DNA knotting in spooling like conformations in bacteriophages

Computational and Mathematical Methods in Medicine

Volumn 9, Issue 3-4, 2008, Pages 303-316

  Arsuaga, J ^a,b   Diao, Y ^c  

^a SAN FRANCISCO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

^c UNIVERSITY OF NORTH CAROLINA AT CHARLOTTE   (United States)

Author keywords

Bacteriophage; DNA packing; Random knots; Random polygons; Spooling model

Indexed keywords

CHIRALITY; CONFORMATIONS; DNA; STEREOCHEMISTRY;

DNA KNOTTING; DNA MOLECULES; DNA PACKING; IDEALIZED MODELS; NUMERICAL RESULTS; RANDOM KNOTS; RANDOM POLYGON;

BACTERIOPHAGES;

BACTERIOPHAGE DNA;

ANALYTIC METHOD; CHIRALITY; CONFERENCE PAPER; CONTROLLED STUDY; DNA CONFORMATION; EXPERIMENTAL DESIGN; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; NONHUMAN; PROBABILITY; RANDOM SAMPLE; RANDOMIZATION; STATISTICAL DISTRIBUTION; THEORETICAL MODEL; VIRUS CAPSID;

MIRIDAE;

EID: 48549100410     PISSN: 1748670X     EISSN: 17486718     Source Type: Journal    
DOI: 10.1080/17486700802167801     Document Type: Conference Paper

References (42)

