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

Biophysical Journal

Volumn 83, Issue 5, 2002, Pages 2408-2418

  Scipioni, Anita ^a   Anselmi, Claudio ^a   Zuccheri, Giampaolo ^b   Samori, Bruno ^b   De Santis, Pasquale ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CURVED DNA; DINUCLEOTIDE; PALINDROMIC DNA; DNA;

ARTICLE; BASE PAIRING; DNA SEQUENCE; DNA STRUCTURE; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR MODEL; SCANNING FORCE MICROSCOPY; STATISTICAL ANALYSIS; VALIDATION PROCESS; YOUNG MODULUS; ATOMIC FORCE MICROSCOPY; BIOPHYSICS; CHEMISTRY; CONFORMATION; DIMERIZATION; METHODOLOGY; STATISTICAL MODEL; THERMODYNAMICS;

BIOPHYSICS; DIMERIZATION; DNA; MICROSCOPY, ATOMIC FORCE; MODELS, STATISTICAL; NUCLEIC ACID CONFORMATION; THERMODYNAMICS;

EID: 0036840332     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(02)75254-5     Document Type: Article

References (52)

1. Anselmi, C., G. Bocchinfuso, P. De Santis, M. Savino, and A. Scipioni. 1999. Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability, J. Mol. Biol. 286:1293-1301.
2. Anselmi, C., G. Bocchinfuso, P. De Santis, M. Savino, and A. Scipioni, 2000. A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability. Biophys. J. 79:601-613.
3. Anselmi, C., P. De Santis, R. Paparcone, M. Savino, and A. Scipioni. 2002. From the sequence to the superstructural properties of DNAs. Biophys. Chem. 95:23-47.
4. Bednar, J., P. Furrer, V. Katritch, A. Z. Stasiak, J. Dubochet, and A. Stasiak. 1995. 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. 254:579-594.
5. Bolshoy, A., P. McNamara, R. E. Harrington, and E. N. Trifonov. 1991. Curved DNA without A·A: Experimental estimation of all 16 DNA wedge angles. Proc. Natl. Acad. Sci. USA. 88:2312-2316.
6. Bustamante, C., J. Vesenka, C. L. Tang, W. Rees, M. Guthold, and R. Keller. 1992. Circular DNA molecules imaged in air by scanning force microscopy. Biochemistry. 31:22-26.
7. Cacchione, S., P. De Santis, A. Foti, A. Palleschi, and M. Savino. 1989. Periodical polydeoxynucleotides and DNA curvature. Biochemistry. 28:8706-8713.
8. Chastain II, P. D., E. E. Eichler, S. Kang, D. L. Nelson, S. D. Levene, and R. R. Sinden. 1995. Anomalous rapid electrophoretic mobility of DNA containing triplet repeats associated with human disease genes. Biochemistry. 34:16125-16131.
9. Chastain, P. D., and R. R. Sinden. 1998. CTG repeats associated with human genetic disease are inherently flexible. J. Mol. Biol. 275:405-411.
10. Cognet, J. A., C. Pakleza, D. Cherny, E. Delain, and E. L. Cam. 1999. DNA bending induced by the archaebacterial histone-like protein MC1. J. Mol. Biol. 285:997-1009.
11. Crothers, D. M. 1998. DNA curvature and deformation in protein-DNA complexes: A step in the right direction. Proc. Natl. Acad. Sci. USA. 95:15163-15165.
12. De Santis, P., M. Fuà, M. Savino, C. Anselmi, and G. Bocchinfuso. 1996. Sequence dependent circularization of DNAs: A physical model to predict the DNA sequence dependent propensity to circularization and its changes in the presence of protein-induced bending. J. Phys. Chem. 100:9968-9976.
13. De Santis, P., A. Palleschi, S. Morosetti, and M. Savino. 1986. Structure and superstructures in periodical polynucleotides. In Structures and Dynamics of Nucleic Acids, Proteins and Membranes. E. Clementi and S. Chin, editors. Plenum Press, New York. 31-49.
14. De Santis, P., A. Palleschi, M. Savino, and A. Scipioni. 1988. A theoretical model of DNA curvature, Biophys. Chem. 32:305-317.
15. De Santis, P., A. Palleschi, M. Savino, and A. Scipioni. 1990. Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature. Biochemistry. 29:9269-9273.
16. Diekmann, S. 1987. DNA methylation can enhance or induce DNA curvature. EMBO J. 6:4213-4217.
17. Flory, P. J., U. W. Suter, and M. Mutter. 1976. Macrocyclization equilibriums. 1. Theory. J. Am. Chem. Soc. 98:5733-5739.
18. Gotoh, O., and Y. Tagashira. 1981. Stabilities of nearest-neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles. Biopolymers. 20:1033-1042.
19. Hagerman, P. J. 1985. Sequence dependence of the curvature of DNA: A test of the phasing hypothesis. Biochemistry. 24:7033-7036.
20. Hagerman, P. J. 1986. Sequence-directed curvature of DNA. Nature. 321:449-450.
21. Hagerman, P. J. 1988. Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17:265-286.
22. Hansma, H. G., and D. E. Laney. 1996. DNA binding to mica correlates with cationic radius: Assay by atomic force microscopy. Biophys. J. 70:1933-1939.
