AIP Publishing manuscript submission and processing system (PXP) is currently unavailable to users in China. We are working to resolve the issue as quickly as possible. We apologize for the inconvenience.

尊敬的中国作者和评审人:AIP Publishing (AIP出版公司) 的论文发布系统(PXP)目前遇到一些技术问题。我们将为您尽快解决。因此带来的不便,我们向您表达我们诚挚的歉意!

Thank you for your patience during this process.

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.
The full text of this article is not currently available.
Communication: Origin of the contributions to DNA structure in phages
Rent this article for
Access full text Article
1. W. C. Earnshaw, J. King, S. C. Harrison, and F. A. Eiserling, Cell 14, 559 (1978).
2. S. C. Riemer and V. A. Bloomfield, Biopolymers 17, 785794 (1978).
3. S. Tzlil, J. T. Kindt, W. M. Gelbart, and A. Ben-Shaul, Biophys. J. 84, 1616 (2003).
4. T. Odijk, Philos. Trans. R. Soc. London, Ser. A 362, 1497 (2004).
5. T. Odijk, Biophys. J. 75, 1223 (1998).
6. P. K. Purohit, M. M. Inamdar, P. D. Grayson, T. M. Squires, J. Kondev, and R. Phillips, Biophys. J. 88, 851 (2005).
7. P. K. Purohit, J. Kondev, and R. Phillips, Proc. Natl. Acad. Sci. U.S.A. 100, 3173 (2003).
8. H. G. Garcia, P. Grayson, L. Han, M. Inamdar, J. Kondev, P. C. Nelson, R. Phillips, J. Widom, and P. A. Wiggins, Biopolymers 85, 115 (2007).
9. J. Müller, S. Oehler, and B. Müller-Hill, J. Mol. Biol. 257, 21 (1996).
10. J. Tang, N. Olson, P. J. Jardine, S. Grimes, D. L. Anderson, and T. S. Baker, Structure 16, 935 (2008).
11. J. E. Johnson and W. Chiu, Curr. Opin. Struct. Biol. 17, 237 (2007).
12. W. Jiang, J. Chang, J. Jakana, P. Weigele, J. King, and W. Chiu, Nature (London) 439, 612 (2006).
13. J. Chang, P. Weigele, J. King, W. Chiu, and W. Jiang, Structure 14, 1073 (2006).
14. C. M. Knobler and W. M. Gelbart, Annu. Rev. Phys. Chem. 60, 367 (2009).
15. J. Tang, G. C. Lander, A. Olia, R. Li, S. Casjens, P. Prevelige, G. Cingolani, T. S. Baker, and J. E. Johnson, Structure 19, 496 (2011).
16. D. E. Smith, S. J. Tans, S. B. Smith, S. Grimes, D. L. Anderson, and C. Bustamante, Nature (London) 413, 748 (2001).
17. D. N. Fuller, D. M. Raymer, J. P. Rickgauer, R. M. Robertson, C. E. Catalano, D. L. Anderson, S. Grimes, and D. E. Smith, J. Mol. Biol. 373, 1113 (2007).
18. D. N. Fuller, J. P. Rickgauer, P. J. Jardine, S. Grimes, D. L. Anderson, and D. E. Smith, Proc. Natl. Acad. Sci. U.S.A. 104, 11245 (2007).
19. A. Evilevitch, L. Lavelle, C. M. Knobler, E. Raspaud, and W. M. Gelbart, Proc. Natl. Acad. Sci. U.S.A. 100, 9292 (2003).
20. A. Evilevitch, L. T. Fang, A. M. Yoffe, M. Castelnovo, D. C. Rau, V. A. Parsegian, W. M. Gelbart, and C. M. Knobler, Biophys. J. 94, 1110 (2008).
21. A. Evilevitch, W. H. Roos, I. L. Ivanovska, M. Jeembaeva, B. Jönsson, and G. J. L. Wuite, J. Mol. Biol. 405, 18 (2011).
22. H. A. Lankes, C. N. Zanghi, K. Santos, C. Capella, C. M. P. Duke, and S. Dewhurst, J. Appl. Microbiol. 102, 1337 (2007).
23. M. E. Cerritelli, N. Cheng, A. H. Rosenberg, C. E. McPherson, F. P. Booy, and A. C. Steven, Cell 91, 271 (1997).
24. A. S. Petrov and S. C. Harvey, J. Struct. Biol. 174, 137 (2011).
25. A. S. Petrov and S. C. Harvey, Structure 15, 21 (2007).
26. A. S. Petrov and S. C. Harvey, Biophys. J. 95, 497 (2008).
27. E. V. Orlova and H. R. Saibil, in Methods in Enzymology, edited by G. J. Jensen (Academic, 2010), pp. 321341.
28. J. Ambia-Garrido and B. M. Pettitt, Commun. Comput. Phys. 3, 1117 (2008).
29. J. Ambia-Garrido, A. Vainrub, and B. M. Pettitt, Comput. Phys. Commun. 181, 20012007 (2010).
30. J. Ambia-Garrido, A. Vainrub, and B. Montgomery Pettitt, J. Phys.: Condens. Matter 23, 325101 (2011).
31. E. J. W. Verwey and J. T. G. Overbeek, Theory of the Stability of Lyophobic Colloids (Courier Dover, 1999).
32. P. E. Smith, M. E. Holder, L. X. Dang, M. Feig, G. C. Lynch, K. Y. Wong, and B. M. Pettitt, Extended System Program (ESP) (University of Houston, 1996).
33. J. D. Weeks, D. Chandler, and H. C. Andersen, J. Chem. Phys. 54, 5237 (1971).
34. W. Humphrey, A. Dalke, and K. Schulten, J. Mol. Graphics 14, 33 (1996).
35. E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, and T. E. Ferrin, J. Comput. Chem. 25, 1605 (2004).
36. C. G. Baumann, S. B. Smith, V. A. Bloomfield, and C. Bustamante, Proc. Natl. Acad. Sci. U.S.A. 94, 6185 (1997).
37. T. E. Cloutier and J. Widom, Mol. Cell 14, 355 (2004).
38. Q. Du, C. Smith, N. Shiffeldrim, M. Vologodskaia, and A. Vologodskii, Proc. Natl. Acad. Sci. U.S.A. 102, 5397 (2005).
39. N. B. Becker and R. Everaers, Science 325, 538 (2009).
40. A. J. Mastroianni, D. A. Sivak, P. L. Geissler, and A. P. Alivisatos, Biophys. J. 97, 1408 (2009).
41. P. A. Wiggins, T. van der Heijden, F. Moreno-Herrero, A. Spakowitz, R. Phillips, J. Widom, C. Dekker, and P. C. Nelson, Nat. Nanotechnol. 1, 137 (2006).
42. R. Vafabakhsh and T. Ha, Science 337, 1097 (2012).
43. P. C. Nelson, Science 337, 1045 (2012).
44. G. L. Randall, L. Zechiedrich, and B. M. Pettitt, Nucleic Acids Res. 37, 5568 (2009).
45. F. Lankas, R. Lavery, and J. H. Maddocks, Structure 14, 1527 (2006).
46. J. Yan and J. F. Marko, Phys. Rev. Lett. 93, 108108 (2004).
47. J. S. Mitchell, C. A. Laughton, and S. A. Harris, Nucleic Acids Res. 39, 3928 (2011).
48. S. A. Harris, C. A. Laughton, and T. B. Liverpool, Nucleic Acids Res. 36, 21 (2008).
49. J. M. Fogg, G. L. Randall, B. M. Pettitt, D. W. L. Sumners, S. A. Harris, and L. Zechiedrich, Q. Rev. Biophys. 45, 257 (2012).
50. C. L. Hetherington, A. Karunakaran, J. Schnitzbauer, P. Jardine, S. Grimes, D. Anderson, and C. Bustamante, Biophys. J. 96, 416a (2008).

