Eternacon PuzzleJam 2020

This is PuzzleJam 2020

PuzzleJam 2020 is going to be a contest to see what players can best design puzzles that have some basic goals.
The following are the generic rules for each category

  1. If a puzzle is published, it has to have the correct tag for your category
  2. If a puzzle is published, the player has to have solved it.
  3. The puzzle needs to be solved in the puzzlemaker
  4. Have fun!

Puzzle 1: The art contest

Design RNA secondary structures to make art
Use tag [PuzzleJam Art]


  1. Use the Eternafold or LinearFold-Eterna free energy engine
  2. Include some level of structural diversity

Puzzle 2: The Switch Puzzle

Design RNA sequences that switch secondary structures
Use tag [PuzzleJam Switch]


  1. Puzzle has to be a 3-state structure switch
  2. Puzzle must contain natively occurring RNA aptamers that will be posted in the forum
  3. Extra points for artistic design!

A list of some current aptamers currently allowed include:


I’ll add to this list, along with sequences, later in the day.

Puzzle 3: The Difficult One

Publish using tag [PuzzleJam Difficult]
You must design a difficult to solve puzzle


  1. Must have all stem lengths be two base pairs or longer
  2. Must not have base or base pair constraints
  3. Must use Eternafold or LinearFold-Eterna free energy model.

Bonus Puzzle: The Science Proposal

Using tag [PuzzleJam Science]
Make a proposal or a puzzle that aims to use RNA design to investigate some aspect of RNA structure, methodology, or medicine

Examples of open design problems in RNA:

RNA Logic Systems
In an effort to make an RNA only computer, the logic systems of an RNA need to expanded significantly. Can you make a proposal or design that incorporates complex logic using RNA? Potential inputs include other RNA, DNA, protein, or small molecules.

mRNA design
While we are currently focusing on the design of mRNA for the coronavirus spike protein, there are other diseases that could benefit from mRNA vaccines. Can we get a headstart on designing these mRNA using the strategies developed by the Das lab currently?

Many state RNA systems
The Das lab has currently only focused on the design of 2-state switches. Can you make a proposal for an RNA system that has more than 2 states? What about other small molecule inputs?

And there are many, many more!

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