RNA molecules often adopt complex 3-dimensional structures in nature. The structure of RNA and other large biomolecules can be broken down into four levels of increasing complexity.
Main article: Sequence
The primary structure of RNA consists of the nucleotide sequence, customarily written in the 5' to 3' direction.
Main article: Secondary Structural Motifs in RNA
The secondary structure of RNA is created by base pairing between complementary regions. Two general types of secondary structure are encountered in EteRNA: stacks and loops. Stacks, or helices, are regions of paired bases, while loops are regions of unpaired bases. An additional type of secondary structure, the pseudoknot, is not present in EteRNA puzzles. The EteRNA game currently displays secondary structure. Puzzles in EteRNA focus on the creation of sequences that adopt a given secondary structure. Secondary structure can be conveniently represented in dot-bracket notation.
Main article: Tertiary Structure
The tertiary structure of RNA refers to the 3-dimensional structure of the molecule. While the secondary structure of a hairpin might specify the paired and unpaired bases, the tertiary structure describes the position of each atom in space. The biological activity of many RNAs requires that the molecule adopt a specific tertiary structure.
The quaternary structure of RNA refers to complexes formed by multiple interacting RNA and/or protein molecules.