Purification of multiplex oligonucleotide libraries by synthesis and selection

Complex oligonucleotide (oligo) libraries are essential materials for diverse applications in synthetic biology, pharmaceutical production, nanotechnology and DNA-based data storage. However, the error rates in synthesizing complex oligo libraries can be substantial, leading to increment in cost and...

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Bibliographic Details
Published in:Nature biotechnology 2022-01, Vol.40 (1), p.47-53
Main Authors: Choi, Hansol, Choi, Yeongjae, Choi, Jaewon, Lee, Amos Chungwon, Yeom, Huiran, Hyun, Jinwoo, Ryu, Taehoon, Kwon, Sunghoon
Format: Article
Language:English
Subjects:
Analysis
Chemical synthesis
Complementarity-determining region
Data storage
Deoxyribonucleic acid
Digital data
DNA
Enzymes
Hybridization
Identification and classification
Libraries
Methods
Multiplexing
Nanotechnology
Oligonucleotides
Oligonucleotides - genetics
Purification
Synthesis
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Summary:Complex oligonucleotide (oligo) libraries are essential materials for diverse applications in synthetic biology, pharmaceutical production, nanotechnology and DNA-based data storage. However, the error rates in synthesizing complex oligo libraries can be substantial, leading to increment in cost and labor for the applications. As most synthesis errors arise from faulty insertions and deletions, we developed a length-based method with single-base resolution for purification of complex libraries containing oligos of identical or different lengths. Our method-purification of multiplex oligonucleotide libraries by synthesis and selection-can be performed either step-by-step manually or using a next-generation sequencer. When applied to a digital data-encoded library containing oligos of identical length, the method increased the purity of full-length oligos from 83% to 97%. We also show that libraries encoding the complementarity-determining region H3 with three different lengths (with an empirically achieved diversity >10 ) can be simultaneously purified in one pot, increasing the in-frame oligo fraction from 49.6% to 83.5%.
ISSN:1087-0156
1546-1696
DOI:10.1038/s41587-021-00988-3