Formal grammars for intermolecular structure

Abstract

Formal grammars can be used to model general forms of intramolecular structure, such as secondary structure of nucleic acids. A new formalism, called cut grammar, is shown to model intermolecular assemblages such as hybridization products, as well. Formal grammars themselves can be modelled by sets of oligonucleotides, and derivations from any context-free grammar can in theory be simulated by hybridization experiments.<>