23. Hockings, S. C., J. D. Kahn, and D. M. Crothers. 1998. Characterization of the ATF/CREB site and its complex with GCN4. Proc. Natl. Acad. Sci. USA. 95:1410-1415.
24. Jacobson, H., and W. H. Stockmayer. 1950. Intramolecular reaction in polycondensations, I. The theory of linear systems. J. Chem. Phys. 18:1600-1606.
25. Kahn, J. D., and D. M. Crothers. 1998. Measurement of the DNA bend angle induced by the catabolite activator protein using Monte Carlo simulation of cyclization kinetics. J. Mol. Biol. 276:287-309.
26. Koo, H. S., and D. M. Crothers. 1988. Calibration of DNA curvature and a unified description of sequence-directed bending. Proc. Natl. Acad. Sci. USA. 85:1763-1767.
27. Koo, H. S., H.-M. Wu, and D. M. Crothers. 1986. DNA bending at adenine-thymine tracts. Nature. 320:501-506.
28. Landau, L. D., and E. M. Lifshitz. 1970. Theory of Elasticity. Pergamon Press, Oxford, New York.
29. Lankas, F., J. Sponer, P. Hobza, and J. Langowski. 2000. Sequence-dependent elastic properties of DNA. J. Mol. Biol. 299:695-709.
30. Levene, S. D., and B. H. Zimm. 1989. Understanding the anomalous electrophoresis of bent DNA molecules: A reptation model. Science. 245:396-399.
31. Levene, S. D., and D. M. Crothers. 1986. Ring closure probabilities for DNA fragments by Monte Carlo simulation. J. Mol. Biol. 189:61-72.
32. Lumpkin, O. J., P. Dejardin, and B. H. Zimm. 1985. Theory of gel electrophoresis of DNA. Biopolymers. 24:1573-1593.
33. Marini, J. C., S. D. Levene, D. M. Crothers, and P. T. Englund. 1982. Bent helical structure in kinetoplast DNA. Proc. Natl. Acad. Sci. USA. 79:7664-7668.
34. Muzard, G., B. Theveny, and B. Revet. 1990. Electron microscopy mapping of pBR322 DNA curvature. Comparison with theoretical models. EMBO J. 9:1289-1298.
35. Olson, W. K., A. A. Gorin, X.-J. Lu, L. M. Hock, and V. B. Zhurkin. 1998. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl. Acad. Sci. USA. 95:11163-11168.
36. Olson, W. K., N. L. Marky, R. L. Jernigan, and V. B. Zhurkin. 1993. Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. J. Mol. Biol. 232:530-554.
37. Olson, W. K., and V. B. Zhurkin. 1996. Twenty years of DNA bending. In Biological Structure and Dynamics. Proceedings of the Ninth Conversation. R. H. Sarma and M. H. Sarma, editors. Adenine Press, New York. 341-370.
38. Ornstein, R. L., R. Rein, D. L. Breen, and R. D. Macelroy. 1978. An optimized potential function for the calculation of nucleic acid interaction energies. I. Base stacking. Biopolymers. 17:2341-2360.
39. Perico, A. 1989. Segmental relaxation in macromolecules. Acc. Chem. Res. 22:336-342.
40. Rivetti, C., M. Guthold, and C. Bustamante. 1996. Scanning force microscopy of DNA deposited onto mica: Equilibration versus kinetic trapping studied by statistical polymer chain analysis. J. Mol. Biol. 264:919-932.
41. Rivetti, C., C. Walker, and C. Bustamante. 1998. Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility. J. Mol. Biol. 280:41-59.
42. Roychoudhury, M., A. Sitlani, J. Lapham, and D. M. Crothers. 2000. Global structure and mechanical properties of a 10-bp nucleosome positioning motif. Proc. Natl. Acad. Sci. USA. 97:13608-13613.
43. Sambrook, J., T. Maniatis, and E. F. Fritsch. 1989. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
44. SantaLucia Jr., J. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA. 95:1460-1465.
45. Shimada, J., and H. Yamakawa. 1984. Ring closure probability for twisted wormlike chains. Application to DNA. Macromolecules. 17:689-698.
46. Sprous, D., R. K.-Z. Tan, and S. C. Harvey. 1996. Molecular modeling of closed circular DNA thermodynamic ensembles. Biopolymers. 39:243-258.
47. Sugimoto, N., S. Nakano, M. Yoneyama, and K. Honda. 1996. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acid. Res. 24:4501-4505.
48. Trifonov, E. N. 1980. Sequence-dependent deformational anisotropy of chromatin DNA. Nucleic Acids Res. 8:4041-4053.
49. Trifonov, E. N., R. K.-Z. Tan, and S. C. Harvey. 1987. DNA bending and curvature. In Structure and Expression, DNA Bending and Curvature, Vol. 3. W. K. Olson, M. H. Sarma, and M. Sundaralingam, editors. Adenine Press, New York. 243.
50. Wu, H.-M., and D. M. Crothers. 1984. The locus of sequence-directed and protein-induced DNA bending. Nature. 308:509-513.
51. Yamakawa, H., and W. H. Stockmayer. 1972. Statistical mechanics of wormlike chains. II. Excluded volume effects. J. Chem. Phys. 57:2843-2854.
52. Zuccheri, G., A. Scipioni, V. Cavaliere, G. Gargiulo, P. De Santis, and B. Samori. 2001. Mapping the intrinsic curvature and the flexibility along the DNA chain. Proc. Natl. Acad. Sci. USA. 98:3074-3079.