School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
Bioinformatics. 2018 Aug 15;34(16):2862-2864. doi: 10.1093/bioinformatics/bty216.
Toehold switches are a class of RNAs with a hairpin loop that can be unfolded upon binding a trigger RNA, thereby exposing a ribosome binding site (RBS) and permitting translation of the reporter protein. They have been shown very useful in detecting a variety of targets including RNAs from Zika and Ebola viruses. The base complementation between the toehold switch and the trigger RNA also makes it sensitive to sequence variations. Design of toehold switches involves a series of considerations related to their sequence properties, structures and specificities.
Here we present the first comprehensive web tool for designing toehold switches. We also propose a score for predicting the efficacy of designed toehold switches based on properties learned from ∼180 experimentally tested switches.
The toehold switch web tool is available at https://yiplab.cse.cuhk.edu.hk/toehold/.
适体开关是一类具有发夹环的 RNA，当与触发 RNA 结合时可以展开，从而暴露核糖体结合位点 (RBS)，并允许报告蛋白的翻译。它们已被证明在检测各种靶标（包括寨卡病毒和埃博拉病毒的 RNA）方面非常有用。适体开关与触发 RNA 之间的碱基互补也使其对序列变异敏感。适体开关的设计涉及一系列与它们的序列特性、结构和特异性相关的考虑因素。
这里我们提出了第一个用于设计适体开关的综合网络工具。我们还提出了一个基于从大约 180 个经过实验测试的开关中学习到的特性来预测设计的适体开关效果的评分。
适体开关网络工具可在 https://yiplab.cse.cuhk.edu.hk/toehold/ 获得。
