The syntactic monoid of hairpin-free languages

Authors:
Lila Kari;Kalpana Mahalingam;Gabriel Thierrin
Affiliations:
University of Western Ontario, Department of Computer Science, London, ON, Canada;University of Western Ontario, Department of Computer Science, London, ON, Canada;University of Western Ontario, Department of Mathematics, N6A 5B7, London, ON, Canada
Venue:
Acta Informatica
Year:
2007

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Abstract

The study of hairpin-free words has been initiated in the context of DNA computing. DNA strands that, theoretically speaking, are finite strings over the alphabet {A, G, C, T} are used in DNA computing to encode information. Due to the fact that A is complementary to T and G to C, DNA single strands that are complementary can bind to each other or to themselves in either intended or unintended ways. One of the structures that is usually undesirable for biocomputation, since it makes the affected DNA string unavailable for future interactions, is the hairpin: if some subsequences of a DNA single string are complementary to each other, the string will bind to itself forming a hairpin-like structure. This paper continues the theoretical study of hairpin-free languages. We study algebraic properties of hairpin-free words and hairpins. We also give a complete characterization of the syntactic monoid of the language consisting of all hairpin-free words over a given alphabet and illustrate it with an example using the DNA alphabet.