Abstract
Background
Short hairpin RNAs (shRNAs) expressed from vectors have been used as an effective means of exploiting the RNA interference (RNAi) pathway in mammalian cells. Genome-scale screening with shRNA libraries has been used to investigate the relationship between genotypes and phenotypes on a large scale. Although several methods have been developed to construct shRNA libraries, their broad application has been limited by the high cost of constructing these libraries.
Objective
We develop a new method that efficiently constructs a shRNA library at low cost, using treatments with several enzymes and an oligonucleotide library.
Methods
The library of shRNA expression cassettes, which were cloned into a lentiviral plasmid, was produced through several enzymatic reactions, starting from a library of 20,000 different short oligonucleotides produced by microarray-based oligonucleotide synthesis.
Results
The NGS sequence analysis of the library shows that 99.8% of them (19,956 from 20,000 sequences) were contained in the library: 63.2% of them represent the correct sequences and the rest showed one or two base pair differences from the expected sequences.
Conclusion
Considering the ease of our method, shRNA libraries of new genomes and of specific populations of genes can be prepared in a short period of time for genome-scale RNAi library screening.
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Acknowledgements
We thank Dr. Sunghoon Kim at the Seoul National University for helping with the oligonucleotide library synthesis. This work was supported by the SGER Program through the NRF by the Ministry of Education to Y. Kee (Grant Number NRF-2015R1D1A1A02060346); by the Basic Science Research Program through the NRF by the Ministry of Education (Grant Number NRF-2015R1D1A3A01015641); by a Grant from the National R&D Program for Cancer Control, Ministry of Health & Welfare, Republic of Korea (Grant Number HA17C0035); and by a 2016 Research Grant from Kangwon National University to B.J. Hwang.
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Park, S.K., Kee, Y., Ryu, T. et al. Enzymatic construction of shRNA library from oligonucleotide library. Genes Genom 41, 573–581 (2019). https://doi.org/10.1007/s13258-019-00800-2
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DOI: https://doi.org/10.1007/s13258-019-00800-2