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. 1990 Apr;9(4):1289–1298. doi: 10.1002/j.1460-2075.1990.tb08238.x

Electron microscopy mapping of pBR322 DNA curvature. Comparison with theoretical models.

G Muzard 1, B Théveny 1, B Révet 1
PMCID: PMC551807  PMID: 2323339

Abstract

A map of local curvature of the pBR322 DNA has been established by electron microscopy analysis of linearized plasmid molecules. To determine their polarity these molecules are one end labelled with an avidin-ferritin-biotin complex and the images are digitized. Local curvature is calculated from two mathematical treatments of the DNA trajectory and expressed in term of a mean dinucleotide wedge angle. Eight regions of curvature are distinguished. The four main regions of curvature have a high content of phased AA runs. The experimental curvature map is compared to theoretical maps of curvature obtained from four available models for DNA curvature.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Burkhoff A. M., Tullius T. D. The unusual conformation adopted by the adenine tracts in kinetoplast DNA. Cell. 1987 Mar 27;48(6):935–943. doi: 10.1016/0092-8674(87)90702-1. [DOI] [PubMed] [Google Scholar]
  2. Cacchione S., De Santis P., Foti D., Palleschi A., Savino M. Periodical polydeoxynucleotides and DNA curvature. Biochemistry. 1989 Oct 31;28(22):8706–8713. doi: 10.1021/bi00448a006. [DOI] [PubMed] [Google Scholar]
  3. Calladine C. R., Drew H. R., McCall M. J. The intrinsic curvature of DNA in solution. J Mol Biol. 1988 May 5;201(1):127–137. doi: 10.1016/0022-2836(88)90444-5. [DOI] [PubMed] [Google Scholar]
  4. Coll M., Frederick C. A., Wang A. H., Rich A. A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. Proc Natl Acad Sci U S A. 1987 Dec;84(23):8385–8389. doi: 10.1073/pnas.84.23.8385. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. De Santis P., Palleschi A., Savino M., Scipioni A. A theoretical model of DNA curvature. Biophys Chem. 1988 Dec;32(2-3):305–317. doi: 10.1016/0301-4622(88)87016-9. [DOI] [PubMed] [Google Scholar]
  6. Definitions and nomenclature of nucleic acid structure parameters. J Mol Biol. 1989 Feb 20;205(4):787–791. doi: 10.1016/0022-2836(89)90324-0. [DOI] [PubMed] [Google Scholar]
  7. Di Capua E., Stasiak A., Koller T., Brahms S., Thomae R., Pohl F. M. Torsional stress induces left-handed helical stretches in DNA of natural base sequence: circular dichroism and antibody binding. EMBO J. 1983;2(9):1531–1535. doi: 10.1002/j.1460-2075.1983.tb01619.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. DiGabriele A. D., Sanderson M. R., Steitz T. A. Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. Proc Natl Acad Sci U S A. 1989 Mar;86(6):1816–1820. doi: 10.1073/pnas.86.6.1816. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Diekmann S., McLaughlin L. W. DNA curvature in native and modified EcoRI recognition sites and possible influence upon the endonuclease cleavage reaction. J Mol Biol. 1988 Aug 20;202(4):823–834. doi: 10.1016/0022-2836(88)90561-x. [DOI] [PubMed] [Google Scholar]
  10. Diekmann S. Sequence specificity of curved DNA. FEBS Lett. 1986 Jan 20;195(1-2):53–56. doi: 10.1016/0014-5793(86)80128-4. [DOI] [PubMed] [Google Scholar]
  11. Diekmann S. Temperature and salt dependence of the gel migration anomaly of curved DNA fragments. Nucleic Acids Res. 1987 Jan 12;15(1):247–265. doi: 10.1093/nar/15.1.247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Dubochet J., Ducommun M., Zollinger M., Kellenberger E. A new preparation method for dark-field electron microscopy of biomacromolecules. J Ultrastruct Res. 1971 Apr;35(1):147–167. doi: 10.1016/s0022-5320(71)80148-x. [DOI] [PubMed] [Google Scholar]
