| Autor: |
Lyons E; Laboratory of Functional Genomics, Department of Computational Biology and Medical Science, School of Frontier Sciences, University of Tokyo, Tokyo, 108-8639, Japan. elilyons@gmail.com., Sheridan P; Department of Active Life Promotion Science, Graduate School of Medicine, Hirosaki University, Hirosaki, 036-8562, Japan., Tremmel G; Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan., Miyano S; Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan., Sugano S; Laboratory of Functional Genomics, Department of Computational Biology and Medical Science, School of Frontier Sciences, University of Tokyo, Tokyo, 108-8639, Japan. |
| Abstrakt: |
High-throughput screens allow for the identification of specific biomolecules with characteristics of interest. In barcoded screens, DNA barcodes are linked to target biomolecules in a manner allowing for the target molecules making up a library to be identified by sequencing the DNA barcodes using Next Generation Sequencing. To be useful in experimental settings, the DNA barcodes in a library must satisfy certain constraints related to GC content, homopolymer length, Hamming distance, and blacklisted subsequences. Here we report a novel framework to quickly generate large-scale libraries of DNA barcodes for use in high-throughput screens. We show that our framework dramatically reduces the computation time required to generate large-scale DNA barcode libraries, compared with a naїve approach to DNA barcode library generation. As a proof of concept, we demonstrate that our framework is able to generate a library consisting of one million DNA barcodes for use in a fragment antibody phage display screening experiment. We also report generating a general purpose one billion DNA barcode library, the largest such library yet reported in literature. Our results demonstrate the value of our novel large-scale DNA barcode library generation framework for use in high-throughput screening applications. |
