences. Particularly, instead of directly measuring the similarity of two sequences by any metric/approach, the proposed SS works in a way to evaluate how more likely will the undesirable hybridizations occur over the desirable hybridizations in the presence of the two measured sequences and their RC pairs. With this SS model, we construct thermodynamically stable DNA codes subject to several combinatorial constraints using a sorting-based algorithm. The proposed scheme results in DNA codes with larger code sizes and wider free energy gaps (hence better cross-hybridization performance) compared to the existing methods.
