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Volumn 40, Issue 11, 2012, Pages 5129-5137

Effective stiffening of DNA due to nematic ordering causes DNA molecules packed in phage capsids to preferentially form torus knots

Author keywords

[No Author keywords available]

Indexed keywords

POLYMER;

EID: 84862225074     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks157     Document Type: Article
Times cited : (56)

References (42)
  • 2
    • 0034797254 scopus 로고    scopus 로고
    • Combined EM/X-Ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions
    • DOI 10.1016/S0969-2126(01)00642-6, PII S0969212601006426
    • Martn, C.S., Burnett, R.M., de Haas, F., Heinkel, R., Rutten, T., Fuller, S.D., Butcher, S.J. and Bamford, D.H. (2001) Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions. Structure, 9, 917-930. (Pubitemid 32972158)
    • (2001) Structure , vol.9 , Issue.10 , pp. 917-930
    • Martin, C.S.1    Burnett, R.M.2    De Haas, F.3    Heinkel, R.4    Rutten, T.5    Fuller, S.D.6    Butcher, S.J.7    Bamford, D.H.8
  • 3
    • 17044395121 scopus 로고    scopus 로고
    • Conservation of the capsid structure in tailed dsDNA bacteriophages: The pseudoatomic structure of phi29
    • Morais, M.C., Choi, K.H., Koti, J.S., Chipman, P.R., Anderson, D.L. and Rossmann, M.G. (2005) Conservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29. Mol. Cell, 18, 149-159.
    • (2005) Mol. Cell , vol.18 , pp. 149-159
    • Morais, M.C.1    Choi, K.H.2    Koti, J.S.3    Chipman, P.R.4    Anderson, D.L.5    Rossmann, M.G.6
  • 4
    • 31844435708 scopus 로고    scopus 로고
    • Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus
    • DOI 10.1038/nature04487, PII NATURE04487
    • Jiang, W., Chang, J., Jakana, J., Weigele, P., King, J. and Chiu, W. (2006) Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus. Nature, 439, 612-616. (Pubitemid 43185387)
    • (2006) Nature , vol.439 , Issue.7076 , pp. 612-616
    • Jiang, W.1    Chang, J.2    Jakana, J.3    Weigele, P.4    King, J.5    Chiu, W.6
  • 5
    • 38649114349 scopus 로고    scopus 로고
    • Three-dimensional architecture of the bacteriophage φ29 packaged genome and elucidation of its packaging process
    • DOI 10.1016/j.virol.2007.07.035, PII S0042682207004990
    • Comolli, L.R., Spakowitz, A.J., Siegerist, C.E., Jardine, P.J., Grimes, S., Anderson, D.L., Bustamante, C. and Downing, K.H. (2008) Three-dimensional architecture of the bacteriophage phi29 packaged genome and elucidation of its packaging process. Virology, 371, 267-277. (Pubitemid 351173222)
    • (2008) Virology , vol.371 , Issue.2 , pp. 267-277
    • Comolli, L.R.1    Spakowitz, A.J.2    Siegerist, C.E.3    Jardine, P.J.4    Grimes, S.5    Anderson, D.L.6    Bustamante, C.7    Downing, K.H.8
  • 6
    • 0037058959 scopus 로고    scopus 로고
    • Investigation of viral DNA packaging using molecular mechanics models
    • DOI 10.1016/S0301-4622(02)00197-7, PII S0301462202001977
    • Arsuaga, J., Tan, R.K., Vazquez, M., Sumners, D.W. and Harvey, S.C. (2002) Investigation of viral DNA packaging using molecular mechanics models. Biophys. Chem., 101-102, 475-484. (Pubitemid 35462066)
    • (2002) Biophysical Chemistry , vol.101-102 , pp. 475-484
    • Arsuaga, J.1    Tan, R.K.-Z.2    Vazquez, M.3    Sumners, D.W.4    Harvey, S.C.5
  • 7
    • 35148817067 scopus 로고    scopus 로고
    • The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape
    • DOI 10.1016/j.jsb.2007.08.012, PII S1047847707002018
    • 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. J. Struct. Biol., 160, 241-248. (Pubitemid 47539199)
    • (2007) Journal of Structural Biology , vol.160 , Issue.2 , pp. 241-248
    • Petrov, A.S.1    Boz, M.B.2    Harvey, S.C.3
  • 10
    • 0034642752 scopus 로고    scopus 로고
    • Twist in chiral interaction between biological helices
