Conformational flexibility of B-DNA at 0.74 Å resolution: d(CCAGTACTGG)2

Journal of Molecular Biology

Volumn 296, Issue 3, 2000, Pages 787-801

  Kielkopf, Clara L ^a   Ding, Sheng ^b   Kuhn, Peter ^c   Rees, Douglas C ^a,b  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b California Institute of Technology   (United States)

^c SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

Author keywords

B DNA; Calcium binding; DNA structure; Nucleic acid structure; Ultrahigh resolution

Indexed keywords

DNA B;

ARTICLE; BASE PAIRING; CALCIUM BINDING; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DNA CONFORMATION; DNA HELIX; DNA STRUCTURE; HYDRATION; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; REPRESSOR GENE;

EID: 0034711942     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3478     Document Type: Article

References (78)

1. A fast algorithm for rendering space filling molecule pictures
2. m6A)TCG: A B-DNA helix with 10.6 base-pairs per turn
3. Crystal structure of rubredoxin from Pyrococcus furiosus at 0.95 Å resolution, and the structures of N-terminal methionine and formylmethionine variants of Pf Rd. Contributions of N-terminal interactions to thermostability
4. Hydration of DNA: Take 2
5. +3 binding to the guanine
6. Crystallography and NMR system: A new software suite for macromolecular structure determination
7. 2+ recognizes the sequence of DNA through its hydration shell
8. 2·poly(rU) helices
9. Influence of base composition, base sequence and duplex structure on DNA hydration: Apparent molar volumes, and apparent molar adiabatic compressibilities of synthetic and natural DNA duplexes at 25°C
10. Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex
11. Crystal structures of B-form DNA-RNA chimeras complexed with distamycin
12. Crystal structures of side-by-side binding of distamycin to AT-containing DNA octamers d(ICI-TACIC) and d(ICATATIC)
13. Absence of minor groove cations in the crosslinked dodecamer C-G-C-G-A-A-T-T-C-G-C-G
14. The benefits of atomic resolution
15. Structural correlations in B-DNA
16. Structure of a B-DNA dodecamer III. Geometry of hydration
17. The tautomerism of heterocycles
18. An extensively modified version of MolScript that includes greatly enhanced coloring capabilities
19. Geometric parameters in nucleic acids: Sugar and phosphate constituents
20. Structure at 0.85 Å resolution of an early protein photocycle intermediate
21. Crystal structure of CTCTCGAGAG. Implications for the structure of the Holliday junction
22. The structure of B-helical CGATCGATCG and comparison with CCAACGTFGG. The effect of base-pair reversals
23. Crystallographic analysis of CCAAGCTFGG and its implications for bending in B-DNA
24. Sequence-dependent structural variation in B-DNA
25. Crystallographic study of one turn of G + C-rich B-DNA
26. m5C)TGG-Helical fine structure, hydration, and comparison with CCAGGCCTGG
27. Cryocrystallography of biological macromolecules - A generally applicable method
28. Base only binding of spermine in the deep groove of the A-DNA octamer d(GTGTACAC)
29. ORTEP-III: Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Illustrations
30. Calcium ion coordination: A comparison with that of beryllium, magnesium, and zinc
31. Oligonucleotide structure: A decade of results from single crystal X-ray diffraction studies
32. Structural basis for G·C recognition in the DNA minor groove
33. A structural basis for recognition of A·T and T·A base-pairs in the minor groove of B-DNA
34. Structural effects of DNA sequence on T·A recognition by Hp/Py pairs in the minor groove
35. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
36. The 0.78 Å structure of a serine protease: Bacillus lentus subtilisin
37. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
38. Tandem binding in crystals of a trp repressor/operator half-site complex
39. Structure of a B-DNA decamer CCAACITTGG in two different space groups: Conformational flexibility of B-DNA
40. Messages from ultrahigh resolution crystal structures
41. Divalent cations stabilize unstacked conformation of DNA and RNA by interacting with base π systems
42. DNA structure: Cations in charge?
43. Raster3D version 2.0- a program for photorealistic molecular graphics
44. Atomic-resolution structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing
45. 2
46. Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide 1-methylimidazole-2-carboxamide netropsin
47. Highly structured water network in crystals of a deoxydinucleoside-drug complex
48. Crystal structure of trp repressor/operator complex at atomic resolution
49. Processing of X-ray diffraction data collected in oscillation mode
50. Aromatic hydrogen bond in sequence-specific protein DNA recognition
51. 2 complex by two-dimensional NMR
52. Towards an understanding of protein-DNA recognition
53. The interpretation of protein structures: Total volume, group volume distributions and packing density
54. Cryocrystallography
55. Determination of the base composition of deoxyribonucleic acid from its buoyant density in CsCl
56. A systematic method for studying the spatial distribution of water molecules around nucleic acid bases
57. Hydration of the DNA bases is local
58. Hydration of the phosphate group in double helical DNA
59. The role of water in protein-DNA interactions
60. Determinants of repressor/operator recognition from the structure of the trp operator binding site
61. SHELXL: High-resolution refinement
62. 2{d(pGpG)}], the principal adduct formed by cis-diamminedichloroplatinum(II) with DNA
63. The B-DNA dodecamer at high resolution reveals a spine of water on sodium
64. Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations
65. Water and ions in a high resolution structure of B-DNA
66. Discrimination of 5'-GGGG-3', 5'-GCGC-3' and 5'-GGCC-3' sequences in the minor groove of DNA by eight-ring hairpin polyamides
67. Crystal structure of a double-stranded DNA containing the major adduct of the anticancer drug cisplatin
68. Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin
69. A 'hydrat-ion' spine in a B-DNA minor groove
70. The Dickerson-Drew dodecamer revisited at atomic resolution
71. B-DNA at atomic resolution reveals extended hydration patterns
72. 5G(A,T)C(A,T)-3' sequences by a dimeric side-by-side motif
73. Effects of the A·T/T·A degeneracy of pyrrole-imidazole polyamide recognition in the minor groove of DNA
74. On the pairing rules for recognition in the minor groove of DNA by pyrrole-imidazole polyamides
75. Recognition of the four Watson-Crick base-pairs in the DNA minor groove by synthetic ligands
76. Crystal structure analysis of a complete turn of B-DNA
77. Analysis of the local helix geometry in three B-DNA decamers and eight dodecamers
78. Alternative structures for alternating poly(dA-dT) tracts: The structure of the B-DNA decamer CGATATATCG