An extended dot-bracket notation for functional nucleic acids

Functional nucleic acids are an attractive substrate for molecular computing. A nucleic acid molecule is a linear chain of covalently bound building blocks assembled in arbitrary order from a set of typically four nucleotides. Certain pairs of nucleotides weakly attract each other through short-range electrostatic interaction and, accordingly, complementary sequences of nucleotides can bind to each other. The complementary stretches of nucleic acids that attract each other can be part of two different molecules or two parts of a single molecule. Binding within a single molecule leads to a folding of the linear chain. This so called secondary structure is of great importance for the function of nucleic acids. The present paper is concerned with the representation of this secondary structure. We propose an extension for the syntax of the standard dot-bracket notation to increase its convenience and expressive power for both its use to communicate nucleic acid secondary structures among humans and machines. The extensions reflect our own requirements for the representation of nucleic acids for molecular computation, but should be useful for functional nucleic acids in general.