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Tuesday, August 1 • 16:00 - 16:40
Oligo-Designer: rational design for easy gene construction and high protein expression

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Each biotech company has to create new genetic constructions and express proteins. The most popular gene synthesis method is PCR-based assembly from a set of oligonucleotides. To increase synthesis purity most scientists often design oligonucleotides intuitively with one or a number of heuristics, but this often leads to loss of protein expression.

 In this work we present Oligo-Designer (a part of BIOCAD YLab computational platform) — a novel oligonucleotides design software that optimizes the probability of successful gene synthesis and protein expression in specified cell culture. We use genetic algorithm and a set of rational physics-based metrics to solve common problems like hairpins, low binding energy and oligonucleotides cross-reactivity. This helps us to obtain an optimum set of oligonucleotides. The algorithm can be used both in single gene or library mode. Using this algorithm in 2016 we created 466 gene constructions (exact or libraries) with average expression after transient transfection between 150 and 200 mg/l. We also present a fully-automated synthesis pipeline using Biosset and Tecan hardware.

avatar for Pavel Yakovlev

Pavel Yakovlev

Director of Computational Biology Department, BIOCAD

Tuesday August 1, 2017 16:00 - 16:40
Graduate School of Management Building, room 309 Volkhovskiy Pereulok, 3, St. Petersburg, Russia