Hairpin Structures Defined by DNA Trajectories

We examine scattered hairpins, which are structures formed when a single strand of nucleotides folds into a partially hybridized stem and a loop. To specify different classes of hairpins, we use the concept of DNA trajectories, which allows precise descriptions of valid bonding patterns on the stem of the hairpin. DNA trajectories have previously been used to describe bonding between separate strands. We are interested in the mathematical properties of scattered hairpins described by DNA trajectories. We examine the complexity of the set of hairpin-free words described by a set of DNA trajectories. In particular, we consider the closure properties of language classes under sets of DNA trajectories of differing complexity. We address decidability of recognition problems for hairpin structures.

• Type: Conference
• Year: 2006
• Where: DNA
• Authors: Michael Domaratzki
• Keywords: Bioinformatics, DNA 2006, DNA Trajectories, Scattered Hairpins, Valid Bonding Patterns