A mesoscale model of DNA and its renaturation

Biophysical Journal

Volumn 96, Issue 5, 2009, Pages 1675-1690

  Sambriski, E J ^a   Schwartz, D C ^b   De Pablo, J J ^a  

^a University of Wisconsin Madison   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; SOLVENT;

ARTICLE; CHEMICAL INTERACTION; COLLOID; DIELECTRIC CONSTANT; ELECTRICITY; FORCE; HEAT; IONIC STRENGTH; MELTING POINT; MOLECULAR DYNAMICS; MOLECULAR MODEL; NUCLEIC ACID ANALYSIS; NUCLEIC ACID RENATURATION; NUCLEOTIDE SEQUENCE; SIMULATION; THEORY; ALGORITHM; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; OSMOLARITY; STATIC ELECTRICITY; TRANSITION TEMPERATURE;

ALGORITHMS; COMPUTER SIMULATION; DNA; HOT TEMPERATURE; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEIC ACID RENATURATION; OSMOLAR CONCENTRATION; STATIC ELECTRICITY; TRANSITION TEMPERATURE;

EID: 63649131960     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2008.09.061     Document Type: Article

References (81)

1. Kornyshev, A. A., and S. Leiken. 1998. Electrostatic interaction between helical macromolecules in aggregates: an impetus for DNA poly- and mesomorphism. Proc. Natl. Acad. Sci. USA. 95:13579-13584.
2. Solis, F. J., and M. Olvera de la Cruz. 1999. Attractive interactions between rodlike polyelectrolytes: polarization, crystallization, and packing. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics. 60:4496-4499.
3. Lyubartsev, A. P., and L. Nordenskiöld. 1997. Monte Carlo simulation study of DNA polyelectrolyte properties in the presence of multivalent polyamine ions. J. Phys. Chem. B. 101:4335-4342.
4. Gil Montoro, J. C., and J. L. F. Abascal. 1995. Ionic distribution around simple DNA models. I. Cylindrically averaged properties. J. Chem. Phys. 103:8273-8284.
5. Schlick, T., and W. K. Olson. 1992. Supercoiled DNA energetics and dynamics by computer simulation. J. Mol. Biol. 223:1089-1119.
6. Barkley, M. D., and B. H. Zimm. 1979. Theory of twisting and bending of chain macromolecules - analysis of the fluorescence depolarization of DNA. J. Chem. Phys. 70:2991-3007.
7. Jian, H., A. Vologodskii, and T. Schlick. 1997. A combined wormlikechain and bead model for dynamic simulations of long linear DNA. J. Comput. Phys. 136:168-179.
8. Chopra, M., and R. G. Larson. 2002. Brownian dynamics simulations of isolated polymer molecules in shear flow near adsorbing and non-adsorbing surfaces. J. Rheol. 46:831-862.
9. Jendrejack, R. M., J. J. de Pablo, and M. D. Graham. 2002. Stochastic simulations of DNA in flow: dynamics and the effects of hydrodynamic interactions. J. Chem. Phys. 116:7752-7759.
10. Jendrejack, R. M., D. C. Schwartz, J. J. de Pablo, and M. D. Graham. 2004. Shear-induced migration in flowing polymer solutions: simulation of long-chain DNA in microchannels. J. Chem. Phys. 120:2513-2529.
11. Hur, J. S., E. S. G. Shaqfeh, and R. G. Larson. 2000. Brownian dynamics simulations of single DNA molecules in shear flow. J. Rheol. 44:713-742.
12. Schroeder, C. M., R. E. Teixiera, E. S. G. Shaqfeh, and S. Chu. 2005. Dynamics of DNA in the flow-gradient plane of steady shear flow: observations and simulations. Macromolecules. 38:1967-1978.
13. Bruant, N., D. Flatters, R. Lavery, and D. Genest. 1999. From atomic to mesoscopic descriptions of the internal dynamics of DNA. Biophys. J. 77:2366-2376.
14. Tepper, H. L., and G. A. Voth. 2005. A coarse-grained model for double-helix molecules in solution: spontaneous helix formation and equilibrium properties. J. Chem. Phys. 122:124906.
