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Low-Bias Manipulation of DNA Oligo Pool for Robust Data Storage
ACS Synthetic Biology ( IF 4.7 ) Pub Date : 2020-11-13 , DOI: 10.1021/acssynbio.0c00419
Yanmin Gao 1, 2 , Xin Chen 3 , Hongyan Qiao 1, 2 , Yonggang Ke 4 , Hao Qi 1, 2
Affiliation  

In DNA data storage, the massive sequence complexity creates challenges in repeatable and efficient information readout. Here, our study clearly demonstrated that PCR created significant DNA amplification biases due to its inherent mechanism of inefficient priming, product-as-template, and error-spreading prone, which greatly hinder subsequent applications such as data retrieval in DNA-based storage. To mitigate the amplification bias, we recruited an isothermal DNA amplification by combining strand displacement amplification (SDA) with magnetic beads (MB) DNA immobilization for robust, repeated, and low-bias amplification of DNA oligo pool, comprising over 100 thousand oligos, in a primer-free and low-error-spreading fashion. Furthermore, we introduced oligo pool normalization (OPN), a cost-effective and scalable method for normalizing an oligo pool, by which oligo pools comprising from 256 to 1024 distinct oligos were simply modified with improved Gini-index. Therefore, we believe that the combination of SDA and OPN can provide an ideal amplification mechanism for a low-bias copy of a large oligo pool, which is of vital importance for successful data retrieval in DNA information storage.

中文翻译:

DNA寡核苷酸池的低偏差操纵,可实现可靠的数据存储

在DNA数据存储中,巨大的序列复杂性给可重复和高效的信息读取带来了挑战。在这里,我们的研究清楚地表明,由于PCR固有的效率低下的引物,模板产物和易错分布的机制,PCR产生了明显的DNA扩增偏差,这极大地阻碍了随后的应用,例如基于DNA的存储中的数据检索。为了减轻扩增偏差,我们通过结合链置换扩增(SDA)和磁珠(MB)DNA固定技术来募集等温DNA扩增,以对包含10万多寡核苷酸的DNA寡聚池进行稳健,重复和低偏置的扩增。无底漆和低错误传播方式。此外,我们引入了寡核苷酸池标准化(OPN),一种经济高效且可扩展的标准化寡核苷酸库的方法,通过该方法可以简单地使用改良的Gini指数修改包含256至1024个不同寡核苷酸的寡核苷酸库。因此,我们认为SDA和OPN的结合可以为大型寡核苷酸池的低偏倚拷贝提供理想的扩增机制,这对于成功地在DNA信息存储中进行数据检索至关重要。
更新日期:2020-12-18
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