Modelling DNA Structure from Sequence

  • Kristian Vlahoviček
  • Sándor Pongor


Biological thinking in recent years has been profoundly influenced by the idea of local structural polymorphism in DNA. DNA is no longer considered as a featureless polymer but rather as a series of individual domains differing in flexibility and curvature. Local structural polymorphism is expected to contribute to the specificity of various biological events as gene regulation, packaging, for example, through regulating the affinity of protein binding (Travers and Klug, 1990). In contrast to traditional structural polymorphism (e,g, B, A or Z structures), here we deal with a localised micropolymorphism in which the original B-DNA structure is only distorted but is not extensively modified. The DNA segments involved in protein-induced and inherent DNA-bending are 10–50 base pairs in length (Olson and Zhurkin, 1996) i.e. they are longer than what can be easily handled by atomic resolution molecular modelling or quantum mechanical approaches. Traditional elastic models of DNA, that represent DNA as an ideally elastic, homogeneous cylindrical rod, were used to model macroscopic behaviour of long DNA segments, such as supercoiling (Langowski et al., 1996; Olson, 1996). However, local DNA conformations and recognition by DNA-binding proteins are clearly sequence-dependent, so conventional elastic rod models of DNA, which do not explicitly represent the dependence of the elasticity on the base sequence, cannot say much about them. Here we attempt to briefly review advantages and limitations of the rod-models of DNA with particular regard to elastic modelling of local bending phenomena.


