Abstract
Based on the model of the strong correlation of counterions condensed on DNA molecule, by tailoring interaction potential, interduplex spacing and correlation spacing between condensed counterions on DNA molecule and interduplex spacing fluctuation strength, toroidal configuration, rod-like configuration and two-hole configurations are possible. The size effects of counterion structure on the toroidal structure can be detected by this model. The autocorrelation function of the tangent vectors is found as an effective way to detect the structure of toroidal conformations and the generic pathway of the process of DNA condensation. The generic pathway of all of the configurations involves an initial nucleation loop, and the next part of the DNA chain is folded on the top of the initial nucleation loop with different manners, in agreement with the recent experimental results.
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References
N. V. Hud and I. D. Vilfan, Toroidal DNA condensates: Un raveling the fine structure and the role of nucleation in determining size, Annu. Rev. Biophys. Biomol. Struct., 2005, 34: 295
V. A. Bloomfield, DNA condensation, Curr. Opin. Struct. Biol., 1996, 6(3): 334
A. Leforestier, A. Siber, F. Livolant, and R. Podgornik, Protein-DNA interactions determine the shapes of DNA toroids condensed in virus capsids, Biophys. J., 2011, 100: 2209
Z. Y. Ou and M. Muthukumar, Langevin dynamics of semi-flexible polyelectrolytes: Rod-toroid-globule-coil structures and counterion distribution, J. Chem. Phys., 2005, 123(7): 074905
W. M. Gelbart, R. F. Bruinsma, P. A. Pincus, V. A. Parsegian, and W. J. Johnson, DNA-inspired electrostatics, Phys. Today, 2000, 53: 38
B. Schnurr, F. C. MacKintosh, and D. R. M. Williams, Dynamical intermediates in the collapse of semiflexible polymers in poor solvents, Europhys. Lett., 2000, 51: 279
W. B. Fu, X. L. Wang, X. H. Zhang, S. Y. Ran, J. Yan, and M. Li, Compaction dynamics of single DNA molecules under tension, J. Am. Chem. Soc., 2006, 128(47): 15040
F. Oosawa, Interaction between parallel rodlike macroions, Biopolymers, 1968, 6(11): 1633
G. S. Manning, Limiting laws and counterion condensation in polyelectrolyte solutions (i): Colligative properties, J. Chem. Phys., 1969, 51(3): 924
B. Y. Ha and A. J. Liu, Counterion-mediated attraction between two like-charged rods, Phys. Rev. Lett., 1997, 79(7): 1289
I. Rouzina and V. A. Bloomfield, Macroion attraction due to electrostatic correlation between screening counterions (1): Mobile surface-adsorbed ions and diffuse ion cloud, J. Phys. Chem., 1996, 100(23): 9977
Y. Levin, J. J. Arenzon, and J. F. Stilck, The nature of attraction between like-charged rods, Phys. Rev. Lett., 1999, 83(13): 2680
A. A. Kornyshev and S. Leikin, Electrostatic zipper motif for DNA aggregation, Phys. Rev. Lett., 1999, 82(20): 4138
K. Besteman, S. Hage, N. H. Dekker, and S. G. Lemay, Role of tension and twist in single-molecule DNA condensation, Phys. Rev. Lett., 2007, 98(5): 058103
K. Besteman, K. Van Eijk, and S. G. Lemay, Charge inversion accompanies DNA condensation by multivalent ions, Nat. Phys., 2007, 3(9): 641
F. Ritort, S. Mihardja, S. B. Smith, and C. Bustamante, Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers, Phys. Rev. Lett., 2006, 96(11): 118301
W. K. Kim and W. Sung, Charge density coordination and dynamics in a rodlike polyelectrolyte, Phys. Rev. E, 2008, 78(2): 021904
L. Dai, Y. G. Mu, L. Nordenskiöld, and J. R. van der Maarel, Molecular dynamics simulation of multivalent-ion mediated attraction between DNA molecules, Phys. Rev. Lett., 2008, 100(11): 118301
F. Oosawa, Polyelectrolyte, New York: Marcel Dekker, INC, 1971
J. Barrat and J. Hansen, Basic Concepts for Simple and Complex Liquids, Cambridge: Cambridge University Press, 2003
Y. H. Liu and L. Hu, Monte Carlo simulation on topology of DNA minicircles, Chinese J. Comput. Phys., 2009, 26: 152 (in Chinese)
J. Marko, Introduction to single-DNA micromechanics in multiple aspects of DNA and RNA from biophysics to bioinformatics Les Houches Session LXXXII, Elsevier, 2005
L. S. Lerman, L. S. Wilkerson, J. H. Venable, Jr, and B. H. Robinson, DNA packing in single crystals inferred from freeze-fracture-etch replicas, J. Mol. Biol., 1976, 108(2): 271
J. A. Schellman and N. Parthasarathy, X-ray diffraction studies on cation-collapsed DNA, J. Mol. Biol., 1984, 175: 313
H. Deng and V. A. Bloomfield, Structural effects of cobaltamine compounds on DNA condensation, Biophys. J., 1999, 77(3): 1556
G. E. Plum, P. G. Arscott, and V. A. Bloomfield, Condensation of DNA by trivalent cations (2): Effects of cation structure, Biopolymers, 1990, 30(5–6): 631
J. Widom and R. L. Baldwin, Monomolecular condensation of lambda-DNA induced by cobalt hexamine, Biopolymers, 1983, 22(6): 1595
J. A. Benbasat, Condensation of bacteriophage phi W14 DNA of varying charge densities by trivalent counterions, Biochemistry, 1984, 23(16): 3609
A. M. Carnerup, M. L. Ainalem, V. Alfredsson, and T. Nylander, Watching DNA condensation induced by poly (amido amine) dendrimer with time-resolved cryo-TEM, Langmuir, 2009, 25(21): 12466
G. S. Manning, The persistence length of DNA is reached from the persistence length of its null isomer through an internal electrostatic stretching force, Biophys. J., 2006, 91(10): 3607
S. Geggier, A. Kotlyar, and A. Vologodskii, Temperature dependence of DNA persistence length, Nucleic Acids Res., 2011, 39(4): 1427
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Liu, YH., Jiang, CM., Guo, XM. et al. DNA condensation and size effects of DNA condensation agent. Front. Phys. 8, 467–471 (2013). https://doi.org/10.1007/s11467-013-0342-8
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DOI: https://doi.org/10.1007/s11467-013-0342-8