1887
banner image
No data available.
Please log in to see this content.
You have no subscription access to this content.
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
oa
Critical behavior of megabase-size DNA toward the transition into a compact state
Rent:
Rent this article for
Access full text Article
/content/aip/journal/jcp/135/22/10.1063/1.3666845
1.
1. Y. Fang and J. H. Hoh, Nucleic Acids Res. 26, 588 (1998).
http://dx.doi.org/10.1093/nar/26.2.588
2.
2. I. Baeza, P. Gariglio, L. M. Rangel, P. Chavez, L. Cervantes, C. Arguello, C. Wong, and C. Montanez, Biochemistry 26, 6387 (1987).
http://dx.doi.org/10.1021/bi00394a012
3.
3. J. Pelta, D. Durand, J. Doucet, and F. Livolant, Biophys. J. 71, 48 (1996).
http://dx.doi.org/10.1016/S0006-3495(96)79232-9
4.
4. K. Tsumoto, F. Luckel, and K. Yoshikawa, Biophys. Chem. 106, 23 (2003).
http://dx.doi.org/10.1016/S0301-4622(03)00138-8
5.
5. A. Yamada, K. Kubo, T. Nakai, K. Yoshikawa, and K. Tsumoto, Appl. Phys. Lett. 86, (2005).
http://dx.doi.org/10.1063/1.1937990
6.
6. C. C. Conwell, I. D. Vilfan, and N. V. Hud, Proc. Natl. Acad. Sci. U.S.A. 100, 9296 (2003).
http://dx.doi.org/10.1073/pnas.1533135100
7.
7. M. Haynes, R. A. Garrett, and W. B. Gratzer, Biochemistry 9, 4410 (1970).
http://dx.doi.org/10.1021/bi00824a600
8.
8. Y. M. Evdokimov, A. L. Platonov, A. S. Tikhonenko, and Y. M. Varshavsky, FEBS Lett. 23, 180 (1972).
http://dx.doi.org/10.1016/0014-5793(72)80335-1
9.
9. L. C. Gosule and J. A. Schellman, Nature (London) 259, 333 (1976).
http://dx.doi.org/10.1038/259333a0
10.
10. S. A. Allison, J. C. Herr, and J. M. Schurr, Biopolymers 20, 469 (1981).
http://dx.doi.org/10.1002/bip.1981.360200305
11.
11. C. B. Post and B. H. Zimm, Biopolymers 21, 2123 (1982).
http://dx.doi.org/10.1002/bip.360211104
12.
12. V. A. Bloomfield, Biopolymers 31, 1471 (1991).
http://dx.doi.org/10.1002/bip.360311305
13.
13. N. V. Hud, M. J. Allen, K. H. Downing, J. Lee, and R. Balhorn, Biochem. Biophys. Res. Commun. 193, 1347 (1993).
http://dx.doi.org/10.1006/bbrc.1993.1773
14.
14. V. A. Bloomfield, Curr. Opin. Struct. Biol. 6, 334 (1996).
http://dx.doi.org/10.1016/S0959-440X(96)80052-2
15.
15. K. Yoshikawa and Y. Matsuzawa, J. Am. Chem. Soc. 118, 929 (1996).
http://dx.doi.org/10.1021/ja952685m
16.
16. V. A. Bloomfield, Biopolymers 44(3), 269 (1997).
http://dx.doi.org/10.1002/(SICI)1097-0282(1997)44:3<269::AID-BIP6>3.0.CO;2-T
17.
17. O. Lambert, L. Letellier, W. M. Gelbart, and J. L. Rigaud, Proc. Natl. Acad. Sci. U.S.A. 97, 7248 (2000).
http://dx.doi.org/10.1073/pnas.130187297
18.
18. N. V. Hud and K. H. Downing, Proc. Natl. Acad. Sci. U.S.A. 98, 14925 (2001).
http://dx.doi.org/10.1073/pnas.261560398
19.
19. I. D. Vilfan, C. C. Conwell, and N. V. Hud, J. Biol. Chem. 279(19), 20088 (2004).
http://dx.doi.org/10.1074/jbc.M312777200
20.
20. N. V. Hud and I. D. Vilfan, Annu. Rev. Biophys. Biomol. Struct. 34, 295 (2005).
http://dx.doi.org/10.1146/annurev.biophys.34.040204.144500
21.
21. I. D. Vilfan, C. C. Conwell, T. Sarkar, and N. V. Hud, Biochemistry 45, 8174 (2006).
http://dx.doi.org/10.1021/bi060396c
22.
22. B. A. Todd and D. C. Rau, Nucleic Acids Res. 36, 501 (2008).