Major Groove Isotropic Elastic Model Strand Symmetry Simple Elastic Model Hydrophobic Moment Plot 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Bansal, M., Bhattacharyya, D. and Ravi, B., 1995, Nuparm and Nucgen: Software for Analysis and Generation of Sequence Dependent Nucleic Acid Structures. Comput Appl Biosci 11:281–7.PubMedGoogle Scholar
  2. Barkley, M. D., Zimm, B., 1979, Theory of Twisting and Bending of Chain Macromolecules: Analysis of the Fluorescence Depolarization of DNA. J. Chem.Phys. 70: 2991–3007.CrossRefGoogle Scholar
  3. Bauer, W. R., Lund, R. A. and White, J. H., 1993, Twist and Writhe of a DNA Loop Containing Intrinsic Bends. Proc. Natl. Acad. Sci. USA 90: 833–7.PubMedCrossRefGoogle Scholar
  4. Bolshoy, A., McNamara, P., Harrington, R. E. and Trifonov, E. N., 1991, Curved DNA without a-A: Experimental Estimation of All 16 DNA Wedge Angles. Proc. Natl. Acad.Sci. USA 88: 2312–6.PubMedCrossRefGoogle Scholar
  5. Brukner, I., Dlakic, M., Savic, A., Susie, S., Pongor, S. and Suck, D., 1993, Evidence for Opposite Groove-Directed Curvature of Gggccc and Aaaaa Sequence Elements [Published Erratum Appears in Nucleic Acids Res 1993 Mar 1 l;2l(5): 1332]. Nucleic Acids Res. 21: 1025–9.PubMedCrossRefGoogle Scholar
  6. Brukner, I., Sanchez, R., Suck, D. and Pongor, S., 1995, Sequence-Dependent Bending Propensity of DNA as Revealed by Dnase I: Parameters for Trinucleotides. Embo J. 14:1812–8.PubMedGoogle Scholar
  7. Calladine, C. R. and Drew, H. R., 1996, A Useful Role for “Static” Models in Elucidating the Behaviour of DNA in Solution. J. Mol. Biol. 257: 479–85.PubMedCrossRefGoogle Scholar
  8. De Santis, P., Palleschi, A., Savino, M. and Scipioni, A., 1990, Validity of the Nearest-Neighbor Approximation in the Evaluation of the Electrophoretic Manifestations of DNA Curvature. Biochemistry 29: 9269–73.PubMedCrossRefGoogle Scholar
  9. Dlakic, M. and Harrington, R. E., 1998, Diamod: Display and Modeling of DNA Bending.Bioinformatics 14: 326–31.PubMedCrossRefGoogle Scholar
  10. Eisenberg, D., Schwarz, E., Komaromy, M. and Wall, R., 1984, Analysis of Membrane and Surface Protein Sequences with the Hydrophobie Moment Plot. J. Mol. Biol. 179: 125–42.PubMedCrossRefGoogle Scholar
  11. el Hassan, M. A. and Calladine, C. R., 1995, The Assessment of the Geometry of Dinucleotide Steps in Double-Helical DNA; a New Local Calculation Scheme. J. Mol.Biol. 251:648–64.PubMedCrossRefGoogle Scholar
  12. Gabrielian, A. and Pongor, S., 1996, Correlation of Intrinsic DNA Curvature with DNA Property Periodicity. Febs Lett. 393: 65–8.PubMedCrossRefGoogle Scholar
  13. Gabrielian, A., Simoncsits, A. and Pongor, S., 1996, Distribution of Bending Propensity in DNA Sequences. Febs Lett. 393: 124–30.PubMedCrossRefGoogle Scholar
  14. Gabrielian, A., Vlahovicek, K., Munteanu, M. G., Gromiha, M. M., Brukner, I., Sanchez, R. and Pongor, S., 1998, Prediction of Bendability and Curvature in Genomic DNA. In Tenth conversation in biomolecular stereodynamics, pp. 117–132.Google Scholar
  15. Goodsell, D. S. and Dickerson, R. E., 1994, Bending and Curvature Calculations in B-DNA.Nucleic Acids Res. 22: 5497–503.PubMedCrossRefGoogle Scholar
  16. Gromiha, M. M., Munteanu, M. G., Gabrielian, A. and Pongor, S., 1996, Anisotropic Elastic Bending Models of DNA. J. Biol. Phys. 22: 227–243.CrossRefGoogle Scholar
  17. Gromiha, M. M., Munteanu, M. G., Simon, I. and Pongor, S., 1997, The Role of DNA Bending in Cro Protein-DNA Interactions. Biophysical Chemistry, in press.Google Scholar
  18. Han, W., Lindsay, S. M., Dlakic, M. and Harrington, R. E., 1997, Kinked DNA [Letter]. Nature 386: 563.PubMedCrossRefGoogle Scholar
  19. Langowski, J., Olson, W. K., Pedersen, S. C., Tobias, I., Westcott, T. P. and Yang, Y., 1996,DNA Supercoiling, Localized Bending and Thermal Fluctuations [Letter]. TrendsBiochem.Sci. 21:50.Google Scholar
