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A double occurrence word (DOW) is a word in which every symbol appears exactly twice. We define the symbol separation of a DOW [Formula: see text] to be the number of letters between the two copies of a symbol, and the separation of [Formula: see text] to be the sum of separations over all symbols in [Formula: see text]. We then analyze relationship among size, reducibility and separation of DOWs. Specifically, we provide tight bounds of separations of DOWs with a given size and characterize the words that attain those bounds. We show that all separation numbers within the bounds can be realized. We present recursive formulas for counting the numbers of DOWs with a given separation under various restrictions, such as the number of irreducible factors. These formulas can be obtained by inductive construction of all DOWs with the given separation. 

We classify rectangular DNA origami structures according to their scaffold and staples organization by associating a graphical representation to each scaffold folding. Inspired by well studied Temperley-Lieb algebra, we identify basic modules that form the structures. The graphical description is obtained by ‘gluing’ basic modules one on top of the other. To each module we associate a symbol such that gluing of molecules corresponds to concatenating the associated symbols. Every word corresponds to a graphical representation of a DNA origami structure. A set of rewriting rules defines equivalent words that correspond to the same graphical structure. We propose two different types of basic module structures and corresponding rewriting rules. For each type, we provide the number of all possible structures through the number of equivalence classes of words. We also give a polynomial time algorithm that computes the shortest word for each equivalence class.