    • Kornyshev, A.A. and Leikin, S. (2000) Twist in chiral interaction between biological helices. Phys. Rev. Lett., 84, 2537-2540.
    • (2000) Phys. Rev. Lett. , vol.84 , pp. 2537-2540
    • Kornyshev, A.A.1    Leikin, S.2
  • 11
    • 0016168104 scopus 로고
    • Location of DNA ends in P2 186, P4 and lambda bacteriophage heads
    • Chattoraj, D.K. and Inman, R.B. (1974) Location of DNA ends in P2, 186, P4 and lambda bacteriophage heads. J. Mol. Biol., 87, 11-22.
    • (1974) J. Mol. Biol. , vol.87 , pp. 11-22
    • Chattoraj, D.K.1    Inman, R.B.2
  • 12
    • 0015829833 scopus 로고
    • On the sequence similarity of the cohesive ends of coliphage P4, P2, and 186 deoxyribonucleic acid
    • 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. Biochemistry, 12, 2119-2123.
    • (1973) Biochemistry , vol.12 , pp. 2119-2123
    • Wang, J.C.1    Martin, K.V.2    Calendar, R.3
  • 17
    • 22244471562 scopus 로고
    • Fractions of particular knots in Gaussian random polygons
    • Tsurusaki, K. and Deguchi, T. (1995) Fractions of particular knots in Gaussian random polygons. J. Phys. Soc. Jpn., 64, 1506-1518.
    • (1995) J. Phys. Soc. Jpn. , vol.64 , pp. 1506-1518
    • Tsurusaki, K.1    Deguchi, T.2
  • 19
    • 0027200062 scopus 로고
    • Knotting of a DNA chain during ring closure
    • Shaw, S.Y. and Wang, J.C. (1993) Knotting of a DNA chain during ring closure. Science, 260, 533-536. (Pubitemid 23161616)
    • (1993) Science , vol.260 , Issue.5107 , pp. 533-536
    • Shaw, S.Y.1    Wang, J.C.2
  • 23
    • 25844439434 scopus 로고    scopus 로고
    • DNA cholesteric pitch as a function of density and ionic strength
    • DOI 10.1529/biophysj.105.064550
    • Stanley, C.B., Hong, H. and Strey, H.H. (2005) DNA cholesteric pitch as a function of density and ionic strength. Biophys. J., 89, 2552-2557. (Pubitemid 41401043)
    • (2005) Biophysical Journal , vol.89 , Issue.4 , pp. 2552-2557
    • Stanley, C.B.1    Hong, H.2    Strey, H.H.3
  • 24
    • 34249308788 scopus 로고    scopus 로고
    • Coarse-grained molecular dynamic simulations for lyotropic liquid-crystalline solutions of semiflexible rod-like molecules
    • DOI 10.1080/15421400701246309, PII 779017268
    • Lin, S., Numasawa, N., Nose, T. and Lin, J. (2007) Corse-grained molecular dynamic simulations for lyotropic liquid-crystalline solutions of semiflexible rod-like molecules. Mol. Cryst. Liq. Cryst., 466, 53-76. (Pubitemid 46806058)
    • (2007) Molecular Crystals and Liquid Crystals , vol.466 , Issue.1 , pp. 53-76
    • Lin, S.1    Numasawa, N.2    Nose, T.3    Lin, J.4
  • 25
    • 39749113170 scopus 로고    scopus 로고
    • Persistence lengths and structure factors of wormlike polymers under confinement
    • DOI 10.1021/jp076355n
    • Cifra, P., Benkova, Z. and Bleha, T. (2008) Persistence lengths and structure factors of wormlike polymers under confinement. J. Phys. Chem. B, 112, 1367-1375. (Pubitemid 351291639)
    • (2008) Journal of Physical Chemistry B , vol.112 , Issue.5 , pp. 1367-1375
    • Cifra, P.1    Benkova, Z.2    Bleha, T.3
  • 26
    • 77955714530 scopus 로고    scopus 로고
    • Shape transition of semi-flexible macromolecules confined in channel and cavity
    • Cifra, P. and Bleha, T. Shape transition of semi-flexible macromolecules confined in channel and cavity. Eur. Phys. J. E., 32, 273-279.
    • Eur. Phys. J. E. , vol.32 , pp. 273-279
    • Cifra, P.1    Bleha, T.2
  • 27
    • 0002313994 scopus 로고
    • A study of statistical globula-coil transition in macromolecules using the Monte-Carlo technique
    • Kron, A.K., Ptitsyn, O.B., Skvortsov, A.M. and Federov, A.K. (1967) A study of statistical globula-coil transition in macromolecules using the Monte-Carlo technique. Molek. Biol., 1, 576-582.
    • (1967) Molek. Biol. , vol.1 , pp. 576-582
    • Kron, A.K.1    Ptitsyn, O.B.2    Skvortsov, A.M.3    Federov, A.K.4
  • 28
    • 75749148281 scopus 로고    scopus 로고
