Structural and tensile properties of self-assembled DNA network on mica surface

CMES - Computer Modeling in Engineering and Sciences

Volumn 46, Issue 2, 2009, Pages 191-207

  Hanasaki, Itsuo ^a   Shintaku, Hirofumi ^a   Matsunami, Satoshi ^a   Kawano, Satoyuki ^a  

^a OSAKA UNIVERSITY   (Japan)

Author keywords

Biodevice; DNA; Molecular dynamics; Network structure; Self assembly; Substrate

Indexed keywords

BIODEVICE; DESIGN REQUIREMENTS; DNA FRAGMENT; DNA MOLECULES; DNA NETWORK; LOADING CONDITION; MANUFACTURING PROCESS; MICA SURFACES; MOLECULAR DYNAMICS SIMULATIONS; NETWORK FORMATION; NETWORK STRUCTURES; PHYSICAL PHENOMENA; SELF-ASSEMBLED; SELF-ASSEMBLED DNA; STRUCTURAL STUDIES; TENSILE LOADS; TENSILE TESTS;

ADSORPTION; DNA; MECHANICAL PROPERTIES; MICA; MOLECULAR DYNAMICS; SELF ASSEMBLY; SILICATE MINERALS; SUBSTRATES; TENSILE TESTING; VIBRATIONS (MECHANICAL);

GENES;

EID: 76249109089     PISSN: 15261492     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (41)