15. Tan, R. K. Z., and S. C. Harvey. 1989. Molecular mechanics model of supercoiled DNA. J. Mol. Biol. 205:573-591.
16. El Hassan, M. A., and C. R. Calladine. 1995. The assessment of the geometry of dinucleotide steps in double-helical DNA - a new local calculation scheme. J. Mol. Biol. 251:648-664.
17. Drukker, K., and G. C. Schatz. 2000. A model for simulating dynamics of DNA denaturation. J. Phys. Chem. B. 104:6108-6111.
18. Sales-Pardo, M.,R.Guimerà, A. A. Moreira, J.Widom,and L.A. N. Amaral. 2005.Mesoscopic modeling for nucleic acid chain dynamics. Phys. Rev. E. 71:051902.
19. Maciejczyk, M., W. R. Rudnicki, and B. Lesyng. 2000. A mesoscopic model of nucleic acids. Part 2. An effective potential energy function for DNA. J. Biomol. Struct. Dyn. 17:1109-1115.
20. Knotts, T. A., IV, N. Rathore, D. C. Schwartz, and J. J. de Pablo. 2007. A coarse grain model for DNA. J. Chem. Phys. 126:084901.
21. Arnott, S., P. J. Campbell Smith, and R. Chandrasekaran. 1975. Atomic coordinates and molecular conformations for DNA-DNA, RNA-RNA and DNA-RNA helices. In Handbook of Biochemistry and Molecular Biology: Nucleic Acids, Vol. 2, 3rd Ed G. D. Fasman, editor. CRC Press, Cleveland, OH.
22. Hagan, M. F., A. R. Dinner, D. Chandler, and A. K. Chakraborty. 2003. Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA. Proc. Natl. Acad. Sci. USA. 100:13922-13927.
23. Piana, S. 2007. Atomistic simulations of the DNA helix-coil transition. J. Phys. Chem. A. 111:12349-12354.
24. Perez, A., J. R. Blas, M. Rueda, J. M. Lopez-Bes, X. de la Cruz, et al. 2005. Exploring the essential dynamics of B-DNA. J. Chem. Theory Comput. 1:790-800.
25. Perez, A., F. J. Luque, and M. Orozco. 2007. Dynamics of B-DNA on the microsecond time scale. J. Am. Chem. Soc. 129:14739-14745.
26. Orozco, M., A. Noy, and A. Perez. 2008. Recent advances in the study of nucleic acid flexibility by molecular dynamics. Curr. Opin. Struct. Biol. 18:185-193.
27. Hoang, T. X., and M. Cieplak. 2000. Molecular dynamics of folding of secondary structures in Gō-type models of proteins. J. Chem. Phys. 112:6851-6862.
28. Schuster, P., and P. Wolschann. 1999. Hydrogen bonding: from small clusters to biopolymers. Monatsh. Chem. 130:947-960.
29. Legon, A. C., and D. J. Millen. 1987. Directional character, strength, and nature of the hydrogen bond in gas-phase dimers. Acc. Chem. Res. 20:39-45.
30. Derewenda, Z. S., L. Lee, and U. Derewenda. 1995. The occurrence of C]H/O hydrogen bonds in proteins. J. Mol. Biol. 252:248-262.
31. Horton, R., L. A. Moran, K. G. Scrimgeour, M. D. Perry, and J. D. Rawn. 2006. Principles of Biochemistry, 4th Ed.. Prentice Hall, Upper Saddle River, NJ.
32. Breslauer, K. J., R. Frank, H. Blöcker, and L. A. Marky. 1986. Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA. 83:3746-3750.
33. SantaLucia, J., Jr. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA. 95:1460-1465.
34. Owczarzy, R., P. M. Vallone, F. J. Gallo, T. M. Paner, M. J. Lane, et al. 1997. Predicting sequence-dependent melting stability of short duplex DNA oligomers. Biopolymers. 44:217-239.
35. Stogryn, A. 1971. Equations for calculating the dielectric constant of saline water. IEEE Trans. Microw. Theory Tech. 19:733-736.
36. Curtis, H. L., and F. M. Defandorf. 1926. Dielectric constant and dielectric strength of elementary pure inorganic compounds and air. In International Critical Tables of Numerical Data, Physics, Chemistry and Technology. E. W. Washburn, editor. McGraw-Hill, New York.
