Sensing DNA-DNA as nanosensor: A perspective towards nanobiotechnology

Journal of Computational and Theoretical Nanoscience

Volumn 2, Issue 3, 2005, Pages 389-395

  Metzler, Ralf ^a   Ambjörnsson, Tobias ^a  

^a NORDITA   (Denmark)

Author keywords

DNA; DNA breathing; Fluorescence correlation spectroscopy; Fluorescence resonance energy transfer; Nanosensors; Single molecule spectroscopy

Indexed keywords

BIOTECHNOLOGY; DNA; DNA SEQUENCES; FLUORESCENCE; MOLECULAR SPECTROSCOPY; MOLECULES; SENSORS;

DNA BREATHING; FLUORESCENCE CORRELATION SPECTROSCOPY; FLUORESCENCE RESONANCE ENERGY TRANSFER; NANOSENSORS; SINGLE MOLECULE SPECTROSCOPY;

NANOTECHNOLOGY;

EID: 27644509796     PISSN: 15461955     EISSN: None     Source Type: Journal    
DOI: 10.1166/jctn.2005.209     Document Type: Article

References (50)

1. K. Pant, R. L. Karpel, and M. C. Williams, J. Mol. Biol. 327, 571 (2003).
2. J. J. Kasianowicz, E. Brandin, D. Branton, and D. W. Deamer, Proc. Natl. Acad. Sci. USA 93, 13770 (1996).
3. A. Meller, J. Phys. C 15, R581 (2003).
4. Berg-Sørensen and H. Flyvbjerg, New J. Phys. 7, (2005).
5. J. Liphardt, S. Dumont, S. B. Smith, I. Tinoco, Jr., and C. Bustamante, Science 296, 1832 (2002).
6. C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997).
7. U. Seifert, Phys. Rev. Lett. 95, 040602 (2005).
8. J. D. Watson and F. H. C. Crick, Nature 171, 737 (1953).
9. S. G. Delcourt and R. D. Blake, J. Biol. Chem. 266, 15160 (1991).
10. A. Kornberg, DNA Synthesis, W. H. Freeman, San Francisco, CA (1974).
11. M. D. Frank-Kamenetskii, Phys. Rep. 288, 13 (1997).
12. M. D. Frank-Kamenetskii, Unraveling DNA: The Most Important Molecule of Life, Perseus (1997).
13. C. R. Calladine and H. Drew, Understanding DNA: The Molecule and How It Works, Academic Press, London (1997).
14. B. H. Zimm, J. Chem. Phys. 33, 1349 (1960).
15. D. Poland and H. Scheraga, Theory of Helix-Coil Transitions in Biopolymers, Academic Press, New York (1970).
16. R. M. Wartell and A. S. Benight, Phys. Rep. 126, 67 (1985).
17. C. Richard and A. J. Guttmann, J. Stat. Phys. 115, 925 (2004).
18. R. D. Blake, J. W. Bizzaro, J. D. Blake, G. R. Day, S. G. Delcourt, J. Knowles, K. A. Marx, and J. SantaLucia, Jr., Bioinformatics 15, 370 (1999).
19. R. Blossey and E. Carlon, Phys. Rev. E 68, 061911 (2003).
20. G. Altan-Bonnet, A. Libchaber, and O. Krichevsky, Phys. Rev. Lett. 90, 138101 (2003).
21. T. Ambjörnsson and R. Metzler, Phys. Rev. E, in press.
22. T. Ambjörnsson and R. Metzler, J. Phys. Cond. Mat. 17, S1841 (2005).
23. T. Ambjörnsson and R. Metzler, J. Phys. Cond. Mat. accepted for publication, E-print cond-mat/0508492.
24. T. Ambjörnsson, S. K. Banik, and R. Metzler, Europhys. Lett. 71, 852 (2005).
25. T. Ambjörnsson and R. Metzler, (2005) unpublished.
26. E. Yeramian, Gene 255, 139 (2000)
27. E. Yeramian, Gene 255, 151 (2000).
28. A. Kornberg and T. A. Baker, DNA Replication, W. H. Freeman, New York, (1992).
29. O. Krichevsky and G. Bonnet, Rep. Prog. Phys. 65, 251 (2002).
30. R. W. Deibler, S. Rahmati, and E. L. Zechiedrich, Genes and Development 15, 748 (2001).
31. R. Metzler and A. Hanke, in Handbook of Theoretical and Computational Nanotechnology, edited by M. Rieth and W. Schommers, American Scientific Publishers (2005).
32. X. R. Bao, H. J. Lee, and S. R. Quake, Phys. Rev. Lett. 91, (2005).
33. D. A. Shultz, Current Opinions in Biotech. 14, 13 (2003).
34. I. L. Medintz, A. R. Clapp, H. Mattoussi, E. R. Goldman, B. Fisher, and J. M. Mauro, Nature Materials 2, 630 (2003).
35. O. G. Berg, R. B. Winter, and P. H. von Hippel, Biochem. 20, 6929 (1981).
36. A. Bakk and R. Metzler, FEBS Lett. 563, 66 (2004)
37. A. Bakk and R. Metzler, J. Theor. Biol. 231, 525 (2004).
38. I. M. Sokolov, R. Metzler, K. Pant, and M. C. Williams, Biophys. J. 89, 895 (2005).
39. B. Alberts, K. Roberts, D. Bray, J. Lewis, M. Raff, and J. D. Watson, The Molecular Biology of the Cell, Garland, New York (1994).
40. T. Ambjörnsson and R. Metzler, Phys. Biol. 1, 77 (2004)
41. T. Ambjörnsson and R. Metzler, E-print q-bio.BM/0508029.
42. H. Salman, D. Zbaida, Y. Rabin, D. Chatenay, and M. Elbaum, Proc. Natl. Acad. Sci. USA 98, 7247 (2001).
43. E. A. Di Marzio and J. J. Kasianowicz, J. Chem. Phys. 119, 6378 (2003).
44. A. Hanke and R. Metzler, Chem. Phys. Lett. 359, 22 (2002).
45. G. Bottari, F. Dehez, D. A. Leigh, P. J. Nash, E. M. Perez, J. K. Y. Wong, and F. Zerbetto, Angew. Chem. Int. Ed. 42, 5886 (2003).
46. P.-G. de Gennes, Scaling Concepts in Polymer Physics, Cornell University Press, Ithaca, (1979).
47. K. Kroy and E. Frey, Phys. Rev. Lett. 77, 306 (1996), and references therein.
48. R. Shusterman, S. Alon, T. Gavrinyov, and O. Krichevsky, Phys. Rev. Lett. 92, art. no. 048303 (2004).
49. M. C. Murphy, I. Rasnik, W. Cheng, T. M. Lohman, and T. Ha, Biophys. J. 86, 2530 (2004).
50. N. L. Goddard, G. Bonnet, O. Krichevsky, and A. Libchaber, Phys. Rev. Lett. 85, 2400 (2000).