1. Bustamante, C.; Bryant, Z.; Smith, S. B. (2003): Ten years of tension: singlemolecule DNA. Nature, vol.421, pp. 423-427.
2. Bustamante, C.; Smith, S. B.; Liphardt, J.; Smith, D. (2000): Single-molecule studies of DNA mechanics. Curr. Opin. Struct. Biol., vol.10, pp. 279-285.
3. Case, D. A.; Darden, T. A.; III, T. E. C.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Pearlman, D. A.; Crawley, M.; Walker, R. C.; Zhang, W.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Wong, K. F.; Paesani, F.; Wu, X.; Brozell, S.; Tsui, V.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Mathews, D. H.; Schafmeister, C.; Ross, W. S.; Kollman, P. A. (2006): Amber9.
4. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T. (2003): A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comp. Chem., vol.24, pp. 1999-2012.
5. Essevaz-Roulet, B.; Bockelmann, U.; Heslot, F. (1997): Mechanical separation of the complementary strands of DNA. Proc. Nat. Acad. Sci., vol.94, pp. 11935-11940.
6. Goodman, R. P.; Schaap, I. A. T.; Tardin, C. F.; Erben, C. M.; Berry, R. M.; Schmidt, C. F.; Turberfield, A. J. (2005): Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. Science, vol.310, pp. 1661-1665.
7. Hanasaki, I.; Haga, T.; Kawano, S. (2008): Antigen-antibody unbinding process through steered molecular dynamics of a complex of fv fragment and lysozyme. J. Phys.: Condens. Matter, vol.20, pp. 255238 (10 pages).
8. Hanasaki, I.; Nakamura, A.; Yonebayashi, T.; Kawano, S. (2008): Structure and stability of water chain in a carbon nanotube. J. Phys.: Condens. Matter, vol.20, pp. 015213.
9. Hanasaki, I.; Takahashi, H.; Sazaki, G.; Nakajima, K.; Kawano, S. (2008): Single-molecule measurements and dynamical simulations of protein molecules near silicon substrates. J. Phys. D: Appl. Phys., vol.41, pp. 095301.
10. Hanasaki, I.; Yonebayashi, T.; Kawano, S. (2009): Molecualr dynamics of a water jet from a carbon nanotube. Phys. Rev. E, vol.79, pp. 046307.
11. Hansma, H. G.; Sinsheimer, R. L.; Li, M. Q.; Hansma, P. K. (1992): Atomic force microscopy of single-and double-stranded dna. Nucleic Acids Research, vol.20, pp. 3585-3590.
12. Harris, S. A.; Sands, Z. A.; Laughton, C. A. (2005): Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA. Biophys. J., vol.88, pp. 1684-1691.
13. Humphrey, W.; Dalke, A.; Schulten, K. (1996): J. Mol. Graphics, vol.14, pp. 33.
14. Kanno, T.; Tanaka, H.; Miyoshi, N.; Kawai, T. (2000): Formation and control of two-dimensional deoxyribonucleic acid network. Appl. Phys. Lett., vol.77, pp. 3848-3850.
15. Kanno, T.; Tanaka, H.; Miyoshi, N.; Kawai, T. (2000): A new self-fabrication of large-scale deoxyribonucleic acid network on mica surfaces. Jpn. J. Appl. Phys., vol.39, pp. L269-L270.
16. Kawano, S. (2005): Fractal dimension analysis in self-assembled poly(dA)·poly(dT) DNA network on mica surface. JSME. Int. J., Ser. B, vol.48, pp. 191-195.
17. Kawano, S.; Maruyama, Y. (2005): Mathematical model for polaronic effects of charge transport in DNA. JSME. Int. J., Ser. B, vol.48, pp. 456-463.
18. Kitagawa, H.; Nakatani, A.; Shibutani, Y. (1994): Molecular dynamics study of crack processes associated with dislocation nucleated at the tip. Materials Science and Engineering, vol.A176, pp. 263.
19. Lee, M. C.; Duan, Y. (2004): Distinguish protein decoys by using a scoring function based on a new amber force field, short molecular dynamics simulations, and the generalized born solvent model. Proteins, vol.55, pp. 620-634.
20. Limary, R.; Green, P. F. (2002): Late-stage coarsening of an unstable structured liquid film. Phys. Rev. E, vol.66, pp. 021601(6 pages).
21. Maeda, Y.; Tabata, H.; Kawai, T. (2001): Two-dimensional assembly of gold nanoparticles with a DNA network template. Appl. Phys. Lett., vol.79, pp. 1181-1183.
22. Maruyama, Y.; Tachikawa, M.; Kawano, S. (2005): Ab initio study of DNA double-strand breaks by hydroxyl radical. JSME. Int. J., Ser. B, vol.48, pp. 196-201.
23. Matsumoto, R.; Nakagaki, M. (2005): Estimation of the mechanical properties of amorphous metal with a dispersed nano-crystalline particle by molecular dynamics simulation. CMES: Computer Modeling in Engineering & Sciences, vol.10, pp. 187-198.
24. Matsumoto, R.; Nakagaki, M.; Nakatani, A.; Kitagawa, H. (2005): Moleculardynamics study on crack growth behavior relevant to crystal nucleation in amorphous metal. CMES: Computer Modeling in Engineering & Sciences, vol.9, pp. 75-84.
25. Nagahiro, S.; Kawano, S.; Kotera, H. (2007): Separation of long DNA chains using a nonuniform electric field: A numerical study. Phys. Rev. E, vol.75, pp. 011902.
26. Nishimura, K.; Miyazaki, N. (2001): Molecular dynamics simulation of crack propagation in polycrystalline material. CMES: Computer Modeling in Engineering & Sciences, vol.2, pp. 143-154.
27. Onufriev, A.; Bashford, D.; Case, D. A. (2004): Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins, vol.55, pp. 383-394.
28. Rief, M.; Clausen-Schaumann, H.; Gaub, H. E. (1999): Sequence-dependent mechanics of single DNA molecules. Nature Struct. Mol. Biol., vol.6, pp. 346-349.
29. Shimizu, N.; Kawano, S.; Tachikawa, M. (2006): Electron correlated and density functional studies on hydrogen-bonded proton transfer in adenine-thymine base pair of DNA. J. Mol. Struct., vol.735-736, pp. 243-248.
30. Shintaku, H.; Kuwabara, T.; Kawano, S.; Suzuki, T.; Kanno, I.; Kotera, H. (2007): Micro cell encapsulation and its hydrogel-beads production using microfluidic device. Microsyst. Technol., vol.13, pp. 951-958.
31. Shintaku, H.; Okitsu, T.; Kawano, S.; Matsumoto, S.; Suzuki, T.; Kanno, I.; Kotera, H. (2008): Effects of fluid dynamic stress on fracturing of cell-aggregated tissue during purification for islets of langerhans transplantation. J. Phys. D: Appl. Phys., vol.41, pp. 115507.
32. Sides, P. J.; Faruqui, D.; Gellman, A. J. (2009): Dynamics of charging of muscovite mica: measurement and modeling. Langmuir, vol.25, pp. 1475-1481.
33. Sotomayor, M.; Schulten, K. (2007): Single-molecule experiments in vitro and in silico. Science, vol.316, pp. 1144-1148.
34. Srivastava, D.; Atluri, S. N. (2002): Computational nanotechnology: A current perspective. CMES: Computer Modeling in Engineering & Sciences, vol.3, pp. 531-538.
35. Tanaka, H.; Nishikawa, Y. (2005): Viscoelastic phase separation of protein solutions. Phys. Rev. Lett., vol.95, pp. 078103 (4 pages).
36. Tanaka, S.; Cai, L.; Tabata, H.; Kawai, T. (2001): Formation of twodimensional network structure of DNA molecules on si substrate. Jpn. J. Appl. Phys., vol.40, pp. L407-L409.
37. Tanaka, S.; Maeda, Y.; Cai, L.; Tabata, H.; Kawai, T. (2001): Formation of two dimensional network structure of DNA molecules on highly ordered pyrolytic graphite surface. Jpn. J. Appl. Phys., vol.40, pp. 4217-4220.
38. Terawaki, A.; Otsuka, Y.; Lee, H.; Matsumoto, T.; Tanaka, H.; Kawai, T. (2005): Conductance measurement of a DNA network in nanoscale by point contact current imaging atomic force microscopy. Appl. Phys. Lett., vol.86, pp. 113901 (3 pages).
39. Tolman, S.; Meakin, P. (1989): Off-lattice and hypercubic-lattice models for diffusion-limited aggregation in dimensionalities 2-8. Phys. Rev. A, vol.40, pp. 428-437.
40. Witten, T. A.; Sander, L. M. (1981): Diffusion-limited aggregation, a kinetic critical phenomenon. Phys. Rev. Lett., vol.47, pp. 1400-1403.
41. Wu, A.; Li, Z.; Wang, E. (2004): DNA network structures on various solid substrates investigated by atomic force microscopy. Anal. Sci., vol.20, pp. 1083-1086.