    • Implementation and performance analysis of bridging Monte Carlo moves for off-lattice single chain polymers in globular states
    • Reith, D. and Virnau, P. (2010) Implementation and performance analysis of bridging Monte Carlo moves for off-lattice single chain polymers in globular states. Comput. Phys. Commun., 181, 800-805.
    • (2010) Comput. Phys. Commun. , vol.181 , pp. 800-805
    • Reith, D.1    Virnau, P.2
  • 29
    • 0028421135 scopus 로고
    • Are there knots in proteins?
    • Mansfield, M.L. (1994) Are there knots in proteins? Nat. Struct. Biol., 1, 213-214.
    • (1994) Nat. Struct. Biol. , vol.1 , pp. 213-214
    • Mansfield, M.L.1
  • 30
    • 78651506437 scopus 로고    scopus 로고
    • Detection and visualization of physical knots in macromolecules
    • Virnau, P. (2010) Detection and visualization of physical knots in macromolecules. Phys. Procedia, 6, 117-125.
    • (2010) Phys. Procedia , vol.6 , pp. 117-125
    • Virnau, P.1
  • 31
    • 39749113170 scopus 로고    scopus 로고
    • Persistence lengths and structure factors of wormlike polymers under confinement
    • DOI 10.1021/jp076355n
    • Cifra, P., Benkova, Z. and Bleha, T. (2008) Persistence lengths and structure factors of wormlike polymers under confinement. J. Phys. Chem. B, 112, 1367-1375. (Pubitemid 351291639)
    • (2008) Journal of Physical Chemistry B , vol.112 , Issue.5 , pp. 1367-1375
    • Cifra, P.1    Benkova, Z.2    Bleha, T.3
  • 32
    • 38949099079 scopus 로고    scopus 로고
    • Production of highly knotted DNA by means of cosmid circularization inside phage capsids
    • Trigueros, S. and Roca, J. (2007) Production of highly knotted DNA by means of cosmid circularization inside phage capsids. BMC Biotechnol., 7, 94.
    • (2007) BMC Biotechnol. , vol.7 , pp. 94
    • Trigueros, S.1    Roca, J.2
  • 35
  • 36
    • 61449215083 scopus 로고    scopus 로고
    • Knot-controlled ejection of a polymer from a virus capsid
    • Matthews, R., Louis, A.A. and Yeomans, J.M. (2009) Knot-controlled ejection of a polymer from a virus capsid. Phys. Rev. Lett., 102, 088101.
    • (2009) Phys. Rev. Lett. , vol.102 , pp. 088101
    • Matthews, R.1    Louis, A.A.2    Yeomans, J.M.3
  • 38
    • 27544511752 scopus 로고    scopus 로고
    • Knots in globule and coil phases of a model polyethylene
    • DOI 10.1021/ja052438a
    • Virnau, P., Kantor, Y. and Kardar, M. (2005) Knots in globule and coil phases of a model polyethylene. J. Am. Chem. Soc., 127, 15102-15106. (Pubitemid 41547376)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.43 , pp. 15102-15106
    • Virnau, P.1    Kantor, Y.2    Kardar, M.3
  • 39
    • 33749347406 scopus 로고    scopus 로고
    • Intricate knots in proteins: Function and evolution
    • Virnau, P., Mirny, L.A. and Kardar, M. (2006) Intricate knots in proteins: Function and evolution. PLoS Comput. Biol., 2, e122.
    • (2006) PLoS Comput. Biol. , vol.2
    • Virnau, P.1    Mirny, L.A.2    Kardar, M.3
  • 40
    • 2342443284 scopus 로고    scopus 로고
    • New developments in topological fluid mechanics: From Kelvin's vortex knots to magnetic knots
    • Stasiak, A., Katritch, V. and Kauffman, L.H. (eds) World Scientific, Singapore
    • Ricca, R.L. (1998) New developments in topological fluid mechanics: from Kelvin's vortex knots to magnetic knots. In: Stasiak, A., Katritch, V. and Kauffman, L.H. (eds), Ideal Knots, Vol. 19. World Scientific, Singapore, pp. 255-273.
    • (1998) Ideal Knots , vol.19 , pp. 255-273
    • Ricca, R.L.1
  • 42
    • 48549100410 scopus 로고    scopus 로고
    • DNA knotting in spooling like configurations in bacteriophages
    • Arsuaga, J. and Diao, Y. (2008) DNA knotting in spooling like configurations in bacteriophages. Comp. Math. Methods Med., 9, 303-316.
    • (2008) Comp. Math. Methods Med. , vol.9 , pp. 303-316
    • Arsuaga, J.1    Diao, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.