The 2012 MIT iGEM team sought to unify aspects from the fields of DNA computing and synthetic biology in one project. We built upon an existing in vitro method of nucleic acid computation, designing new components and extending strand displacement to in vivo applications.

Over the past few months we have:

• established the viability of RNA as an alternative processing medium to DNA
• demonstrated RNA strand displacement in vivo and in vitro
• delivered DNA and RNA into mammalian cells successfully
• designed, modeled, and tested a DNA-based NOT gate, compatible with strand displacement circuits
• designed, modeled, and tested a modular mRNA sensor along with an inverting sensor, both compatible with strand displacement circuits
• designed, modeled, and tested various forms of regulating gene expression at the RNA level, compatible with strand displacement circuits, using:
  • miRNA-induced RNAi knockdown
  • Decoy & TuD mediated double-repression systems
  • self-cleaving Hammerhead ribozymes
• characterized various new MammoBlock parts for transcribing short pieces of RNA in mammalian cells.
• physically submitted 22 of our best standard parts to the Registry of Biological Parts

In addition to our experimental results, we programmed computational models to inform our design decisions. We used Visual DSD to design a strand displacement NOT gate, and we used Visual GEC to design the mRNA sensor and an inverted mRNA sensor.