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Boosting
Certain combinations of nucleotides can lower energy when they occur at the first unpaired positions of a loop. These positions are sometimes called "boost points". The energy of loops in EteRNA is determined by the -
Welcome
The EteRNA wiki has been moved to a new domain. If you have a question and can't find an answer on the wiki, you may want to browse the EteRNA forum on GetSatisfaction, consult -
Dot-Bracket Notation
Dot-bracket notation is a convenient way of representing secondary structure. Each character represents a base. Open parentheses indicate that the base is paired to another base ahead of it. Closed parenthesees indicate that a -
Base Pairing
Base pairs with unusual geometries and the interactions between mismatched bases are not explicitly depicted in EteRNA. Base pairs can be considered the "glue" that holds together a folded RNA. Breaking a base pair that -
Frequently Asked Questions
Have a question regarding the game? See if it has been answered here. Frequently asked questions are organized by topic, but it may be helpful to search this page for for a keyword specific to -
GC Pairs
GC pairs (or CG pairs) are base pairs that form between guanine and cytosine. GC pairs are stronger than AU or GU pairs. Most successful lab designs contain between 50-70% GC pairs. Designs that -
RNA
Ribonucleic acid, or RNA, is molecule present in all living organisms. Like DNA, RNA consists of a chain of simple building blocks called nucleotides. The chemical properties of RNA allow this chain to fold back -
Pairing Probabilities Plot
The pairing probabilities plot, also called a dot plot, is a visual representation of the likelihood that any two bases in a sequence will form a base pair. The numbering of the dot plot begins -
Nucleotides
Nucleotides are the building block from which RNA and DNA are constructed. Each nucleotide consists of a nitrogen-containing base, a sugar, and a phosphate group. Nucleotides are connected by bonds between the phosphate group -
Lab
This article is an overview of the RNA lab. For the lab FAQ, click here Labs are type of puzzle in EteRNA where player solutions are synthesized and scored on their ability to fold properly -
Bases
Bases are components of nucleotides, which in turn are the building blocks of RNA and DNA. The four bases commonly enountered in RNA are adenine, guanine, cytosine, and uracil. Bases are sometimes called nitrogenous bases -
Free Energy
In the context of the EteRNA game, free energy can be thought of as the energy released by folding a completely unfolded RNA molecule. Conversely, it can be thought of as the amount of energy -
Multiloop
A multiloop, sometimes called a junction or multi-branched loop, is a region where three or more stacks come together. These stacks may or may not be separated by unpaired bases. One convenient way of -
Hidden Instabilities
Hidden instabilities are features that indirectly stabilize the target structure by destabilizing misfolded structures. These instabilities are usually only revealed when base pairs in the target structure are broken. In some cases, placing hidden instabilities -
Shape Notation
Shape notation is the method by which you may manually code for the shape that you desire your RNA to fold into. This feature is only available in the player puzzle maker, which is unlocked -
Target structure
The target structure is a secondary structure that players attempt to satisfy when solving puzzles and designing lab submissions. The puzzle designer is used to create target structures for puzzles. To view the target structure -
Restrictions
Many puzzles place restrictions on player solutions. Restrictions increase difficulty and help players avoid sequences that can cause synthesis of lab submissions to fail. In player puzzles not designed as lab candidates, players can require -
Special Sequences
Certain structures in EteRNA can only be solved using one or a few sequences. Zigzags have a large number of solutions, but they are not always immediately apparent and are unlikely to be found by -
Internal Loop
An internal loop is a region of unpaired bases with two adjacent stacks. In an internal loop, unpaired bases are found on both sides of the stack. This differs from a bulge, where only one -
Base Pair Flipping
Base pair flipping, usually referred to as simply "flipping," refers to switching the two nucleotides that are paired in a structure. The flipping tool in EteRNA can be selected by clicking the two white dots -
Suboptimal Structure
Alternative, or suboptimal structures are structures that a given sequence could fold into aside from the minimum free energy structure. As an RNA folds, it may pass through several suboptimal structures before it adopts a -
Puzzle Design
300px The ability to design puzzles is unlocked once a player has earned 20000 points. Only three puzzles can be submitted in any given 24-hour period. All player puzzles are worth 100 points. -
Sugar
Sugars are carbohydrates - organic molecules with the empirical formula Cx(H2O)y - that are used as energy sources and structural components by all life on earth. Simple sugars contain one sugar unit, or saccharide. Other -
Zigzag
A zigzag is a series of alternating bulges or asymmetric internal loops. Solving zigzags requires the use of specific sequences. Zigzags may be viewed as a "collapsed" symmetric internal loop. -
Hairpin Loop
A hairpin loop is a region of unpaired bases with only one adjoining stack. Hairpin loops are described in terms of the number of unpaired bases in the loop. A prefix (tri-, tetra-, penta-, hexa
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