http://dx.doi.org/10.1093/nar/gkm1038
23.
23. D. K. Chattoraj, L. C. Gosule, and J. A. Schellman, J. Mol. Biol. 121, 327 (1978).
http://dx.doi.org/10.1016/0022-2836(78)90367-4
24.
24. W. Wilson and V. A. Bloomfield, Biochemistry 18, 2192 (1979).
http://dx.doi.org/10.1021/bi00578a009
25.
25. K. A. Marx and T. C. Reynolds, Biochim. Biophys. Acta 741, 279 (1983).
http://dx.doi.org/10.1016/0167-4781(83)90146-X
26.
26. D. Porschke, Biochemistry 23(21), 4821 (1984).
http://dx.doi.org/10.1021/bi00316a002
27.
27. D. Jary and J. L. Sikorav, Biochemistry 38, 3223 (1999).
http://dx.doi.org/10.1021/bi982770h
28.
28. J. Widom and R. L. Baldwin, Biopolymers 22, 1595 (1983).
http://dx.doi.org/10.1002/bip.360220612
29.
29. J. A. Schellman and N. Parthasarathy, J. Mol. Biol. 175, 313 (1984).
http://dx.doi.org/10.1016/0022-2836(84)90351-6
30.
30. D. Gersanovski, P. Colson, C. Houssier, and E. Fredericq, Biochim. Biophys. Acta 824, 313 (1985).
http://dx.doi.org/10.1016/0167-4781(85)90037-5
31.
31. H. A. Tajmir-Riahi, R. Ahmad, and M. Naoui, J. Biomol. Struct. Dyn. 10, 865 (1993).
32.
32. C. L. Ma and V. A. Bloomfield, Biophys. J. 67, 1678 (1994).
http://dx.doi.org/10.1016/S0006-3495(94)80641-1
33.
33. L. S. Lerman, Cold Spring Harb. Symp. Quant. Biol. 38, 59 (1974).
http://dx.doi.org/10.1101/SQB.1974.038.01.009
34.
34. U. K. Laemmli, Proc. Natl. Acad. Sci. U.S.A. 72, 4288 (1975).
http://dx.doi.org/10.1073/pnas.72.11.4288
35.
35. D. E. Olins and A. L. Olins, J. Mol. Biol. 57, 437 (1971).
http://dx.doi.org/10.1016/0022-2836(71)90102-1
36.
36. D. J. Clark and J. O. Thomas, J. Mol. Biol. 187, 569 (1986).
http://dx.doi.org/10.1016/0022-2836(86)90335-9
37.
37. M. Garciaramirez and J. A. Subirana, Biopolymers 34, 285 (1994).
http://dx.doi.org/10.1002/bip.360340214
38.
38. K. Yoshikawa and Y. Yoshikawa, in Pharmaceutical Perspectives of Nucleic Acid-Based Therapy, edited by R. I. Mahato and S. W. Kim (Taylor & Francis, London, 2002), p. 136.
39.
39. Y. Matsuzawa and K. Yoshikawa, Nucleosides Nucleotides 13, 1415 (1994).
http://dx.doi.org/10.1080/15257779408012161
40.
40. Y. Yoshikawa and K. Yoshikawa, FEBS Lett. 361, 277 (1995).
http://dx.doi.org/10.1016/0014-5793(95)00190-K
41.
41. M. Takahashi, K. Yoshikawa, V. V. Vasilevskaya, and A. R. Khokhlov, J. Phys. Chem. B 101, 9396 (1997).
http://dx.doi.org/10.1021/jp9716391
42.
42. S. M. Melnikov, V. G. Sergeyev, and K. Yoshikawa, J. Am. Chem. Soc. 117, 2401 (1995).
http://dx.doi.org/10.1021/ja00114a004
43.
43. K. Yoshikawa, S. Kidoaki, M. Takahashi, V. V. Vasilevskaya, and A. R. Khokhlov, Ber. Bunsenges. Phys. Chem. 100, 876 (1996).
http://dx.doi.org/10.1002/bbpc.19961000631
44.
44. K. Yoshikawa, Y. Yoshikawa, Y. Koyama, and T. Kanbe, J. Am. Chem. Soc. 119, 6473 (1997).
http://dx.doi.org/10.1021/ja970445w
45.
45. Y. Yoshikawa, Y. S. Velichko, Y. Ichiba, and K. Yoshikawa, Eur. J. Biochem. 268, 2593 (2001).
http://dx.doi.org/10.1046/j.1432-1327.2001.02144.x
46.
46. Y. Katsuda, Y. Yoshikawa, T. Sato, Y. Saito, M. Chikuma, M. Suzuki, and K. Yoshikawa, Chem. Phys. Lett. 473, 155 (2009).
http://dx.doi.org/10.1016/j.cplett.2009.03.026
47.
