Quantitative determination of size and shape of surface-bound DNA using an acoustic wave sensor

Biophysical Journal

Volumn 94, Issue 7, 2008, Pages 2706-2715

  Tsortos, Achilleas ^a   Papadakis, George ^a,b   Mitsakakis, Konstantinos ^a,b   Melzak, Kathryn A ^a,b   Gizeli, Electra ^a,b  

^a INSTITUTE OF MOLECULAR BIOLOGY AND BIOTECHNOLOGY   (Greece)

^b UNIVERSITY OF CRETE   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ACOUSTICS; ARTICLE; CHEMISTRY; EQUIPMENT; EQUIPMENT DESIGN; EVALUATION; GENETIC PROCEDURES; INSTRUMENTATION; METHODOLOGY; MICROELECTRODE; MOLECULAR WEIGHT; TRANSDUCER; ULTRASTRUCTURE;

ACOUSTICS; BIOSENSING TECHNIQUES; DNA; EQUIPMENT DESIGN; EQUIPMENT FAILURE ANALYSIS; MICROELECTRODES; MOLECULAR WEIGHT; TRANSDUCERS;

EID: 41649109444     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.119271     Document Type: Article

References (40)

1. Luscombe, N. M., S. E. Austin, H. M. Berman, and J. M. Thornton. 2000. An overview of the structures of protein-DNA complexes. Genome Biol. 1:1-37.
2. Dlakic, M., and T. K. Kerppola. 2001. DNA changes coupled to protein binding. In Encyclopedia of Life Sciences. Nature Publishing Group. 1-10. Available at http://www.mrw.interscience.wiley.com/emrw/9780470015902/search/ firstpage.
3. Kahn, J. D., E. Yun, and D. M. Crothers. 1994. Identification of localized DNA flexibility. Nature. 368:163-166.
4. Allen, M. J., E. M. Bradbury, and R. Balhorn. 1997. AFM analysis of DNA-protamine complexes bound to mica. Nucleic Acids Res. 25:2221-2226.
5. Hansma, H. G., I. Revenko, K. Kim, and D. E. Laney. 1996. Atomic force microscopy of long and short double-stranded, single-stranded and triple-stranded nucleic acids. Nucleic Acids Res. 24:713-720.
6. Lehner, R., J. Koota, G. Maret, and T. Gisler. 2006. Segment distributions of end-tethered polymers in a good solvent. Phys. Rev. Lett. 96:107801.
7. Moiseev, L., M. S. Ünlü, A. K. Swan, B. B. Goldberg, and C. R. Cantor. 2006. DNA conformation on surfaces measured by fluorescence self-interference. Proc. Natl. Acad. Sci. USA. 103:2623-2628.
8. Liley, M. 2002. Optical transducers. In Biomolecular Sensors. E. Gizeli and C. R. Lowe, editors. Taylor & Francis, London. 123-175.
9. Ballantine, D. S., R. M. White, S. J. Martin, A. J. Ricco, E. T. Zellers, G. C. Frye, and H. Wohltjen. 1997. Acoustic Wave Sensors. Academic Press, San Diego, CA.
10. Cantor, C. R., and P. R. Schimmel. 1980. Biophysical Chemistry, Part II. Freeman, San Francisco.
11. Tanford, C. 1961. Physical Chemistry of Macromolecules. Wiley, New York.
12. Saha, K., F. Bender, A. Rasmusson, and E. Gizeli. 2003. Probing the viscoelasticity and mass of a surface-bound protein layer with an acoustic waveguide device. Langmuir. 19:1304-1311.
13. Su, H., and M. Thompson. 1995. Kinetics of interfacial nucleic acid hybridization studied by acoustic network analysis. Biosens. Bioelectron. 10:329-340.
14. Crothers, D. M., T. A. Haran, and J. G. Nadeau. 1990. Intrinsically bent DNA. J. Biol. Chem. 265:7093-7096.
15. Gohlke, C. DNA Curvature Analysis. http://www.lfd.uci.edu/~gohlke/curve/.
16. Gizeli, E. 1997. Design considerations for the acoustic waveguide biosensor. Smart Mater. Struct. 6:700-706.
17. Martin, S. J., A. J. Ricco, T. M. Niemczyk, and G. C. Frye. 1989. Characterization of SH acoustic plate mode liquid sensors. Sensor Actuator. 20:253-268.
18. Josse, F., and Z. Shana. 1988. Analysis of shear horizontal surface waves at the boundary between a piezoelectric crystal and a viscous fluid medium. J. Acoust. Soc. Am. 84:978-984.
19. Ricco, A. J., and S. J. Martin. 1987. Acoustic wave viscosity sensor. Appl. Phys. Lett. 50:1474-1476.
