title: Effect of inert tails on the thermodynamics of DNA hybridization.
abstract: The selective hybridization of DNA is of key importance for many practical applications such as gene detection and DNA-mediated self-assembly. These applications require a quantitative prediction of the hybridization free energy. Existing methods ignore the effects of non-complementary ssDNA tails beyond the first unpaired base. We use experiments and simulations to show that the binding strength of complementary ssDNA oligomers is altered by these sequences of non-complementary nucleotides. Even a small number of non-binding bases are enough to raise the hybridization free energy by approximately 1 kcal/mol at physiological salt concentrations. We propose a simple analytical expression that accounts quantitatively for this variation as a function of tail length and salt concentration.
authors.affiliation: Cavendish Laboratory, Department of Physics, University of Cambridge , J.J. Thomson Avenue, CB3 0HE Cambridge, United Kingdom.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Di Michele
authors.forename: Bortolo M
authors.initials: BM
authors.lastname: Mognetti
authors.forename: Taiki
authors.initials: T
authors.lastname: Yanagishima
authors.forename: Patrick
authors.initials: P
authors.lastname: Varilly
authors.forename: Zachary
authors.initials: Z
authors.lastname: Ruff
authors.forename: Daan
authors.initials: D
authors.lastname: Frenkel
authors.forename: Erika
authors.initials: E
authors.lastname: Eiser
mesh_terms: D004247:DNA / Q000737:chemistry*; D009693:Nucleic Acid Hybridization; D013816:Thermodynamics
chemical_list: D004247:DNA