Stanford
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Docket #: S15-015

Platform for Engineering Molecular Sensor RNA Devices

Researchers in Professor Christina Smolke's laboratory have developed an advanced, high-throughput directed evolution platform for designing and discovering RNA devices that can sense and respond to various target ligands in real-time. This automated system employs a robotic platform to evaluate hundreds of thousands of RNA sequences from libraries of functional RNA sequences (aptamers with genetic control elements) under identical conditions with or without the target molecule. The assay uses ligand molecules in their natural state and does not require prior knowledge of their structure. The aptamers and control elements are jointly optimized and function through conformational changes, resulting in more sensitive and effective RNA-based sensors than previous devices. These sensors can be used in various applications, including synthetic biology, cell or gene therapy, research, or diagnostics..

Stage of Research

The inventors have validated their high-throughput platform by building biosensors for diverse ligands, demonstrating superior performance in gene silencing, activation ratio, and ligand sensitivity compared to traditional RNA devices.

Related Inventions

Applications

  • RNA-based molecular biosensors and gene switches - high-throughput platform to generate novel RNA devices that sense and respond to other molecules

Advantages

  • Robust, scalable, high-throughput process:
    • rate of ~2 hours/cycle and less than 1 week total elapsed time to develop a new sensor to a target of interest
    • solution-based process can be automated and implemented on a robotic platform (no complex separation steps)
    • readily parallelizable – measures activities of hundreds of thousands of sequences from RNA device libraries in the absence or presence of ligands
  • Selection for diverse molecules in natural state:
    • target ligand is not immobilized
    • can sense unidentified or unisolated targets – no structural or detailed knowledge of targets are needed
    • generates new aptamers in context with switching components such that they work together
  • Advantages of RNA devices created with this system:
    • fast switching based on conformational changes in tertiary structure of RNA molecule
    • better ligand sensitivity, dynamic range, gene silencing, and activation ratio compared with than traditional RNA devices

Publications

End User Applications of RNA Devices

  • Synthetic biology: sensing key molecules in a pathway to control biological production
  • Agriculture: controlling crop traits with RNA device tools
  • Drug development: targeting therapeutic agents to particular cell types by coupling them to a riboswitch that is sensitive to cell-specific markers
  • Gene therapy: controlling gene expression in real time with riboswitches that respond to small, non-toxic, bioavailable molecules
  • Cell therapy: employing drug-responsive riboswitches to control activities of cell therapies such as cytolytic activity, proliferation, and survival of CAR-engineered T cells
  • Environmental sensing: biological monitoring for toxins or other compounds with a riboswitch coupled to fluorescent proteins or other visual readout
  • Diagnostics: detecting disease markers
  • Research: identifying and analyzing molecules of interest in live cells, tissues or organisms
  • Aptamer design: developing modular aptamers that could be used in different systems that require high-affinity binding

Patents

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