47. N. Kida, Y. Katsuda, Y. Yoshikawa, S. Komeda, T. Sato, Y. Saito, M. Chikuma, M. Suzuki, T. Imanaka, and K. Yoshikawa, J. Biol. Inorg. Chem. 15, 701 (2010).
http://dx.doi.org/10.1007/s00775-010-0637-y
48.
48. H. H. Heng, J. B. Stevens, G. Liu, S. W. Bremer, and C. J. Ye, Cell Chromosome 3, 1 (2004).
http://dx.doi.org/10.1186/1475-9268-3-1
49.
49. N. Makita, Y. Yoshikawa, Y. Takenaka, T. Sakaue, M. Suzuki, C. Watanabe, T. Kanai, T. Kanbe, T. Imanaka, and K. Yoshikawa, J. Phys. Chem. B 115, 4453 (2011).
http://dx.doi.org/10.1021/jp111331q
50.
50. K. Minagawa, Y. Matsuzawa, K. Yoshikawa, A. R. Khokhlov, and M. Doi, Biopolymers 34, 555 (1994).
http://dx.doi.org/10.1002/bip.360340410
51.
51. H. Oana, K. Tsumoto, Y. Yoshikawa, and K. Yoshikawa, FEBS Lett. 530, 143 (2002).
http://dx.doi.org/10.1016/S0014-5793(02)03448-8
52.
52. W. Fukuda, K. Yamada, Y. Miyoshi, H. Okuno, H. Atomi, and T. Imanaka, “Rhodoligotrophos appendicifer gen. nov., sp. nov., a bacterium with projections isolated from a lake in Skarvsnes, Antartica,” Int. J. Syst. Evol. Microbiol. (in press).
53.
53. I. Flink and D. E. Pettijohn, Nature (London) 253, 62 (1975).
http://dx.doi.org/10.1038/253062a0
54.
54. Z. Lin, C. Wang, X. Z. Feng, M. Z. Liu, J. W. Li, and C. L. Bai, Nucleic Acids Res. 26, 3228 (1998).
http://dx.doi.org/10.1093/nar/26.13.3228
55.
55. H. S. Rye, S. Yue, D. E. Wemmer, M. A. Quesada, R. P. Haugland, R. A. Mathies, and A. N. Glazer, Nucleic Acids Res. 20, 2803 (1992).
http://dx.doi.org/10.1093/nar/20.11.2803
56.
56. Y. Fang and J. H. Hoh, J. Am. Chem. Soc. 120, 8903 (1998).
http://dx.doi.org/10.1021/ja981332v
57.
57. Y. T. A. Chim, J. K. W. Lam, Y. Ma, S. P. Armes, A. L. Lewis, C. J. Roberts, S. Stolnik, S. J. B. Tendler, and M. C. Davies, Langmuir 21, 3591 (2005).
http://dx.doi.org/10.1021/la047480i
58.
58. K. Besteman, K. van Eijk, I. D. Vilfan, U. Ziese, and S. G. Lemay, Biopolymers 87, 141 (2007).
http://dx.doi.org/10.1002/bip.20806
59.
59. F. Oosawa, Biopolymers 9, 677 (1970).
http://dx.doi.org/10.1002/bip.1970.360090606
60.
60. G. S. Manning, Q. Rev. Biophys. 11, 179 (1978).
http://dx.doi.org/10.1017/S0033583500002031
61.
61. Y. Yamasaki, Y. Teramoto, and K. Yoshikawa, Biophys. J. 80, 2823 (2001).
http://dx.doi.org/10.1016/S0006-3495(01)76249-2
62.
62. N. Yoshinaga, K. Yoshikawa, and S. Kidoaki, J. Chem. Phys. 116, 9926 (2002).
http://dx.doi.org/10.1063/1.1475759
63.
63. P. G. De Gennes and J. Prost, The Physics of Liquid Crystals, 2nd edition. (Oxford University Press, Oxford, 1993).
64.
64. Y. Matsuzawa, Y. Yonezawa, and K. Yoshikawa, Biochem. Biophys. Res. Commun. 225, 796 (1996).
http://dx.doi.org/10.1006/bbrc.1996.1253
65.
65. E. Raspaud, M. Olvera de la Cruz, J. L. Sikorav, and F. Livolant, Biophys. J. 74, 381 (1998).
http://dx.doi.org/10.1016/S0006-3495(98)77795-1
66.
66. T. Iwaki and K. Yoshikawa, Europhys. Lett. 68, 113 (2004).
http://dx.doi.org/10.1209/epl/i2004-10171-0
67.
67. H. G. Hansma, Annu. Rev. Phys. Chem. 52, 71 (2001).
http://dx.doi.org/10.1146/annurev.physchem.52.1.71
68.
journal-id:
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/22/10.1063/1.3666845
Loading
/content/aip/journal/jcp/135/22/10.1063/1.3666845
Loading

