Poster Presentation 2014 International Biophysics Congress

Temperature dependence of DNA hairpin disorder: Effects of adsorption onto gold (#370)

Kurt L.M. Drew 1 , J.P. Palafox-Hernandez 1 , Zak E. Hughes 1 , Tiffany R. Walsh 1
  1. Deakin University, Waurn Ponds, VIC, Australia

The hairpin loop for nucleic acids is an important structural motif that has many possible practical applications.1-4 One such application is the use of a DNA hairpin as a linker between two structures, where the hairpin conformation will change with temperature, modifying the distance between the structures. While there is a lot of information on DNA hairpins tethered onto a gold surface,5 currently there is very little information regarding how the non-covalent adsorption at the gold interface affects the structure and function of the DNA hairpin. It is of interest to know what possible effects gold will have on the conformation of a DNA hairpin linker. Molecular Dynamics (MD) simulations at the atomistic level were used to model the DNA hairpin sequence (5’)GGATAATTTTTTATCC(3’) alone in solution and also at the aqueous Au(111) surface. The “in solution” simulations were performed as a reference for the subsequent DNA-on-gold simulations where the GolP-CHARMM Au(111) force-field6 was used to describe the DNA/water/gold interface. As a measure of the degree of order/disorder in the hairpin structure, we have calculated the root mean square deviation in atomic positions, the number of hydrogen bonds between base pairs and native stacking numbers7 as well as the number of bases in close contact with the gold surface. These analyses indicate that the presence of the gold surface creates an earlier onset of disorder for the DNA hairpin with respect to temperature. Our findings also suggest that there is a strong interaction between the bases and the gold surface.

  1. C. M. Strohsahl, B. L. Miller and T. D. Krauss, Nat. Protoc., 2007, 2, 2105–2110
  2. G. Zauner, Y. Wang, M. Lavesa-Curto, A. MacDonald, A. G. Mayes, R. P. Bowater and J. N. Butt, Analyst, 2005, 130, 345–349.
  3. V. Lavalley, A. Laurent, A. Zebda, J. E. Mendez and V. Stambouli, Sens. Actuat B-Chem, 2007, 124, 564–571.
  4. C. Huang, T. Stakenborg, Y. Cheng, F. Colle, T. Steylaerts, K. Jans, P. Van Dorpe and L. Lagae, Biosens Bioelectron, 2011, 26, 3121–3126.
  5. O.-S. Lee, V. Y. Cho and G. C. Schatz, J Phys Chem. B, 2012, 116, 7000–7005.
  6. L. B. Wright, P. M. Rodger, S. Corni and T. R. Walsh, J Chem Theor Comp, 2013, 9, 1616–1630.
  7. G. Portella and M. Orozco, Angew Chemie Int Ed, 2010, 49, 7673–7676.
  8. K. L. M. Drew, J. P. Palafox-Hernandez, Z. E. Hughes and T. R. Walsh, in preparation 2014.