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. 2002 Nov;83(5):2408–2418. doi: 10.1016/S0006-3495(02)75254-5

Sequence-dependent DNA curvature and flexibility from scanning force microscopy images.

Anita Scipioni 1, Claudio Anselmi 1, Giampaolo Zuccheri 1, Bruno Samori 1, Pasquale De Santis 1
PMCID: PMC1302329  PMID: 12414677

Abstract

This paper reports a study of the sequence-dependent DNA curvature and flexibility based on scanning force microscopy (SFM) images. We used a palindromic dimer of a 1878-bp pBR322 fragment and collected a large pool of SFM images. The curvature of each imaged chain was measured in modulus and direction. It was found that the ensemble curvature modulus does not allow the separation of static and dynamic contributions to the curvature, whereas the curvature, when its direction in the two dimensions is taken into account, permits the direct separation of the intrinsic curvature contributions static and dynamic contributions. The palindromic symmetry also acted as an internal gauge of the validity of the SFM images statistical analysis. DNA static curvature resulted in good agreement with the predicted sequence-dependent intrinsic curvature. Furthermore, DNA sequence-dependent flexibility was found to correlate with the occurrence of A.T-rich dinucleotide steps along the chain and, in general, with the normalized basepair stacking energy distribution.

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Selected References

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  1. Anselmi C., Bocchinfuso G., De Santis P., Savino M., Scipioni A. A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability. Biophys J. 2000 Aug;79(2):601–613. doi: 10.1016/S0006-3495(00)76319-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Anselmi C., Bocchinfuso G., De Santis P., Savino M., Scipioni A. Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability. J Mol Biol. 1999 Mar 12;286(5):1293–1301. doi: 10.1006/jmbi.1998.2575. [DOI] [PubMed] [Google Scholar]
  3. Anselmi C., De Santis P., Paparcone R., Savino M., Scipioni A. From the sequence to the superstructural properties of DNAs. Biophys Chem. 2002 Jan 23;95(1):23–47. doi: 10.1016/s0301-4622(01)00246-0. [DOI] [PubMed] [Google Scholar]
  4. Bednar J., Furrer P., Katritch V., Stasiak A. Z., Dubochet J., Stasiak A. Determination of DNA persistence length by cryo-electron microscopy. Separation of the static and dynamic contributions to the apparent persistence length of DNA. J Mol Biol. 1995 Dec 8;254(4):579–594. doi: 10.1006/jmbi.1995.0640. [DOI] [PubMed] [Google Scholar]
  5. Bolshoy A., McNamara P., Harrington R. E., Trifonov E. N. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2312–2316. doi: 10.1073/pnas.88.6.2312. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bustamante C., Vesenka J., Tang C. L., Rees W., Guthold M., Keller R. Circular DNA molecules imaged in air by scanning force microscopy. Biochemistry. 1992 Jan 14;31(1):22–26. doi: 10.1021/bi00116a005. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Chastain P. D., 2nd, Eichler E. E., Kang S., Nelson D. L., Levene S. D., Sinden R. R. Anomalous rapid electrophoretic mobility of DNA containing triplet repeats associated with human disease genes. Biochemistry. 1995 Dec 12;34(49):16125–16131. doi: 10.1021/bi00049a027. [DOI] [PubMed] [Google Scholar]
  9. Chastain P. D., Sinden R. R. CTG repeats associated with human genetic disease are inherently flexible. J Mol Biol. 1998 Jan 23;275(3):405–411. doi: 10.1006/jmbi.1997.1502. [DOI] [PubMed] [Google Scholar]
  10. Cognet J. A., Pakleza C., Cherny D., Delain E., Cam E. L. Static curvature and flexibility measurements of DNA with microscopy. A simple renormalization method, its assessment by experiment and simulation. J Mol Biol. 1999 Jan 22;285(3):997–1009. doi: 10.1006/jmbi.1998.2322. [DOI] [PubMed] [Google Scholar]
  11. Crothers D. M. DNA curvature and deformation in protein-DNA complexes: a step in the right direction. Proc Natl Acad Sci U S A. 1998 Dec 22;95(26):15163–15165. doi: 10.1073/pnas.95.26.15163. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. 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]
  13. De Santis P., Palleschi A., Savino M., Scipioni A. Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature. Biochemistry. 1990 Oct 2;29(39):9269–9273. doi: 10.1021/bi00491a023. [DOI] [PubMed] [Google Scholar]
