Uranyl photoprobing of nonbent A/T- And bent A-Tracts. A difference of flexibility?

Biochemistry

Volumn 44, Issue 21, 2005, Pages 7855-7863

  Møllegaard, Niels Erik ^a   Lindemose, Søren ^a   Nielsen, Peter E ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

BENDING (DEFORMATION); CONFORMATIONS; DNA; PHOTOCHEMICAL REACTIONS;

DNA HELIX; MACROSCOPIC BENDING; PHOTOCLEAVAGE; PHOTOPROBING;

BIOLOGICAL ORGANS;

CURVED DNA; DNA FRAGMENT; UNCLASSIFIED DRUG; URANIUM DERIVATIVE; URANYL DERIVATIVE;

ARTICLE; BASE PAIRING; DNA CONFORMATION; DNA PROBE; MATHEMATICAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; ADENINE; BASE PAIRING; DNA; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; PHOTOAFFINITY LABELS; SUGAR PHOSPHATES; THYMINE; URANYL NITRATE;

EID: 19644392719     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0502083     Document Type: Article

References (47)

1. Hagerman, P. J. (1990) Sequence-directed curvature of DNA, Annu. Rev. Biochem. 59, 755-781.
2. Ulanovsky, L. E., and Trifonov, E. N. (1987) Estimation of wedge components in curved DNA, Nature 326, 720-722.
3. Trifonov, E. N., and Sussman, J. L. (1980) The pitch of chromatin DNA is reflected in its nucleotide sequence, Proc. Natl. Acad. Sci. U.S.A. 77, 3816-3820.
4. Goodsell, D. S., Kaczor-Grzeskowiak, M., and 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.
5. Grzeskowiak, K., Goodsell, D. S., Kaczor-Grzeskowiak, M., Cascio, D., and Dickerson, R. E. (1993) Crystallographic analysis of C-C-A-A-G-C-T-T-G-G and its implications for bending in B-DNA, Biochemistry 32, 8923-8931.
6. Wu, H. M., and Crothers, D. M. (1984) The locus of sequence-directed and protein-induced DNA bending, Nature 308, 509-513.
7. Koo, H.-S., Wu, H.-M., and Crothers, D. M. (1986) DNA bending at adenine.thymine tracts, Nature 320, 501-506.
8. Koo, H.-S., Wu, H.-M., and Crothers, D. M. (1988) Calibration of DNA curvature and a unified description of sequence-directed bending, Proc. Natl. Acad. Sci. U.S.A. 85, 1763-1767.
9. Burkhoff, A. M., and Tullius, T. D. (1987) The unusual conformation adopted by the adenine tracts in kinetoplast DNA, Cell 48, 935-943.
10. MacDonald, D., Herbert, K., Zhang, X., Pologruto, T., Lu, P., and Polgruto, T. (2001) Solution structure of an A-tract DNA bend, J. Mol. Biol. 306, 1081-1098.
11. Katahira, M., Sugeta, H., and Kyogoku, Y. (1990) A new model for the bending of DNAs containing the oligo(dA) tracts based on NMR observations, Nucleic Acids Res. 18, 613-618.
12. Leroy, J. L., Charretier, E., Kochoyan, M., and Gueron, M. (1988) Evidence from base-pair kinetics for two types of adenine tract structures in solution: Their relation to DNA curvature, Biochemistry 27, 8894-8898.
13. Nadeau, J. G., and Crothers, D. M. (1989) Structural basis for DNA bending, Proc. Natl. Acad. Sci. U.S.A. 86, 2622-2626.
14. Nelson, H. C., Finch, J. T., Luisi, B. F., and Klug, A. (1987) The structure of an oligo(dA).oligo(dT) tract and its biological implications, Nature 330, 221-216.
15. Digabrielle, A. D., Sanderson, M. R., and Steitz, T. A. (1993) A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend, J. Mol. Biol. 231, 1024-1039.
16. Chuprina, V. P. (1987) Anomalous structure and properties of poly(dA).poly(dT), Computer simulation of the polynucleotide structure with the spine of hydration in the minor groove, Nucleic Acids Res. 12, 293-311.
17. Kopka, M. L., Fratini, A. V., Drew, H. R., and Dickerson, R. E. (1983) Ordered water structure around a B-DNA dodecamer. A quantitative study, J. Mol. Biol. 163, 129-146.
18. Coll, M., Frederick, C. A., Wang, A. H., and Rich, A. (1987) 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. 84, 8385-8389.
19. Dickerson, R. E., and Drew, H. R. (1981) Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure, J. Mol. Biol. 149, 761-786.
20. Edwards, K. J., Brown, D. G., Spink, N., Skelly, J. V., and Neidle, S. (1993) Molecular structure of the B-DNA dodecamer d(CGCAAATTTGCG)2. An examination of propeller twist and minor-groove water structure at 2.2 Å resolution, J. Mol. Biol. 20, 1161-1173.
21. Møllegaard, N. E., Bailly, C., Waring, M. J., and Nielsen, P. E. (1997) Effects of diaminopurine and inosine substitutions on A-tract induced DNA curvature. Importance of the 3′-A-tract junction, Nucleic Acids Res. 25, 3497-3502.