Data & Media loading...

Loading

Article metrics loading...

/content/aip/journal/jcp/135/22/10.1063/1.3666845
2011-12-08
2014-07-26

Abstract

We studied the changes in the higher-order structure of a megabase-size DNA (S120-1 DNA) under different spermidine (SPD) concentrations through single-molecule observations using fluorescence microscopy (FM) and atomic force microscopy(AFM). We examined the difference between the folding transitions in S120-1 DNA and sub-megabase-size DNA, T4 DNA (166 kbp). From FM observations, it is found that S120-1 DNA exhibits intra-chain segregation as the intermediate state of transition, in contrast to the all-or-none nature of the transition on T4 DNA. Large S120-1 DNA exhibits a folding transition at lower concentrations of SPD than T4 DNA.AFM observations showed that DNA segments become aligned in parallel on a two-dimensional surface as the SPD concentration increases and that highly intense parallel alignment is achieved just before the compaction. S120-1 DNA requires one-tenth the SPD concentration as that required by T4 DNA to achieve the same degree of parallel ordering. We theoretically discuss the cause of the parallel ordering near the transition into a fully compact state on a two-dimensional surface, and argue that such parallel ordering disappears in bulk solution.

Loading

Full text loading...

/deliver/fulltext/aip/journal/jcp/135/22/1.3666845.html;jsessionid=6updetnstafid.x-aip-live-06?itemId=/content/aip/journal/jcp/135/22/10.1063/1.3666845&mimeType=html&fmt=ahah&containerItemId=content/aip/journal/jcp
true
true
This is a required field
Please enter a valid email address
This feature is disabled while Scitation upgrades its access control system.
This feature is disabled while Scitation upgrades its access control system.
752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Critical behavior of megabase-size DNA toward the transition into a compact state
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/22/10.1063/1.3666845
10.1063/1.3666845
SEARCH_EXPAND_ITEM