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EteRNA 3D 8/20/14

Puzzle 1

MS2 RNA

Puzzle 2

Switch enabled with flavin mononucleotide (FMN)

Making computers based of certain conditions. Eg: Virus + RNA + FMN -> Viral Sphere Eg: RNA + FMN + GACAAG - ACAUUG -> Viral Sphere

Readouts

  1. Chemical mapping (SHAPE) -> Can handle 1000s. Ok, but not exciting
  2. RNA array (Johan) -> 10^6 variants, but not detailed. Use to monitor cleavage in RNA possibly.
  3. Plain sequencing:
    • Challenges are RNA that edit their own sequences
    • Challenge: RNA only cuts itself when FMN is added

Why we need to explore 3D

Take 5 inputs, get 2^5 conditions. We want to make RNA micro computers that take these inputs both in 2D and 3D - Some scientists believe that 3D is required, others believe it is not. - Give players the opportunity to use both methods, see which one is better.

Whereas 3D is more compact and requires less things to keep track off when adding pairs, 2D is more flexible.

MAIN NARRATIVE: RNA COMPUTING, for both 2D and 3D

General Ideas

  1. Gamification of 3D

Two words: simplify & juciy.

  • No bases
  • Color code 5', and 3'
  • Explore on-the-fly motif creation to follow 2D mouse
  • Automatic finishing
  • No motif list (only for advanced)
  • Adrien (1 hr/week), full-time coder, designer
  1. Interaction of 2D to 3D

In 3D, "minimap" of 2D, expands into puzzzle -> solve -> publish

  1. Possible Puzzles
  1. Integrate FMN aptamer into 3D fold, ribozyme

Needed: 1) FMN aptamer in a box glowing red until used 2) Topology checker