Low-Bias Manipulation of DNA Oligo Pool for Robust Data Storage

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.