Abstract
The present study presents the results of molecular modelling of base sequence effects on the structure of the DNA double helix. An appropriate choice of the modelling algorithm and the use of helical symmetry has enabled a very thorough investigation of the conformational space of all unique tetranucleotide repeating sequences. The results indicate that each sequence is associated with a considerable number of stable sub-states characterised by their sugar puckers. Using this data it is possible to envisage predicting the conformation of much longer pieces of DNA using the superposition of tetranucleotide fragments.
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
R. E. Dickerson: in Unusual DNA Structures ,R. D. Wells and S. C. Harvey (Eds.), Springer-Verlag, p. 287 (1988).
K. Yanagi, G. G. Privé and R. E. Dickerson: J. Mol. Biol. 217, 201 (1991).
R. Lavery: in Structure and Expression ,Vol. 3, DNA Bending and Curvature ,W. K. Olson, R. H. Sarma, M. H. Sarma and M. Sundaralingam (Eds.), Adenine Press, New York, p. 191 (1988).
M. Poncin, B. Hartmann and R. Lavery: J. Mol. Biol. 226, 775 (1992).
M. Poncin, D. Piazzola and R. Lavery: Biopolymers 32, 1077 (1992).
K. Zakrzewska: J. Biomol. Struct. Dynam. 9, 681 (1992).
O. Mauffret, B. Hartmann, O. Convert, R. Lavery and S. Fermandjian: J. Mol. Biol. 227, 852 (1992).
K. Zakrzewska, V. I. Poltev, C. Oguey and R. Lavery: J. Mol.. Struct. (Theochem) 286, 219 (1993).
M. Ouali, R. Letellier, F. Adnet, J. Liquier, J. S. Sun, R. Lavery and E. Taillandier: Biochemistry 32, 2098 (1993).
B. Hartmann, D. Piazzola and R. Lavery: Nucleic Acids Res. 21, 561 (1993).
F. Briki, J. Ramstein, R. Lavery and D. Genest: J. Am. Chem. Soc. 113, 2490 (1991).
V. B. Zhurkin, V. I. Poltev and V. L. Florent’ev: Mol. Biol. 14, 1116 (1980).
R. Lavery, K. Zakrzewska and A. Pullman: J. Comp. Chem. 5, 363 (1984).
R. Lavery, H. Sklenar, K. Zakrzewska and B. Pullman: J. Biomol. Struct. Dynam. 3, 989 (1986).
R. Lavery, I. Parker and J. Kendrick: J. Biomol. Struct. Dynam. 4, 443 (1986).
B. Hingerty, R. H. Richie, T. L. Ferrel and T. E. Turner: Biopolymers 24, 427 (1985).
R. Lavery and H. Sklenar: J. Biomol. Struct. Dynam. 6, 655 (1989).
R. Lavery and H. Sklenar: in Structure and Methods ,Vol. 2, DNA Protein Complexes and Proteins ,R. H. Sarma and M. H. Sarma (Eds.), Adenine Press, p. 215 (1990).
R. E. Dickerson, M. Bansal, C. R. Calladine, S. Diekmann, W. N. Hunter, O. Kennard, R. Lavery, H. C. M. Nelson, W. K. Olson, W. Saenger, Z. Shakked, H. Sklenar, D. M. Soumpasis, C.-S. Tung, E. von Kitzing, A. H.J. Wang and V. B. Zhurkin: J. Mol. Biol. 205, 787 (1989).
R. Lavery and B. Hartmann: Biophys. Chem. 50, 33 (1994).
A. Lipanov, M. L. Kopka, M. Kaczor-Grzeskowiak, J. Quintana and R. E. Dickerson: Biochemistry 32, 1373 (1993).
S. Arnott, R. Chandrasekaran, D. L. Birdsall, A. G. W. Leslie and R. L. Ratliff: Nature 283, 743 (1980) and coordinates communicated to our laboratory by S. Arnott.
R. Lavery: in Advances in Computational Biology ,Vol. 1, H. O. Villar (Ed.), JAI Press, Connecticut, p. 69 (1994).
M. R. Montminy, K. A. Sevarino, J. A. Wagner, G. Mandel and R. H. Goodman: Proc. Natl. Acad. Sci. USA ,83, 6682 (1988).
A. Bolshoy, P. McNamara, R. E. Harrington and E. N. Trifonov: Proc. Natl. Acad. Sci. USA 88, 2312 (1991).
S. Cacchione, P. De Santis, D. Foti, A. Palleschi and M. Savino: Biochemistry 28, 8076 (1989).
R. K.-Z. Tan and S. C. Harvey: J. Biomol. Struct. Dynam. 5, 497 (1987).
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1995 Springer Science+Business Media Dordrecht
About this paper
Cite this paper
Lavery, R. (1995). Twists and Turns in DNA: Predicting Base Sequence Effects on the Conformation of the Double Helix. In: Pullman, A., Jortner, J., Pullman, B. (eds) Modelling of Biomolecular Structures and Mechanisms. The Jerusalem Symposia on Quantum Chemistry and Biochemistry, vol 27. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-0497-5_18
Download citation
DOI: https://doi.org/10.1007/978-94-011-0497-5_18
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-010-4222-2
Online ISBN: 978-94-011-0497-5
eBook Packages: Springer Book Archive