Data & Media loading...


Article metrics loading...



Cryo electron microscopy (cryo-EM) data of the interior of phages show ordering of the interior DNA that has been interpreted as a nearly perfectly ordered polymer. We show surface-induced correlations, excluded volume, and electrostatic forces are sufficient to predict most of the major features of the current structural data for DNA packaged within viral capsids without additional ordering due to elastic bending forces for the polymer. Current models assume highly-ordered, even spooled, hexagonally packed conformations based on interpretation of cryo-EM density maps. We show herein that the surface induced packing of short (6mer), unconnected DNA polymer segments is the only necessary ingredient in creating ringed densities consistent with experimental density maps. This implies the ensemble of possible conformations of polymeric DNA within the capsid that are consistent with cryo-EM data may be much larger than implied by traditional interpretations where such rings can only result from highly-ordered spool-like conformations. This opens the possibility of a more disordered, entropically-driven view of phage packaging thermodynamics. We also show the electrostatics of the DNA contributes a large portion of the internal hydrostatic and osmotic pressures of a phage virion, suggesting that nonlinear elastic anomalies might reduce the overall elastic bending enthalpy of more disordered conformations to have allowable free energies.


Full text loading...

This is a required field
Please enter a valid email address

Oops! This section, does not exist...

Use the links on this page to find existing content.

752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Communication: Origin of the contributions to DNA structure in phages