Abstract
As a coarse-gained model, a super-thin elastic rod subjected to interfacial interactions is used to investigate the condensation of DNA in a multivalent salt solution. The interfacial traction between the rod and the solution environment is determined in terms of the Young–Laplace equation. Kirchhoff’s theory of elastic rod is used to analyze the equilibrium configuration of a DNA chain under the action of the interfacial traction. Two models are established to characterize the change of the interfacial traction and elastic modulus of DNA with the ionic concentration of the salt solution, respectively. The influences of the ionic concentration on the equilibrium configuration of DNA are discussed. The results show that the condensation of DNA is mainly determined by competition between the interfacial energy and elastic strain energy of the DNA itself, and the interfacial traction is one of forces that drive DNA condensation. With the change of concentration, the DNA segments will undergo a series of alteration from the original configuration to the condensed configuration, and the spiral-shape appearing in the condensed configuration of DNA is independent of the original configuration.
Similar content being viewed by others
References
Huang, Z.: Modulating DNA configuration by interfacial traction: an elastic rod model to characterize DNA folding and unfolding. J. Biol. Phys. 37, 79–90 (2011)
Benham, C.J.: Elastic model of super-coiling. Proc. Natl. Acad. Sci. U.S.A. 74, 2397–2401 (1977)
Benham, C.J.: An elastic model of the large-scale structure of duplex DNA. Biopolymers 18, 609–623 (1979)
Le Bret, M.: Relationship between the energy of superhelix formation, the shear modulus and the torsional Brownian motion of DNA. Biopolymers 17, 1939–1955 (1978)
Le Bret, M.: Twist and writhing on short circular DNAs according to first-order elasticity. Biopolymers 23, 1835–1867 (1984)
Gelbart, W.M., Bruinsma, R.F., Pincus, P.A., Parsegian, V.A.: DNA-inspired electrostatics. Phys. Today 53, 38–44 (2000)
Shi, Y., Borovik, A.E., Hearst, J.E.: Elastic rod model incorporating shear and extension, generalized nonlinear Schrodinger equations, and novel closed-form solutions for supercoiled DNA. J. Chem. Phys. 103, 3166–3183 (1995)
Manning, R.S., Maddocks, J.H., Kahn, J.D.: A continuum rod model of sequence–dependent DNA structure. J. Chem. Phys. 105, 5626–5646 (1996)
Cherstvy, A.G.: Torque-induced deformations of charged elastic DNA rods: thin helices, loops, and precursors of DNA supercoiling. J. Biol. Phys. 37, 227–238 (2011)
Cherstvy, A.G.: Collapse of highly charged polyelectrolytes triggered by attractive dipole-dipole and correlation-induced electrostatic interactions. J. Phys. Chem. 114, 5241–5249 (2010)
Cherstvy, A.G.: Effect of a low-dielectric interior on DNA electrostatic response to twisting and bending. J. Phys. Chem. 111, 12933–12937 (2007)
Tobias, I., Swigon, D., Coleman, B.D.: Elastic stability of DNA configuration: I general theory. Phys. Rev. E 61, 747–758 (2000)
Coleman, B.D., Swigon, D., Tobias, I.: Elastic stability of DNA configuration: II Supercoiled plasmids with self-contact. Phys. Rev. E 61, 759–770 (2000)
Munteanu, M.G., Vlahovicek, K., Parthasarathy, S., Simon, I., Pongor, S.: Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena. Trends Biochem. Sci. 23, 341–347 (1998)
Eslami-Mossallam, B., Ejtehadi, M.R.: An asymmetric elastic rod model for DNA. Phys. Rev. E 80, 011919 (2009)
Coleman, B.D., Olson, W.K., Swigon, D.: Theory of sequence-dependent DNA elasticity. J. Chem. Phys. 118, 7127–7140 (2003)
Slita, A.V., Kasyanenko, N.A., Nazarova, O.V., Gavrilova, I.I., Eropkina, E.M., Sirotkin, A.K., Smirnova, T.D., Kiselev, O.I., Panarin, E.F.: DNA–polycation complexes effect of polycation structure on physico-chemical and biological properties. J. Biotechnol. 127, 679–693 (2007)
