A useful role for "static" models in elucidating the behaviour of DNA in solution

Journal of Molecular Biology

Volumn 257, Issue 3, 1996, Pages 479-485

  Calladine, C R ^a   Drew, H R ^b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b CSIRO   (Australia)

Author keywords

Curvature; DNA; Gel electrophoresis; Persistence length; Static models

Indexed keywords

DNA;

ARTICLE; DNA CONFORMATION; DNA DETERMINATION; DNA HELIX; DNA SEQUENCE; DNA STRUCTURE; DNA SUPERCOILING; ELECTRON MICROSCOPY; GEL ELECTROPHORESIS; KINETICS; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; X RAY CRYSTALLOGRAPHY;

EID: 0029872258     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0177     Document Type: Editorial

References (36)

1. Azizov, M., Ul'yanov, A., Kuprash, D., Shakov, A., Gavin, I. & Nedospasov, S. (1992). Production and characterization of a library of mononucleosomal DNA from the chromatin of human cells, and its use to study the affinity of nucleosomal DNA for histones. Doklady Biochemistry (Russia), 322, 415-420.
2. Benfante, R., Landsberger, N., Tubiello, G. & Badaracco, G. (1989). Sequence-directed curvature of repetitive AluI DNA in constitutive heterochromatin of Artemia franciscana. Nucl. Acids Res. 17, 8273-8282.
3. Biburger, M., Niederweis, M. & Hillen, W. (1994). Oligo[d(C)·(G)] runs exhibit a helical repeat of 11.1 bp in solution and cause slight DNA curvature when properly phased. Nucl. Acids Res. 22, 1562-1566.
4. Brukner, I, Dlakic, M., Savic, A., Susic, S., Pongor, S. & Suck, D. (1993). Evidence for opposite groove-directed curvature of GGGCCC and AAAAA sequence elements. Nucl. Acids Res. 21, 1025-1029.
5. Brukner, I., Susic, S., Dlakic, M., Savic, A. & Pongor, S. (1994). Physiological concentration of magnesum ions induces a strong macroscopic curvature in GGGCCC-containing DNA. J. Mol. Biol. 236, 26-32.
6. Burlatsky, S. & Deutsch, J. (1993). Influence of solid friction on polymer motion in gel electrophoresis. Science, 260, 1782-1784.
7. Calladine, C. R. & Drew, H. R. (1992). Understanding DNA: The Molecule and How It Works. Academic Press, London.
8. Calladine, C. R., Drew, H. R. & McCall, M. J. (1988). The intrinsic curvature of DNA in solution. J. Mol. Biol. 201, 127-137.
9. Calladine, C. R., Collis, C. M., Drew, H. R. & Mott, M. R. (1991). A study of electrophoretic mobility of DNA in agarose and polyacrylamide gels. J. Mol. Biol. 221, 981-1005.
10. +3: probes of propeller twisting in solution. Biochemistry, 33, 4130-4139.
11. De Santis, P., Palleschi, A. & Savino, M. (1993). A simple theoretical model for predicting the sequence dependent gel electrophoretic manifestations of DNAs. Electrophoresis, 14, 699-703.
12. Dickerson, R. E., Goodsell, D. & Neidle, S. (1994). "...the tyranny of the lattice..." Proc. Natl Acad. Sci. USA, 91, 3579-3583.
13. Goodsell, D. S., Kaczor-Grzeskowiak, M. & Dickerson, R. E. (1994). The crystal structure of C-C-A-T-T-A-A-T-G-G: implications for bending of B-DNA at T-A steps. J. Mol. Biol. 239, 79-96.
14. Hagerman, P. J. (1985). Sequence-dependence of the curvature of DNA: a test of the phasing hypothesis. Biochemistry, 24, 7033-7036.
15. Hagerman, P. J. & Ramadevi, V. A. (1990). Application of the method of phage T4 DNA legase-catalyzed ring-closure to the study of DNA structure. J. Mol. Biol. 212, 351-362.
