Monte Carlo molecular simulations of DNA decamer-hexamer strands were carried out over a range of temperatures, both free in solution and bound to a surface in several possible fashions, to investigate the effect of dangling end nucleotides on hybridization. For comparison, analogous hexamer duplexes were also studied in solution. Duplex stability was analyzed in terms of energetic, hydrogen bonding, and structural properties. Of the systems studied, shorter solution sequences interacting with longer surface-bound sequences generally had weaker interactions than the opposite. (C) 2015 Elsevier B.V. All rights reserved.