  13. Eckdahl T. T., Anderson J. N. Computer modelling of DNA structures involved in chromosome maintenance. Nucleic Acids Res. 1987 Oct 26;15(20):8531–8545. doi: 10.1093/nar/15.20.8531. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Fratini A. V., Kopka M. L., Drew H. R., Dickerson R. E. Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. J Biol Chem. 1982 Dec 25;257(24):14686–14707. [PubMed] [Google Scholar]
  15. Goulet I., Zivanovic Y., Prunell A., Revet B. Chromatin reconstitution on small DNA rings. I. J Mol Biol. 1988 Mar 20;200(2):253–266. doi: 10.1016/0022-2836(88)90238-0. [DOI] [PubMed] [Google Scholar]
  16. Griffith J., Bleyman M., Rauch C. A., Kitchin P. A., Englund P. T. Visualization of the bent helix in kinetoplast DNA by electron microscopy. Cell. 1986 Aug 29;46(5):717–724. doi: 10.1016/0092-8674(86)90347-8. [DOI] [PubMed] [Google Scholar]
  17. Hagerman P. J. Evidence for the existence of stable curvature of DNA in solution. Proc Natl Acad Sci U S A. 1984 Aug;81(15):4632–4636. doi: 10.1073/pnas.81.15.4632. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hagerman P. J. Investigation of the flexibility of DNA using transient electric birefringence. Biopolymers. 1981 Jul;20(7):1503–1535. doi: 10.1002/bip.1981.360200710. [DOI] [PubMed] [Google Scholar]
  19. Hagerman P. J. Sequence dependence of the curvature of DNA: a test of the phasing hypothesis. Biochemistry. 1985 Dec 3;24(25):7033–7037. doi: 10.1021/bi00346a001. [DOI] [PubMed] [Google Scholar]
  20. Hagerman P. J. Sequence-directed curvature of DNA. Nature. 1986 May 22;321(6068):449–450. doi: 10.1038/321449a0. [DOI] [PubMed] [Google Scholar]
  21. Haran T. E., Crothers D. M. Cooperativity in A-tract structure and bending properties of composite TnAn blocks. Biochemistry. 1989 Apr 4;28(7):2763–2767. doi: 10.1021/bi00433a003. [DOI] [PubMed] [Google Scholar]
  22. Hofmann H., Voss T., Kühn K., Engel J. Localization of flexible sites in thread-like molecules from electron micrographs. Comparison of interstitial, basement membrane and intima collagens. J Mol Biol. 1984 Jan 25;172(3):325–343. doi: 10.1016/s0022-2836(84)80029-7. [DOI] [PubMed] [Google Scholar]
  23. Hsieh C. H., Griffith J. D. The terminus of SV40 DNA replication and transcription contains a sharp sequence-directed curve. Cell. 1988 Feb 26;52(4):535–544. doi: 10.1016/0092-8674(88)90466-7. [DOI] [PubMed] [Google Scholar]
  24. Joanicot M., Revet B. DNA conformational studies from electron microscopy. I. Excluded volume effect and structure dimensionality. Biopolymers. 1987 Feb;26(2):315–326. doi: 10.1002/bip.360260211. [DOI] [PubMed] [Google Scholar]
  25. Kabsch W., Sander C., Trifonov E. N. The ten helical twist angles of B-DNA. Nucleic Acids Res. 1982 Feb 11;10(3):1097–1104. doi: 10.1093/nar/10.3.1097. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Kitchin P. A., Klein V. A., Ryan K. A., Gann K. L., Rauch C. A., Kang D. S., Wells R. D., Englund P. T. A highly bent fragment of Crithidia fasciculata kinetoplast DNA. J Biol Chem. 1986 Aug 25;261(24):11302–11309. [PubMed] [Google Scholar]
  27. Koo H. S., Crothers D. M. Calibration of DNA curvature and a unified description of sequence-directed bending. Proc Natl Acad Sci U S A. 1988 Mar;85(6):1763–1767. doi: 10.1073/pnas.85.6.1763. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Koo H. S., Crothers D. M. Chemical determinants of DNA bending at adenine-thymine tracts. Biochemistry. 1987 Jun 16;26(12):3745–3748. doi: 10.1021/bi00386a070. [DOI] [PubMed] [Google Scholar]
  29. Koo H. S., Wu H. M., Crothers D. M. DNA bending at adenine . thymine tracts. Nature. 1986 Apr 10;320(6062):501–506. doi: 10.1038/320501a0. [DOI] [PubMed] [Google Scholar]
  30. Levene S. D., Crothers D. M. A computer graphics study of sequence-directed bending in DNA. J Biomol Struct Dyn. 1983 Oct;1(2):429–435. doi: 10.1080/07391102.1983.10507452. [DOI] [PubMed] [Google Scholar]
