Characterizing DNA Bond Shapes Using Trajectories

Article type: Research Article

Authors: Domaratzki, Michael

Affiliations: Department of Computer Science, University of Manitoba, Winnipeg, MB, R3T 2T2, Canada. mdomarat@cs.umanitoba.ca

Note: [] Address for correspondence: Department of Computer Science, University of Manitoba, Winnipeg, MB, R3T 2T2, Canada

Abstract: We consider the use of DNA trajectories to characterize DNA bond shapes. This is an extension of recent work on the bond-free properties of a language. Using a new definition of bondfreeness, we show that we can increase the types of DNA bond shapes which are expressible. This is motivated by the types of bond shapes frequently found in DNA computing. We examine the algebraic properties of sets of DNA trajectories. In particular, we consider rotation of trajectories and weakening of the bonding conditions expressed by a set of DNA trajectories. We also consider decidability results for bond-freeness with respect to our definition.

Journal: Fundamenta Informaticae, vol. 87, no. 3-4, pp. 269-285, 2008