37. Fernández, D. P., A. R. H. Goodwin, E. W. Lemmon, J. M. H. L. Sengers, and R. C. Williams. 1997. A formulation for the static permittivity of water and steam at temperatures from 238 K to 873 K at pressures up to 1200 MPa, including derivatives and Debye-Hückel coefficients. J. Phys. Chem. Ref. Data. 26:1125-1166.
38. Catenaccio, A., Y. Daruich, and C. Magallanes. 2003. Temperature dependence of the permittivity of water. Chem. Phys. Lett. 367:669-671.
39. Rau, D. C., and V. A. Parsegian. 1992. Direct measurement of the intermolecular forces between counterion-condensed DNA double helices: evidence for long range attractive hydration forces. Biophys. J. 61:246-259.
40. Rau, D. C., and V. A. Parsegian. 1992. Direct measurement of temperature-dependent solvation forces between DNA double helices. Biophys. J. 61:260-271.
41. Qiu, X., L. W. Kwok, H. Y. Park, J. S. Lamb, K. Andersen, et al. 2006. Measuring inter-DNA potentials in solution. Phys Rev. Lett. 96:138101.
42. Raspaud, E., M. Olvera de la Cruz, J. -L. Sikorav, and F. Livolant. 1998. Precipitation of DNA by polyamines: a polyelectrolyte behavior. Biophys. J. 74:381-393.
43. Allahyarov, E., and H. Löwen. 2000. Effective interaction between helical biomolecules. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics. 62:5542-5556.
44. Allahyarov, E., G. Gompper, and H. Löwen. 2004. Attraction between DNA molecules mediated by multivalent ions. Phys Rev. E. 69:041904.
45. Ha, B.-Y., and A. J. Liu. 1998. Charge oscillations and many-body effects in bundles of like-charged rods. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics. 58:6281-6286.
46. Ha, B.-Y., and A. J. Liu. 1999. Counterion-mediated, non-pairwiseadditive attractions in bundles of like-charged rods. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics. 60:803-813.
47. Rouzina, I., and V. A. Bloomfield. 1996. Macroion attraction due to electrostatic correlation between screening counterions. 1. Mobile surface-adsorbed ions and diffuse ion cloud. J. Phys. Chem. 100:9977-9989.
48. Chocholousova, J., and M. Feig. 2006. Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment. J. Phys. Chem. B. 110:17240-17251.
49. Anderson, M. L. M. 1999. Nucleic Acid Hybridization. Bios Scientific, Oxford, United Kingdom.
50. Carlon, E., E. Orlandini, and A. L. Stella. 2002. Roles of stiffness and excluded volume in DNA denaturation. Phys. Rev. Lett. 88:198101.
51. Kafri, Y., D. Mukamel, and L. Peliti. 2000. Why is the DNA denaturation transition first order? Phys. Rev. Lett. 85:4988-4991.
52. Owczarzy, R., Y. You, B. G. Moreira, J. A. Manthey, L. Huang, et al. 2004. Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. Biochemistry. 43:3537-3554.
53. Chodera, J. D., W. C. Swope, J. W. Pitera, C. Seok, and K. A. Dill. 2007. Use of the Weighted Histogram Analysis Method for the analysis of simulated and parallel tempering simulations. J. Chem. Theory Comput. 3:26-41.
54. Rathore, N., M. Chopra, and J. J. de Pablo. 2005. Optimal allocation of replicas in parallel tempering simulations. J. Chem. Phys. 122:024111.
55. Abraham, M. J., and J. E. Gready. 2008. Ensuring mixing efficiency of replica-exchange molecular dynamics simulations. J. Chem. Theory Comput. 4:1119-1128.
56. Sugita, Y., A. Kitao, and Y. Okamoto. 2000. Multidimensional replicaexchange method for free-energy calculations. J. Chem. Phys. 113:6042-6051.
