面向DNA存储低串扰信息检索的引物设计方法

Primer Design Method for Low Interference Information Retrieval in DNA Storage

摘要

在DNA信息存储中，从寡核苷酸池中准确有效地检索信息是提升其实用性的关键．目前，基于PCR扩增的信息检索方法因具备技术成熟、操作简单和成本低等优势被广泛应用．该方法通过引物与目标文件DNA序列上引物结合位点的特异性结合并扩增实现信息检索，若引物间的正交性不强，极易造成引物与非目标DNA序列的错误结合从而导致信息检索出错．为了提升DNA存储信息检索的准确性，提出一种面向DNA存储低串扰信息检索的引物设计方法，该方法主要包括随机引物生成、引物间加权汉明距离设计和强正交性引物筛选3个部分．首先随机生成满足CGC、均聚物长度、熔化温度和吉布斯自由能等基本引物设计规则的引物；然后设计加权汉明距离以确保对引物间正交性的衡量更加精准；最终构建以引物为节点、以加权汉明距离为路径的全耦合网络，并基于网络路径优化的策略筛选出具备强正交性的引物用于DNA存储信息检索，以降低信息检索出错的概率．实验结果表明，通过该方法设计的引物与传统方法相比具有更强的正交性，并且采用该方法设计的引物进行DNA存储信息检索可将误检可能性降低1/5左右，有效提升了DNA存储信息检索的准确性，有助于推动DNA存储的实用化进程．

Abstract

The accurate and efficient retrieval of data from an oligonucleotide pool is crucial for enhancing the practi- cality of DNA information storage systems. Currently，PCR amplication is widely used as an information retrieval method due to its advantages，such as its advanced technological nature，ease of operation，and low cost. This method retrieves information by specifically binding primers to primer binding sites in the target DNA sequences， followed by amplification. However，a lack of primer orthogonality most likely leads to nonspecific binding， resulting in errors. To improve the accuracy of DNA storage information retrieval，this study proposed a novel method for designing primers that enable low-interference information retrieval. It consisted of three main components： random primer generation，the design of weighted Hamming distance for primers，and screening of primers with strong orthogonality. First，primers that met basic primer design rules such as CGC，homopolymer length，melting temperature，and Gibbs free energy were randomly generated. Then，the weighted Hamming distance was designed to ensure a more accurate measurement of primer orthogonality. Finally，a fully-coupled network with primers as nodes and weighted Hamming distances as paths was constructed. From this complex，primers with strong or- thogonality were selected using a network path optimization strategy，thereby reducing the likelihood of errors. The experimental results confirmed that these primers were more orthogonal than those obtained using traditional methods，reducing the risk of false retrieval by about one-fifth. Thus，they effectively improved the accuracy of DNA storage information retrieval and advanced the practical applications of DNA information storage systems.

关键词

DNA 存储 / 信息检索 / 引物 / 引物正交性

Key words

DNA storage / information retrieval / primer / primer orthogonality

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基金资助

天津市科技计划资助项目(22JCYBJC01390)

合成生物技术全国重点实验室自主创新基金资助项目(HCZC-202610A)