Parsegian, V.A., Rand, R.P., Rau, D.C.: Osmotic stress, crowding, preferential hydration, and binding: a comparison of perspectives. Proc. Natl. Acad. Sci. U.S.A. 97, 3987 (2000)
Hud, N.V., Vilfan, I.D.: Toroidal DNA condensates: Unraveling the fine structure and the role of nucleation in determining size. Ann. Rev. Biophys. Biomol. Struct. 34, 295 (2005)
Keyser, U.F., van Dorp, S., Lemay, S.G.: Tether forces in DNA electrophoresis. Chem. Soc. Rev. 39, 939 (2010)
Leonard, C., Gousle, J.A.S.: Compact form of DNA induced by supermidine. Nature 259, 333 (1976)
Li, W., Wang, P.-Y., Yan, J., Li, M.: Impact of DNA twist accumulation on progressive helical wrapping of torsionally constrained DNA. Phys. Rev. Lett. 109, 218–102 (2012)
Benham, C.J., Mielke, S.P.: DNA mechanics. Ann. Rev. Biomed. Eng. 7, 21–53 (2005)
Travers, A.A., Thompson, J.M.: An introduction to the mechanics of DNA. Philos. Trans. R. Soc. A 362, 1265–1279 (2004)
Liu, Y.-Z.: Nonlinear Mechanics of Thin Elastic Rod: Theoretical Basis of Mechanical Model of DNA (in Chinese). Tsinghua Press, Beijing (2006)
Bednar, J., Furrer, P., Stasiak, A., Dubochet, J.: The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. J. Mol. Biol. 235, 825–847 (1994)
Brady, G., Foos, D., Benham, C.J.: Evidence for an interwound form of the superhelix in circular DNA. Biopolymers 23, 2963–2966 (1984)
Swigon, D.: The mathematics of DNA structure, mechanics, and dynamics. In: Benham C.J. et al. (eds.) Mathematics of DNA Structure, Function and Interactions, pp. 293–320. Springer, Berlin (2009)
Podgornik, R.: DNA off the Hooke. Nat. Nanotechnol. 1, 100–101 (2006)
Gosule, L.C., Schellman, J.A.: Compact form of DNA induced by spermidine. Nature 59, 333–335 (1972)
Hud, N.V., Downing, K.H., Balhorn, R.: A constant radius of curvature model for the organization of DNA in toroidal condensates. Proc. Nat. Acad. Sci. USA 92, 3581–3585 (1995)
Hud, N.V., Downing, K.H.: Cryoelectron microscopy of λ phage DNA condensates in vitreous ice: the fine structure of DNA toroids. Proc. Nat. Acad. Sci. USA 98, 14925–14930 (2001)
Westcott, T.P., Tobias, I., Olson, W.K.: Modeling self-contact forces in the elasticity of DNA supercoiling. J. Chem. Phys. 107, 3967–3980 (1997)
Leforestier, A., Livolant, F.: Structure of toroidal DNA collapsed inside the phage capsid. Proc. Nat. Acad. Sci. USA 106, 9157–9162 (2009)
Wang, M.D., Yin, H., Landick, R., Gelles, J., Block, S.M.: Stretching DNA with optical tweezers. Biophys. J. 72, 1335–1346 (1997)
Hamley, W.I. : Introduction to soft matter : synthetic and biological self-assembling materials. Reading (2008)
Futian, Z.: Fundamentals of Molecular Interface Chemistry (in Chinese). Shanghai Scientific and Technology Literature Publishing House, Shanghai (2006)
Daoud, M., Williams, C.E.: Soft Matter Physics. Springer, Berlin (1999)
Baumann, C.G., Smith, S.B., Bloomfield, V.A., Bustamante, C.: Ionic effects on the elasticity of single DNA molecules. Proc. Nat. Acad. Sci. USA 94, 6185–6190 (1997)
Chen, W.: Differential geometry (in Chinese). Beijing University Press, Beijing (2006)
Zhao, Z.: Adsorption Principle in Application (in Chinese). Chemical Industry Press, Beijing (2005)
Liu, F., Tang, X.: Polymer Physics (in Chinese). Higher Education Press, Beijing (2004)
Smith, S.B., Finzi, L., Bustamante, C.: Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258, 5085 (1992)
Schlick, T.: Modeling Superhelical DNA: recent analytical and dynamic approaches. Current Opin. Struct. Biol. 5, 245–265 (1995)
Acknowledgements
Support of the National Nature Science Foundation of China through Grant No. 11172130 is gratefully acknowledged.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Xiao, Y., Huang, Z. & Wang, S. An elastic rod model to evaluate effects of ionic concentration on equilibrium configuration of DNA in salt solution. J Biol Phys 40, 179–192 (2014). https://doi.org/10.1007/s10867-014-9344-1
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10867-014-9344-1