  14. Diekmann S. DNA methylation can enhance or induce DNA curvature. EMBO J. 1987 Dec 20;6(13):4213–4217. doi: 10.1002/j.1460-2075.1987.tb02769.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hagerman P. J. Flexibility of DNA. Annu Rev Biophys Biophys Chem. 1988;17:265–286. doi: 10.1146/annurev.bb.17.060188.001405. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. Hagerman P. J. Sequence-directed curvature of DNA. Nature. 1986 May 22;321(6068):449–450. doi: 10.1038/321449a0. [DOI] [PubMed] [Google Scholar]
  18. Hansma H. G., Laney D. E. DNA binding to mica correlates with cationic radius: assay by atomic force microscopy. Biophys J. 1996 Apr;70(4):1933–1939. doi: 10.1016/S0006-3495(96)79757-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Hockings S. C., Kahn J. D., Crothers D. M. Characterization of the ATF/CREB site and its complex with GCN4. Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1410–1415. doi: 10.1073/pnas.95.4.1410. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kahn J. D., Crothers D. M. Measurement of the DNA bend angle induced by the catabolite activator protein using Monte Carlo simulation of cyclization kinetics. J Mol Biol. 1998 Feb 13;276(1):287–309. doi: 10.1006/jmbi.1997.1515. [DOI] [PubMed] [Google Scholar]
  21. 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]
  22. 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]
  23. Lankas F., Sponer J., Hobza P., Langowski J. Sequence-dependent elastic properties of DNA. J Mol Biol. 2000 Jun 9;299(3):695–709. doi: 10.1006/jmbi.2000.3781. [DOI] [PubMed] [Google Scholar]
  24. Levene S. D., Crothers D. M. Ring closure probabilities for DNA fragments by Monte Carlo simulation. J Mol Biol. 1986 May 5;189(1):61–72. doi: 10.1016/0022-2836(86)90381-5. [DOI] [PubMed] [Google Scholar]
  25. Levene S. D., Zimm B. H. Understanding the anomalous electrophoresis of bent DNA molecules: a reptation model. Science. 1989 Jul 28;245(4916):396–399. doi: 10.1126/science.2756426. [DOI] [PubMed] [Google Scholar]
  26. Lumpkin O. J., Déjardin P., Zimm B. H. Theory of gel electrophoresis of DNA. Biopolymers. 1985 Aug;24(8):1573–1593. doi: 10.1002/bip.360240812. [DOI] [PubMed] [Google Scholar]
  27. 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]
  28. Muzard G., Théveny B., Révet B. Electron microscopy mapping of pBR322 DNA curvature. Comparison with theoretical models. EMBO J. 1990 Apr;9(4):1289–1298. doi: 10.1002/j.1460-2075.1990.tb08238.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Olson W. K., Gorin A. A., Lu X. J., Hock L. M., Zhurkin V. B. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci U S A. 1998 Sep 15;95(19):11163–11168. doi: 10.1073/pnas.95.19.11163. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Olson W. K., Marky N. L., Jernigan R. L., Zhurkin V. B. Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. J Mol Biol. 1993 Jul 20;232(2):530–554. doi: 10.1006/jmbi.1993.1409. [DOI] [PubMed] [Google Scholar]
  31. Rivetti C., Guthold M., Bustamante C. Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis. J Mol Biol. 1996 Dec 20;264(5):919–932. doi: 10.1006/jmbi.1996.0687. [DOI] [PubMed] [Google Scholar]
  32. Rivetti C., Walker C., Bustamante C. Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility. J Mol Biol. 1998 Jul 3;280(1):41–59. doi: 10.1006/jmbi.1998.1830. [DOI] [PubMed] [Google Scholar]
  33. Roychoudhury M., Sitlani A., Lapham J., Crothers D. M. Global structure and mechanical properties of a 10-bp nucleosome positioning motif. Proc Natl Acad Sci U S A. 2000 Dec 5;97(25):13608–13613. doi: 10.1073/pnas.250476297. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. SantaLucia J., Jr A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1460–1465. doi: 10.1073/pnas.95.4.1460. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sprous D., Tan R. K., Harvey S. C. Molecular modeling of closed circular DNA thermodynamic ensembles. Biopolymers. 1996 Aug;39(2):243–258. doi: 10.1002/(SICI)1097-0282(199608)39:2%3C243::AID-BIP11%3E3.0.CO;2-F. [DOI] [PubMed] [Google Scholar]
  36. Sugimoto N., Nakano S., Yoneyama M., Honda K. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res. 1996 Nov 15;24(22):4501–4505. doi: 10.1093/nar/24.22.4501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. 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]
  38. Wu H. M., Crothers D. M. The locus of sequence-directed and protein-induced DNA bending. Nature. 1984 Apr 5;308(5959):509–513. doi: 10.1038/308509a0. [DOI] [PubMed] [Google Scholar]
  39. Zuccheri G., Scipioni A., Cavaliere V., Gargiulo G., De Santis P., Samorì B. Mapping the intrinsic curvature and flexibility along the DNA chain. Proc Natl Acad Sci U S A. 2001 Feb 27;98(6):3074–3079. doi: 10.1073/pnas.051631198. [DOI] [PMC free article] [PubMed] [Google Scholar]

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