Dot-Bracket Notation

Encoding pseudoknot
The basic unit of the RNA double stranded secondary structure ("hairpin"). You can edit the nucleotide sequence or dot-bracket interaction pattern, the visualization changes accordingly. Brackets must be balanced.
RNA (ribonucleic acids) are an important biological molecules, deeply involved in bringing cell genetic information (stored in other molecule, DNA) into action by actually building the real plant or animal, whatever it be (through regulated synthesis of proteins).

RNA secondary structure is often defined using Dot-Bracket Notation (DBN). Valid structures in DBN format are well-parenthesized words consisting of dots '.', opening '(' and closing ')' parentheses. Dotted positions are unpaired, whereas matching parenthesized positions represent base-pairing nucleotides. As the number of nucleotides interacting is always even (everyone must have a parter), the brackets must be balanced.

A structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem is called pseudoknot. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982.[1] Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots as they are understood in mathematics. Pseudoknots are marked using alternative [ .. ] or { .. } bracket pairs.

RNA is along chain of four repeating elementary units (nucleotides) that have agreed letter codes G, A, C and U. In addition to the main sequence (primary structure), G can form a weak (non covalent) connection to C anywhere in the chain, and A similarly can pair with U. These interactions (largely) simply and predictably build the actual shape of the molecule, determining its ability the required biochemical function. While most of the chemical reactions in the cell are catalysed by proteins, not by RNA, a hypothesis exist that RNA is evolutionary older than protein and in the deep past was able to do all tasks required to support a living system, on its own. Not just it still plays key role in protein synthesis; many proteins cannot perform they reactions without involving either directly nucleotides (like ATP) or clearly similar molecules (such as NAD). Such RNA, carying catalytic function, is called ribozyme.

The widely known way to determine RNA secondary structure from its sequence (primary structure) is to use the Nussinov algorithm, while other similar methods are used as well. In many cases experimental research is also required.


  1. 1 Staple DW, Butcher SE (2005). Pseudoknots: RNA structures with diverse functions. PLoS Biol.3 (6), e213