toehold

toehold designs and scores toehold switch RNA sensors for sequence-specific detection of trigger RNAs by generating hairpin-forming sequences that expose a ribosome binding site upon trigger binding to initiate reporter protein translation.

Key Features:

• Design and optimization: Generates and optimizes toehold switch sequences that form hairpin structures which unfold upon binding a specific trigger RNA to expose a ribosome binding site (RBS) and initiate translation of a reporter protein.
• Base-complementation specificity: Accounts for base complementation between switch and trigger RNA to enable tuning for sequence-specific detection.
• Sequence and structural evaluation: Evaluates sequence properties, structural configurations, and specificities during design.
• Predictive scoring: Implements a scoring system that predicts switch efficacy using empirical data derived from approximately 180 experimentally tested switches.
• Target applicability: Supports design for detecting targets including viral RNAs such as Zika and Ebola viruses.

Scientific Applications:

• Molecular diagnostics: Designs RNA-based sensors for detecting viral RNAs, including Zika and Ebola.
• Synthetic biology: Provides modular RNA sensors to control translation of reporter proteins in synthetic biology applications.
• RNA biology research: Enables study of sequence-structure-function relationships and base complementation effects in RNA-mediated regulation.
• Molecular biology assays: Facilitates construction of translation-based reporter assays via RBS exposure upon trigger binding.

Methodology:

Designs are generated and evaluated by considering sequence properties and structural configurations, and are scored by a predictive model trained on empirical data from approximately 180 experimentally tested switches.