Abstract
Bending is a local conformational micropolymorphism of DNA in which the original B-DNA structure is only distorted but is not extensively modified Bending can be predicted by simple static geometry models as well as by a recently developed elastic model that incorporate sequence dependent anisotropic bendability (SDAB). The SDAB model qualitatively explains phenomena including affinity of protein binding, kinking, as well as sequence-dependent vibrational properties of DNA. The vibrational properties of DNA segments can be studied by finite element analysis of a model subjected to an initial bending moment. The frequency spectrum is obtained by applying Fourier analysis to the displacement values in the time domain. This analysis shows that the spectrum of the bending vibrations quite sensitively depends on the sequence, for example that spectrum of a curved sequence is characteristically different from the spectrum of straight sequence motifs of identical basepair composition. Curvature distributions are genome-specific, and pronounced differences are found between protein-coding and regulatory regions, respectively, i.e. sites of extreme curvature and/or bendability are less frequent in protein-coding regions. A WWW server is set up for prediction of curvature and generation of 3D models from DNA sequences (http://www.icgeb.trieste.it/dna)
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Travers, A.A. and Klug, A. (1990), Bending of DNA, in: DNA topology and its biological effects, pp. 57–106 (Cozzarelli, N.R. and Wang, J.C., Eds.) Cold Spring Harbor laboratory, Cold Spring Harbor.
Olson, W.K. and Zhurkin, V.B. (1996),Twenty years of DNA bending, in: Biological Structure and Dynamics, Vol. 2, pp. 341–370 (Sarma, R.H. and Sarma, M.H., Eds.) Adenine Press, Schenectady.
Olson, W.K. (1996) Simulating DNA at low resolution, Curr Opin StructBiol 6 242–56.
Langowski, J., Olson, W.K., Pedersen, S.C., Tobias, I., Westcott, T.P. and Yang, Y. (1996) DNA supercoiling, localized bending and thermal fluctuation s [letter], Trends Biochem Sci 21 50.
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.
Wu, H.M. and Crothers, D.M. (1984) The locus of sequence-directed and protein-induced DNA bending, Nature 308 509–13.
Satchwell, S.C., Drew, H.R. and Travers, A.A. (1986) Sequence periodicities in chicken nucleosome core DNA, J Mol Biol 191 659–75.
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, Nucleic Acids Res 21 1025–9.
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.
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.
Olson, W.K. et al. (1995) Flexing and folding double helical DNA, Biophys Chem 55, 7–29.
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.
Ulyanov, N.B. and James, T.L. (1995) Statistical analysis of DNA duplex structural features, Methods Enzymol 261 90–120.
Gabrielian, A. and Pongor, S. (1996) Correlation of intrinsic DNA curvature with DNA property periodicity, Febs Lett 393 65–8.
Goodsell, D.S. and Dickerson, R.E. (1994) Bending and curvature calculations in B-DNA, Nucleic Acids Res 22 5497–503.
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, JMoI Biol 251648–64.
Wheeler, D. (1993) A gel-concentration-independent retardation detected in two fragments of the rrnB P 1 promoter of E. coli using transverse polyacrylamide pore gradient gel electrophoresis, Biochem Biophys Res Commun 193 413–9.
Shpigelman, E.S., Trifonov, E.N. and Bolshoy, A. (1993) CURVATURE: software for the analysis of curved DNA, Comput Appl Biosci 9, 435–40.
Dlakic, M. (1998) DIAMOD: display and modeling of DNA bending, Bioinformatics, 14 326–31.
Barkley, M. and Zimm, B. (1979) Models of DNA J. Chem. Phys 70 2991–2997.
Vologodskii, A.V. and Frank-Kamenetskii, M.D. (1992) Modeling supercoiled DNA, Methods Enzymol 211 467–80.
Zienkiewicz, O.C. and Taylor, R.L. (1991) The finite element method McGraw-Hill.
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 U S A 90 833–7.
Yang, Y., Tobias, I. and Olson, W.K. (1993) Finite element analysis of DNA supercoiling, JChem Phy 98 1673–1686.
Zhang, P., Tobias, I. and Olson, W.K. (1994) Computer simulation of protein-induced structural changes in closed circular, J Mol Biol 242 271–90.
Rippe, K., von Hippel, P. and Langowski, J. (1995) Action at a distance: DNA-looping and initiation of transcription., Trends Biochem Sci 20 500–6.
Schellman, J.A. (1974) Flexibility of DNA, Biopolymers 13 217–26.
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.
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.
Gromiha, M.M., Munteanu, M.G., Gabrielian, A. and Pongor, S. (1996) Anisotropic elastic bending models of DNA, JBiol Phys 22 227–243.
Gabrielian, A., Vlahovicek, K., Munteanu, M.M., Gromiha, M.M., Brukner, I Sanchez, R. and Pongor, S. (1998) Prediction of bendability and curvature in genomic DNA, in: Structure,Motion, Interaction and Expression, Vol. 1, pp. 117–132 (Sarma, R.H. and Sarma, M.H., Eds.) Adenine Press, Inc., Cincinnati, N.Y.
Han, W., Lindsay, S.M., Dlakic, M. and Harrington, R.E. (1997) Kinked DNA [letter], Nature 386 563.
Gromiha, M.M., Munteanu, M.G., Simon, I. and Pongor, S. (1997) The role of DNA bending in Cro protein-DNA interactions, Biophys Chem 69 153–160.
Eisenberg, D., Schwarz, E., Komaromy, M. and Wall, R. (1984) Analysis of membrane and surface protein sequences with the hydrophobic moment plot, J Mol Biol 179 125–42
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.
Gabrielian, A., Simoncsits, A. and Pongor, S. (1996) Distribution of bending propensity in DNA sequences, Febs Lett 393 124–30.
Schatz, T. and Langowski, J. (1997)J Biomol Struct Dynam 15 265–275.
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.
Yakushevich, L.V. (1994) Nonlinear DNA dynamics: hierarchy of the models, Physica D 79, 77–86.
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.
Gorin, A.A., Zhurkin, V.B. and Olson, W.K. (1995) B-DNA twisting correlates with base-pair morphology, J Mol Biol 247 34–48.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1999 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
VlahoviČek, K., Munteanu, M.G., Pongor, S. (1999). Sequence-Dependent Modelling of Local DNA Bending Phenomena: Curvature Prediction and Vibrational Analysis. In: Bradbury, E.M., Pongor, S. (eds) Structural Biology and Functional Genomics. NATO Science Series, vol 71. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-4631-9_6
Download citation
DOI: https://doi.org/10.1007/978-94-011-4631-9_6
Publisher Name: Springer, Dordrecht
Print ISBN: 978-0-7923-5782-7
Online ISBN: 978-94-011-4631-9
eBook Packages: Springer Book Archive