20. Larsson, C., M. Rodahl, and F. Höök. 2003. Characterization of DNA immobilization and subsequent hybridization on a 2D arrangement of streptavidin on a biotin-modified lipid bilayer supported on SiO2. Anal. Chem. 75:5080-5087.
21. Rosano, C., P. Arosio, and M. Bolognesi. 1999. The x-ray three-dimensional structure of avidin. Biomol. Eng. 16:5-12.
22. Eimer, W., and R. Pecora. 1991. Rotational and translational diffusion of short rodlike molecules in solution: oligonucleotides. J. Chem. Phys. 94:2324-2329.
23. Maher, L. J. 1998. Mechanisms of DNA bending. Curr. Opin. Chem. Biol. 2:688-694.
24. Liberles, D. A., and P. B. Dervan. 1996. Design of artificial sequence-specific DNA bending ligands. Proc. Natl. Acad. Sci. USA. 93:9510-9514.
25. Sun, Y., X. Li, N. Duzgunes, Y. Takaoka, S. Ohi, and S. Hirota. 2003. The shape parameter of liposomes and DNA-lipid complexes determined by viscometry utilizing small sample volumes. Biophys. J. 85:1223-1232.
26. Moore, W. R. 1967. Viscosities of dilute polymer solutions. Prog. Polym. Sci. 1:3-43.
27. Wierenga, A. M., and A. P. Philipse. 1998. Low-shear viscosity of isotropic dispersions of (Brownian) rods and fibres; a review of theory and experiments. Colloids Surf. A Physicochem. Eng. Asp. 137:355-372.
28. Levicky, R., T. M. Herne, M. J. Tarlov, and S. K. Satija. 1998. Using self-assembly to control the structure of DNA monolayers on gold: a neutron reflectivity study. J. Am. Chem. Soc. 120:9787-9792.
29. Garcia de la Torre, J., and V. A. Bloomfield. 1978. Hydrodynamic properties of macromolecular complexes IV. Intrinsic viscosity theory, with applications to once-broken rods and multisubunit proteins. Biopolymers. 17:1605-1627.
30. Garcia de la Torre, J., and V. A. Bloomfield. 1981. Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications. Q. Rev. Biophys. 14:81-139.
31. Suto, R. K., M. J. Clarkson, D. J. Tremethick, and K. Luger. 2000. Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nat. Struct. Biol. 7:1121-1124.
32. White, E. M., D. L. Shapiro, C. D. Allis, and A. M. Gorovsky. 1988. Sequence and properties of the message encoding Tetrahymena hv1, a highly evolutionarily conserved histone H2A variant that is associated with active genes. Nucleic Acids Res. 16:179-198.
33. Wolffe, A. P., and D. Guschin. 2000. Chromatin structural features and targets that regulate transcription. J. Struct. Biol. 129:102-122.
34. Su, X., Y. J. Wu, and W. Knoll. 2005. Comparison of surface plasmon resonance spectroscopy and quartz crystal microbalance techniques for studying DNA assembly and hybridization. Biosens. Bioelectron. 21:719-726.
35. Martin, S. J., G. C. Frye, A. J. Ricco, and S. D. Senturia. 1993. Effect of surface roughness on the response of thickness-shear mode resonators in liquids. Anal. Chem. 65:2910-2922.
36. Koç, M., A. Carcaterra, Z. Xu, and A. Akay. 2005. Energy sinks: vibration absorption by an optimal set of undamped oscillators. J. Acoust. Soc. Am. 118:3031-3042.
37. Manghi, M., X. Schlagberger, Y. W. Kim, and R. R. Netz. 2006. Hydrodynamic effects in driven soft matter. Soft Matter. 2:653-658.
38. Wang, C. Y. 2001. Stokes flow through a rectangular array of circular cylinders. Fluid Dyn. Res. 29:65-80.
39. Friedt, J. M., L. Francis, K. H. Choi, F. Frederix, and A. Campitelli. 2003. Combined atomic force microscope and acoustic wave devices: application to electrodeposition. J. Vac. Sci. Technol. A. 21:1500-1505.
40. Peh, W. Y. X., E. Reimhult, H. F. Teh, J. S. Thomsen, and X. Su. 2007. Understanding ligand binding effects on the conformation of estrogen receptor α-DNA complexes: a combinational quartz crystal microbalance with dissipation and surface plasmon resonance study. Biophys. J. 92:4415-4423.