1. Adams, C. (2004) American Mathematical Society, Providence, RI
2. Arsuaga, J., Tan, R. K. -Z., Vazquez, M., Sumners, D. W. and Harvey, S. C. (2002) Investigation of viral DNA packaging using molecular mechanics models. 101, pp. 475-484.
3. Arsuaga, J., Vazquez, M., Trigueros, S., Sumners, D. W. and Roca, J. (2002) Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids. 99, pp. 5373-5377.
4. Arsuaga, J., Vazquez, M., McGuirk, P., Trigueros, S., Sumners, D. W. and Roca, J. (2005) DNA knots reveal a chiral organization of DNA in phage capsids. 102, pp. 9165-9169.
5. Arsuaga, J., Blackstone, T., Diao, Y., Hinson, K., Karadayi, E. and Saito, M. (2007) Sampling large random knots in a confined space. 40, pp. 11697-11711.
6. Black, L., Newcomb, W., Boring, J. and Brown, J. (1985) Ion etching bacteriophage T4: Support for a spiral-fold model of packaged DNA. 82, pp. 7960-7964.
7. Booy, F. P., Newcomb, W. W., Trus, B. L., Brown, J. C., Baker, T. S. and Steven, A. C. (1991) Liquid-crystalline, phage-like packing of encapsidated DNA in herpes simplex virus. 64, pp. 1007-1015.
8. Cerritelli, M. E., Cheng, N., Rosenberg, A. H., McPherson, C. E., Booy, F. P. and Steven, A. C. (1997) Encapsidated conformation of bacteriophage T7 DNA. 91, pp. 271-280.
9. Chattoraj, D. K. and Inman, R. B. (1974) Location of DNA ends in P2, 186, P4 and lambda bacteriophage heads. 87, pp. 11-22.
10. Comolli, L. R., Spakowitz, A. J., Siegerist, C. E., Jardine, P. J., Grimes, S., Anderson, D. L., Bustamante, C. and Downing, K. H. Three-dimensional architecture of the bacteriophage phi29 packaged genome and elucidation of its packaging process. 371, pp. 267-277.
11. Dokland, T., Lindqvist, B. H. and Fuller, S. D. (1992) Image reconstruction from cryo-electron micrographs reveals the morphopoietic mechanism in the P2-P4 bacteriophage system. 11, pp. 839-846.
12. Earnshaw, W. C. and Casjens, S. R. (1980) DNA packaging by the double-stranded DNA bacteriophages. 21, pp. 319-331.
13. Evilevitch, A., Lavelle, L., Knobler, C. M., Raspaud, E. and Gelbart, W. M. (2003) Osmotic pressure inhibition of DNA ejection from phage. 100, pp. 9292-9295.
14. Freedman, M. H. and He, Z. (1991) Divergence-free fields: Energy and asymptotic crossing number. 134, pp. 189-229.
15. Fuller, D. N., Rickgauer, J. P., Jardine, P. J., Grimes, S., Anderson, D. L. and Smith, D. E. (2007) Ionic effects on viral DNA packaging and portal motor function in bacteriophage phi 29. 104, pp. 11245-11250.
16. Hud, N. (1995) Double-stranded DNA organization in bacteriophage heads: An alternative toroid-based model. 69, pp. 1355-1362.
17. Jardine, P. J. and Anderson, D. L. (2006) DNA packaging in double-stranded DNA phages. pp. 49-65. Oxford University Press, Oxford
18. Kellenberger, E., Carlemalm, E., Sechaud, J., Ryter, A. and Haller, G. (1986) Considerations on the condensation and the degree of compactness in non-eukaryotic DNA-containing plasmas. pp. 11-25. Springer, Berlin
19. LaMarque, J. C., Le, T. L. and Harvey, S. C. (2004) Packaging double-helical DNA into viral capsids. 73, pp. 348-355.
20. Lepault, J. et al. (1987) Organization of double-stranded DNA in bacteriophages: A study by cryo-electron microscopy of vitrified samples. 6, pp. 1507-1512.
21. Liu, L. F., Davis, J. L. and Calendar, R. (1981) Novel topologically knotted DNA from bacteriophage P4 capsids: Studies with DNA topoisomerases. 9, pp. 3979-3989.
22. Liu, L. F., Perkocha, L., Calendar, R. and Wang, J. C. (1981) Knotted DNA from bacteriophage capsids. 78, pp. 5498-5502.
23. Locker, C. R., Fuller, S. D. and Harvey, S. C. (2007) DNA organization and thermodynamics during viral packing. 93, pp. 2861-2869.
24. Micheletti, C. et al. (2006) Knotting of random ring polymers in confined spaces. 124, p. 64903.
25. Millett, K. (1994) Knotting of regular polygons in 3-space. pp. 31-46. World Scientific Publishing, Singapore
26. Morton, H. R. (1986) Seifert circles and knot polynomials. 99, pp. 107-109.
27. Odijk, T. Hexagonally packed DNA within bacteriophage T7 stabilized by curvature stress. 75, pp. 1223-1227.
28. Petrov, A. S., Boz, M. B. and Harvey, S. C. (2007) The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape. 160, pp. 241-248.
29. Pruss, G. R., Wang, J. C. and Calendar, R. (1974) In vitro packaging of satellite phage P4 DNA. 71, pp. 2367-2371.
30. Richards, K., Williams, R. and Calendar, R. (1973) Mode of DNA packing within bacteriophage heads. 78, pp. 255-259.
31. Rishov, S., Holzenburg, A., Johansen, B. V. and Lindqvist, B. H. (1998) Bacteriophage P2 and P4 morphogenesis: Structure and function of the connector. 245, pp. 11-17.
32. Schmutz, M., Durand, D., Debin, A., Palvadeau, Y., Eitienne, E. R. and Thierry, A. R. (1999) DNA packing in stable lipid complexes designed for gene transfer imitates DNA compaction in bacteriophage. 96, pp. 12293-12298.
33. Serwer, P. (1986) Arrangement of double-stranded DNA packaged in bacteriophage capsids: An alternative model. 190, pp. 509-512.
34. Smith, D. E., Tans, S. J., Smith, S. B., Grimes, S., Anderson, D. L. and Bustamante, C. (2001) The bacteriophage phi29 portal motor can package DNA against a large internal force. 413, pp. 748-752.
35. Starostin, E. L. (2006) On the perfect hexagonal packing of rods. 18, pp. S187-S204.
36. Trigueros, S. and Roca, J. (2007) Production of highly knotted DNA by means of cosmid circularization inside phage capsids. 7:1, p. 94.
37. Trigueros, S., Arsuaga, J., Vazquez, M., Sumners, D. W. and Roca, J. (2001) Novel display of knotted DNA molecules by two dimensional gel electrophoresis. 29, p. e67.
38. Tzill, S., Kindt, J. T., Gelbart, W. and Ben-Shaul, A. (2003) Forces and pressures in DNA packaging and release from viral capsids. 84, pp. 1616-1627.
39. Vologodskii, A. V., Crisona, N. J., Laurie, B., Pieranski, P., Katritch, V., Dubochet, J. and Stasiak, A. (1998) Sedimentation and electrophoretic migration of DNA knots and catenanes. 278, pp. 1-3.
40. Wang, J. C., Martin, K. V. and Calendar, R. (1973) On the sequence similarity of the cohesive ends of coliphage P4, P2, and 186 deoxyribonucleic acid. 12, pp. 2119-2123.
41. Wang, S., Chang, J. R. and Dokland, T. (2006) Assembly of bacteriophage P2 and P4 procapsids with internal scaffolding protein. 348, pp. 133-140.
42. Wolfson, J. S., McHugh, G. L., Hooper, D. C. and Swartz, M. N. (1985) Knotting of DNA molecules isolated from deletion mutants of intact bacteriophage P4. 13, pp. 6695-6702.