16. Harrington, R. E. & Winicon, I. (1994). New concepts in protein-DNA recognition: sequence-directed DNA bending and flexibility. Prog. Nucl Acids Res. 47, 195-270.
17. Holliday R. (1990). The history of the DNA heteroduplex. BioEssays, 12, 133-142.
18. Hunter, C. A. (1993). Sequence-dependent DNA structure: the role of base stacking interactions. J. Mol. Biol. 230, 1025-1054.
19. Koo, H.-S., Wu, H.-W. & Crothers, D. M. (1986). DNA bending at adenine-thymine tracts. Nature, 320, 501-506.
20. Koudelka, G. B., Harrison, S. C. & Ptashne, M. (1987). Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro. Nature, 326, 886-888.
21. McCall, M. J., Brown, T. & Kennard, O. (1985). The crystal structure of d(GGGGCCCC): a model for poly[(dG).(dC)]. J. Mol. Biol. 183, 385-396.
22. McClellan, J. A. & Lilley D. M. J. (1991). Structural alternation in alternating adenine-thymine sequences in positively-supercoiled DNA. J. Mol. Biol. 219, 145-149.
23. Millar, D. P., Robbins, R. J. & Zewail, A. H. (1982). Torsion and bending of nucleic acids studied by subnanosecond time-resolved fluorescence depolarization of intercalated dyes. J. Chem. Phys. 76, 2080-2094.
24. Mott, M. R., Cox, D., Drew, H. R., Collis, C. M. & Calladine, C. R. (1993). Review on visualization by electron microscopy of double stranded curved DNA in relation to migration through electrophoretic gels. J. Comp. Assist. Microsc. 5, 131-134.
25. Nelson, H. C. M., Finch, J. T., Luisi, B. F. & Klug, A. (1987). The structure of an oligo(dA)-oligo(dT) tract and its biological implications. Nature, 330, 221-226.
26. Niederweis, M., Lederer, T. & Hillen, W. (1994). Matrix effects suggest an important influence of DNA polyacrylamide interactions on the electrophorectic mobility of DNA. J. Biol. Chem. 269, 10156-10162.
27. Olson, W. K., Marky, N. L., Jernigan, R. L. & Zhurkin, V. B. (1993). Influence of fluctuations on DNA curvature: a comprison of flexible and static wedge models of intrinsically bent DNA. J. Mol. Biol. 232, 530-554.
28. Pavletich, N. P. & Pabo, C. O. (1993). Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers. Science, 261, 1701-1707.
29. Satchwell, S. C., Drew, H. R. & Travers, A. A. (1986). Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191, 659-675.
30. Steitz, T. (1990). Structural studies of protein-nucleic interaction: sources of sequence-specific binding. Quart. Rev. Biophys. 23, 205-280.
31. Travers, A. A. (1989). DNA conformation and protein binding. Annu. Rev. Biochem. 58, 427-452.
32. Travers, A. A. & Klug, A. (1987). The bending of DNA in nucleosomes and its wider implications. Phil. Trans. Roy. Soc. ser. B, 317, 537-561.
33. Weston, S. A., Lahm, A. & Suck, D. (1992). X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 Å resolution. J. Mol. Biol. 226, 1237-1256.
34. Yanagida, M., Hiraoka, Y. & Katoura, I. (1982). Dynamic behaviour of DNA molecules in solution studied by fluorescence spectroscopy. Cold Spring Harbor Symp. Quant. Biology, 47, 177-187.
35. Zimm, B. H. (1993). Mechanisms of gel electrophoresis of DNA: unexpected findings. Curr. Opin. Struct. Biol. 3, 373-376.
36. Zimm, B. H. & Lumpkin, O. (1993). Reptation of a polymer chain in an irregular matrix: diffusion and electrophoresis. Macromolecules, 26, 226-234.