  31. Levene S. D., Wu H. M., Crothers D. M. Bending and flexibility of kinetoplast DNA. Biochemistry. 1986 Jul 15;25(14):3988–3995. doi: 10.1021/bi00362a003. [DOI] [PubMed] [Google Scholar]
  32. Lilley D. DNA structure. Bent molecules--how and why? Nature. 1986 Apr 10;320(6062):487–488. doi: 10.1038/320487a0. [DOI] [PubMed] [Google Scholar]
  33. Marini J. C., Levene S. D., Crothers D. M., Englund P. T. Bent helical structure in kinetoplast DNA. Proc Natl Acad Sci U S A. 1982 Dec;79(24):7664–7668. doi: 10.1073/pnas.79.24.7664. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Nelson H. C., Finch J. T., Luisi B. F., Klug A. The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nature. 1987 Nov 19;330(6145):221–226. doi: 10.1038/330221a0. [DOI] [PubMed] [Google Scholar]
  35. Revet B., Malinge J. M., Delain E., Le Bret M., Leng M. Electron microscopic measurement of chain flexibility of poly(dG-dC).poly(dG-dC) modified by cis-diamminedichloroplatinum(II). Nucleic Acids Res. 1984 Nov 26;12(22):8349–8362. doi: 10.1093/nar/12.22.8349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Selsing E., Wells R. D., Alden C. J., Arnott S. Bent DNA: visualization of a base-paired and stacked A-B conformational junction. J Biol Chem. 1979 Jun 25;254(12):5417–5422. [PubMed] [Google Scholar]
  37. Srinivasan A. R., Torres R., Clark W., Olson W. K. Base sequence effects in double helical DNA. I. Potential energy estimates of local base morphology. J Biomol Struct Dyn. 1987 Dec;5(3):459–496. doi: 10.1080/07391102.1987.10506409. [DOI] [PubMed] [Google Scholar]
  38. Stellwagen N. C. Anomalous electrophoresis of deoxyribonucleic acid restriction fragments on polyacrylamide gels. Biochemistry. 1983 Dec 20;22(26):6186–6193. doi: 10.1021/bi00295a023. [DOI] [PubMed] [Google Scholar]
  39. Tan R. K., Harvey S. C. A comparison of six DNA bending models. J Biomol Struct Dyn. 1987 Dec;5(3):497–512. doi: 10.1080/07391102.1987.10506410. [DOI] [PubMed] [Google Scholar]
  40. Theveny B., Revet B. DNA orientation using specific avidin-ferritin biotin end labelling. Nucleic Acids Res. 1987 Feb 11;15(3):947–958. doi: 10.1093/nar/15.3.947. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Trifonov E. N. Curved DNA. CRC Crit Rev Biochem. 1985;19(2):89–106. doi: 10.3109/10409238509082540. [DOI] [PubMed] [Google Scholar]
  42. Trifonov E. N. Sequence-dependent deformational anisotropy of chromatin DNA. Nucleic Acids Res. 1980 Sep 11;8(17):4041–4053. doi: 10.1093/nar/8.17.4041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Trifonov E. N., Sussman J. L. The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc Natl Acad Sci U S A. 1980 Jul;77(7):3816–3820. doi: 10.1073/pnas.77.7.3816. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Tung C. S., Harvey S. C. Computer graphics program to reveal the dependence of the gross three-dimensional structure of the B-DNA double helix on primary structure. Nucleic Acids Res. 1986 Jan 10;14(1):381–387. doi: 10.1093/nar/14.1.381. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Ulanovsky L. E., Trifonov E. N. Estimation of wedge components in curved DNA. Nature. 1987 Apr 16;326(6114):720–722. doi: 10.1038/326720a0. [DOI] [PubMed] [Google Scholar]
  46. Ulanovsky L., Bodner M., Trifonov E. N., Choder M. Curved DNA: design, synthesis, and circularization. Proc Natl Acad Sci U S A. 1986 Feb;83(4):862–866. doi: 10.1073/pnas.83.4.862. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Zhurkin V. B. Sequence-dependent bending of DNA and phasing of nucleosomes. J Biomol Struct Dyn. 1985 Feb;2(4):785–804. doi: 10.1080/07391102.1985.10506324. [DOI] [PubMed] [Google Scholar]

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