22. Yoon, C., Prive, G. G., Goodsell, D. S., and Dickerson, R. E. (1988) Structure of an alternating-B DNA helix and its relationship to A-tract DNA, Proc. Natl. Acad. Sci. U.S.A. 85, 6332-6336.
23. Johannesson, H., and Halle, B. (1998) Minor groove hydration of DNA in solution: Dependence on base composition and sequence, J. Am. Chem. Soc. 120, 6859-6870.
24. Sonnichsen, S. H., and Nielsen, P. E. (1996) Enhanced uranyl photocleavage across the minor groove of all (A/T)4 sequences indicates a similar narrow minor groove conformation, J. Mol. Recognit. 9, 219-227.
25. Jeppesen, C., and Nielsen, P. E. (1989) Uranyl mediated photofootprinting reveals strong E. coli RNA polymerase - DNA backbone contacts in the +10 region of the DeoP1 promoter open complex, Nucleic Acids Res. 17, 4947-4956.
26. Møllegaard, N. E., Rasmussen, P. B., Valentin-Hansen, P., and Nielsen, P. E. (1993) Characterization of promoter recognition complexes formed by CRP and CytR for repression and by CRP and RNA polymerase for activation of transcription on the Escherichia coli deoP2 promoter, J. Biol. Chem. 268, 17471-17477.
27. Møllegaard, N. E., Murchie, A. I., Lilley, D. M., and Nielsen, P. E. (1994) Uranyl photoprobing of a four-way DNA junction: Evidence for specific metal ion binding, EMBO J. 13, 1508-13.28.
28. Møllegaard, N. E., and Nielsen, P. E. (1997) Uranyl photoprobing of DNA structures and drug-DNA complexes, Methods Mol. Biol. 90, 43-49.
29. Bassi, G. S., Møllegaard, N. E., Murchie, A. I., von Kitzing, E., and Lilley, D. M. (1995) Ionic interactions and the global conformations of the hammerhead ribozyme, Nat. Struct. Biol. 2, 45-55.
30. Nielsen, P. E., Mollegaard, N. E., and Jeppesen, C. (1990) DNA conformational analysis in solution by uranyl mediated photocleavage, Nucleic Acids Res. 1990 Jul 11;18(13):3847-3851.
31. 2+) salts, J. Am. Chem. Soc. 114, 4967-4975.
32. Møllegaard, N. E., and Nielsen, P. E. (2003) Increased temperature and 2-methyl-2,4-pentanediol change the DNA structure of both curved and uncurved adenine/thymine-rich sequences, Biochemistry 42, 8587-8593.
33. Chuprina, V. P., Fedoroff, O. Y., and Reid, B. R. (1991) New insights into the structure of An tracts and B′-B′ bends in DNA, Biochemistry 30, 561-568.
34. 1H NMR and restrained molecular dynamics, Biochemistry 29, 7214-7222.
35. Haran, T. E., and Crothers, D. M. (1989) Cooperativity in A-tract structure and bending properties of composite TuAn blocks, Biochemistry 28, 2763-2767.
36. Hagerman, P. J. (1985) Sequence dependence of the curvature of DNA: A test of the phasing hypothesis, Biochemistry 24, 7033-7037.
37. Mack, D. R., Chiu, T. K., and Dickerson, R. E. (2001) Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: A comparative analysis of T-A and A-T steps within A-tracts, J. Mol. Biol. 312, 1037-1049.
38. Hud, N. V., Sklenar, V., and Feigon, J. (1999) Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending, J. Mol. Biol. 286, 651-660.
39. Burkhoff, A. M., and Tullius, T. D. (1988) Structural details of an adenine tract that does not cause DNA to bend, Nature 331, 455-457.
40. Goodsell, D. S., Kaczor-Grzeskowiak, M., and 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.
41. Quintana, J. R., Grzeskowiak, K., Yanagi, K., and Dickerson, R. E. (1992) Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G, J. Mol. Biol. 225, 379-395.
42. Liepinsh, E., Leupin, W., and Otting, G. (1994) Hydration of DNA in aqueous solution: NMR evidence for a kinetic destabilization of the minor groove hydration of d-(TTAA)2 versus d-(AATT)2 segments, Nucleic Acids Res. 22, 2249-2254.
43. Hagerman, P. J. (1986) Sequence-directed curvature of DNA, Nature 321, 449-450.
44. 1H NMR spectroscopy and manganese(II), Biochemistry 41, 9900-9910.
45. McFail-Isom, L., Sines, C. C., and Williams, L. D. (1999) DNA structure: Cations in charge? Curr. Opin. Struct. Biol. 9, 298-304.
46. Laughton, C., and Luisi, B. (1999) The mechanics of minor groove width variation in DNA, and its implications for the accommodation of ligands, J. Mol. Biol. 288, 953-963.
47. Bostock-Smith, C. E., Harris, S. A., Laughton, C. A., and Searle, M. A. (2001) Induced fit DNA recognition by a minor groove binding analogue of Hoechst 33258: Fluctuations in DNA A tract structure investigated by NMR and molecular dynamics simulations, Nucleic Acids Res. 29, 693-702.