57. Nymeyer, H., S. Gnanakaran, and A. E. García. 2004. Atomic simulations of protein folding, using the replica exchange algorithm. Methods Enzymol. 383:119-149.
58. Sugita, Y., and Y. Okamoto. 1999. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314:141-151.
59. Wetmur, J. G., and N. Davidson. 1968. Kinetics of renaturation of DNA. J. Mol. Biol. 31:349-370.
60. Bussi, G., and M. Parrinello. 2007. Accurate sampling using Langevin dynamics. Phys. Rev. E. 75:056707.
61. Baumann, C. G., S. B. Smith, V. A. Bloomfield, and C. Bustamante. 1997. Ionic effects on the elasticity of single DNA molecules. Proc. Natl. Acad. Sci. USA. 94:6185-6190.
62. Smith, S. B., Y. Cui, and C. Bustamante. 1996. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 271:795-799.
63. Murphy, M. C., I. Rasnik, W. Cheng, T. M. Lohman, and T. Ha. 2004. Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy. Biophys. J. 86:2530-2537.
64. Ullner, M., and C. E. Woodward. 2002. Orientational correlation function and persistence lengths of flexible polyelectrolytes. Macromolecules. 35:1437-1445.
65. Hagerman, P. J. 1988. Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17:265-286.
66. Wiggins, P. A., and P. C. Nelson. 2006. Generalized theory of semiflexible polymers. Phys. Rev. E. 73:031906.
67. Williams, L. D., and L. J. Maher, III.. 2000. Electrostatic mechanism of DNA deformation. Annu. Rev. Biophys. Biomol. Struct. 29:497-521.
68. Skolnick, J., and M. Fixman. 1977. Electrostatic persistence length of a wormlike polyelectrolyte. Macromolecules. 10:944-948.
69. Rathore, N., and J. J. de Pablo. 2002. Monte Carlo simulation of proteins through a random walk in energy space. J. Chem. Phys. 116:7225-7230.
70. Rathore, N., T. A. Knotts, IV, and J. J. de Pablo. 2003. Density of states simulations of proteins. J. Chem. Phys. 118:4285-4290.
71. Nelson, P. 2004. Biological Physics: Energy, Information, Life. W. H. Freeman, New York.
72. Mikulecky, P. J., and A. L. Feig. 2006. Heat capacity changes associated with DNA duplex formation: salt- and sequence-dependent effects. Biochemistry. 45:604-616.
73. Holbrook, J. A., M. W. Capp, R. M. Saecker, and M. T. Record, Jr. 1999. Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices. Biochemistry. 38:8409-8422.
74. Cho, S. S., P. Weinkam, and P. G. Wolynes. 2008. Origins of barriers and barrierless folding in BBL. Proc. Natl. Acad. Sci. USA. 105: 118-123.
75. Eastwood, M. P., and P. G. Wolynes. 2001. Role of explicitly cooperative interactions in protein folding funnels: a simulation study. J. Chem. Phys. 114:4702-4716.
76. Wetmur, J. G. 1976. Hybridization and renaturation kinetics of nucleic acids. Annu. Rev. Biophys. Bioeng. 5:337-361.
77. Eimer, W., and R. Pecora. 1991. Rotational and translational diffusion of short rodlike molecules in solution: oligonucleotides. J. Chem. Phys. 94:2324-2329.
78. Stellwagen, N. C., S. Magnusdottir, C. Gelfi, and P. G. Righetti. 2001. Measuring the translational diffusion coefficients of small DNA molecules by capillary electrophoresis. Biopolymers. 58:390-397.
79. Likhachev, E. 2003. Dependence of water viscosity on temperature and pressure. Tech. Phys. 48:514-515.
80. Stellwagen, E., Y. Lu, and N. C. Stellwagen. 2003. Unified description of electrophoresis and diffusion for DNA and other polyions. Biochemistry. 42:11745-11750.
81. Wilk, A., J. Gapinski, A. Patkowski, and R. Pecora. 2004. Self-diffusion in solutions of a 20 base pair oligonucleotide: effects of concentration and ionic strength. J. Chem. Phys. 121:10794-10802.