  20. Langst, G., Schatz, T., Langowski, J. and Grummt, I., 1997, Structural Analysis of Mouse Rdna: Coincidence between Nuclease Hypersensitive Sites, DNA Curvature and Regulatory Elements in the Intergenic Spacer. Nucleic Acids Res. 25: 511–7.PubMedCrossRefGoogle Scholar
  21. Olson, W. K., 1996, Simulating DNA at Low Resolution. Curr. Opin. Struct. Biol. 6: 242–56.PubMedCrossRefGoogle Scholar
  22. Olson, W. K., Babcock, M. S., Gorin, A., Liu, G., Marky, N. L., Martino, J. A., Pedersen, S.C., S rinivasan, A. R., Tobias, I., Westcott, T. P. and et, al., 1995, Flexing and Folding Double Helical DNA. Biophys. Chem. 55: 7–29.PubMedCrossRefGoogle Scholar
  23. Olson, W. K. and Zhurkin, V. B., 1996, Twenty Years of DNA Bending, In Biological Structure and Dynamics, (Sarma, R. H. and Sarma, M. H., Eds), Adenine Press, Schenectady, pp. 341–370.Google Scholar
  24. Rippe, K., von Hippel, P. H. and Langowski, J., 1995, Action at a Distance: DNA-Looping and Initiation of Transcription. Trends Biochem. Sci. 20: 500–6.PubMedCrossRefGoogle Scholar
  25. Sanghani, S. R., Zakrzewska, K., Harvey, S. C. and Lavery, R., 1996, Molecular Modelling of (A4t4nn)N and (T4a4nn)N: Sequence Elements Responsible for Curvature. Nucleic Acids Res. 24: 1632–7.PubMedCrossRefGoogle Scholar
  26. Satchwell, S. C., Drew, H. R. and Travers, A. A., 1986, Sequence Periodicities in Chicken Nucleosome Core DNA. J. Mol. Biol. 191: 659–75.PubMedCrossRefGoogle Scholar
  27. Schatz, T. and Langowski, J., 1997, Curvature and Sequence Analysis of Eukaryotic Promoters.J. Biomol. Struct. Dyn. 15: 265–75.PubMedCrossRefGoogle Scholar
  28. Schellman, J. A., 1974, Flexibility of DNA. Biopolymers 13: 217–26.PubMedCrossRefGoogle Scholar
  29. Shpigelman, E. S., Trifonov, E. N. and Bolshoy, A., 1993, Curvature: Software for the Analysis of Curved DNA. Comput. Appl. Biosci. 9: 435–40.PubMedGoogle Scholar
  30. Travers, A. A. and Klug, A., 1990, Bending of DNA, In DNA Topology and Its Biological Effects, (Cozzarelli, N. R. a. W., J.C., Ed.), Cold Spring Harbor laboratory, Cold Spring Harbor, pp. 57–106.Google Scholar
  31. Trifonov, E. N. and Sussman, J. L., 1980, The Pitch of Chromatin DNA Is Reflected in Its Nucleotide Sequence. Proc. Natl. Acad. Sci. USA 77: 3816–20.PubMedCrossRefGoogle Scholar
  32. Ulyanov, N. B. and James, T. L., 1995, Statistical Analysis of DNA Duplex Structural Features. Methods Enzymol. 261: 90–120.PubMedCrossRefGoogle Scholar
  33. Vologodskii, A. V. and Frank-Kamenetskii, M. D., 1992, Modeling Supercoiled DNA. Methods Enzymol. 211: 467–80.PubMedCrossRefGoogle Scholar
  34. Wheeler, D., 1993, A Gel-Concentration-Independent Retardation Detected in Two Fragments of the Rrnb Pl Promoter of E. Coli Using Transverse Polyacrylamide Pore Gradient Gel Electrophoresis. Biochem. Biophys. Res. Comm. 193: 413–9.PubMedCrossRefGoogle Scholar
  35. Wu, H. M. and Crothers, D. M., 1984, The Locus of Sequence-Directed and Protein-Induced DNA Bending. Nature 308: 509–13.PubMedCrossRefGoogle Scholar
  36. Yakushevich, L. V., 1994, Nonlinear DNA Dynamics. Physica D 79: 77–86.CrossRefGoogle Scholar
  37. Yang, Y., Tobias, I. and Olson, W.K., 1993, Finite Element Analysis of DNA Supercoiling. J.Chem.Phys. 98: 1673–1686.CrossRefGoogle Scholar
  38. Zhang, P., Tobias, I. and Olson, W. K., 1994, Computer Simulation of Protein-Induced Structural Changes in Closed Circular DNA [Published Erratum Appears in J Mol Biol 1995 Sep l;25l(5):72l].J. Mol. Biol. 242: 271–90.PubMedCrossRefGoogle Scholar
  39. Zhurkin, V. B., Lysov, Y. P. and Ivanov, V. I., 1979, Anisotropic Flexibility of DNA and the Nucleosomal Structure. Nucleic Acids Res. 6: 1081–96.PubMedCrossRefGoogle Scholar
  40. Zienkiewicz, O. C. a. T., R.L., 1991, The Finite Element Methods. McGraw-Hill.Google Scholar

Copyright information

© Springer Science+Business Media New York 2001

Authors and Affiliations

  • Kristian Vlahoviček
    • 1
  • Sándor Pongor
    • 1
  1. 1.International Center for Genetic Engineering and BiotechnologyTriesteItaly

Personalised recommendations