1 Å crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium

Journal of Molecular Biology

Volumn 301, Issue 4, 2000, Pages 915-945

  Chiu, Thang Kien ^a   Dickerson, Richard E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Anisotropy; Divalent cations; DNA sequence specific binding; Groove specific bending; Shelxdna

Indexed keywords

CALCIUM ION; DIVALENT CATION; DNA BASE; MAGNESIUM ION; CALCIUM; DNA; MAGNESIUM; MONOVALENT CATION; SINGLE STRANDED DNA; SOLVENT; WATER;

ARTICLE; BASE PAIRING; COMPUTER PROGRAM; CRYSTAL STRUCTURE; DNA BINDING; DNA HELIX; DNA SEQUENCE; DNA STRUCTURE; HYDROGEN BOND; PRIORITY JOURNAL; SEQUENCE ANALYSIS; ANISOTROPY; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; CRYSTALLIZATION; DRUG EFFECT; ENZYME SPECIFICITY; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; TEMPERATURE; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

ANISOTROPY; BASE PAIRING; BASE SEQUENCE; BINDING SITES; CALCIUM; CATIONS, DIVALENT; CATIONS, MONOVALENT; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DNA; DNA, SINGLE-STRANDED; HYDROGEN BONDING; MAGNESIUM; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; SOFTWARE; SOLVENTS; SUBSTRATE SPECIFICITY; TEMPERATURE; THERMODYNAMICS; WATER;

EID: 0034714010     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2000.4012     Document Type: Article

References (59)

1. The crystal structure of the trigonal decamer CGATCG-A(6ME)-TCG: A B-DNA helix with 10.6 base-pairs per turn
2. A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor
3. Effects of methylation on a synthetic polynucleotide: The B-Z transition in poly(dG-m5dC)·poly(dG-m5dC)
4. Crystal structures of B-DNA with incorporated 2 2'-deoxy-2'-fluoro-arabino- furanosyl thymines: Implications of conformational preorganization for duplex stability
5. NMR studies of cation-binding environments on nucleic acids
6. 2+ ions induces a strong macroscropic curvature in GGGCCC-containing DNA
7. Crystal structure of a group I ribozyme domain: Principles of RNA packing
8. Absence of minor groove monovalent cations in the crosslinked dodecamer CGCGA-ATTCGCG
9. Charge density-dependent strength of hydration and biological structure
10. Sequence-specific binding of counterions to B-DNA
11. DNA bending: The prevalence of kinkiness and the virtues of normality
12. Helix bending as a factor in protein/DNA recognition
13. On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities
14. RNA shows its metal
15. Structure of a B-DNA dodecamer: III. Geometry of hydration
16. Interactions of metal ions with polynucleotides and related compounds. XII. The relative effect of various metal ions on DNA helicity
17. The assessment of the geometry of dinucleotide steps in double-helical DNA: A new local calculation scheme
18. Sodium and chlorine ions as part of the DNA solvation shell
19. Crystal structure of CATGGCCATG and its implications for A-tract bending models
20. Crystal structure of CTCTCGAGAG: Implications for the structure of the Holliday junction
21. The structure of B-helical CGATC-GATCG and comparison with CCAACGTTGG. The effect of base-pair reversals
22. Crystallographic analysis of CCAAGCTTGG and its implications for bending in B-DNA
23. DNA base-stacking interactions: A comparison of theoretical calculations with oligonucleotides X-ray crystal structures
24. How proteins recognize the TATA Box
25. DNA sequence recognition in the minor groove by polyamides, using a GC-specific reading element: A perspective from crystallography
26. + ions to DNA in oriented DNA fibers: Experimental and monte carlo simulation results
27. 2+ ions on calf thymus DNA: Binding sites and conformational changes
28. The definition of generalised helicoidal parameters and of axis curvature for irregular nucleic acids
29. Crystal and molecular structure of d(CGTAGATCTACG) at 2.25 Å resolution
30. A gel electrophoresis study of the competitive effects of monovalent counterion on the extent of divalent counterions binding to DNA
31. The structure of the B-DNA decamer CCAACITTGG in two different space groups: Conformational flexibility of B-DNA
32. The structure of the most studied DNA fragment changes under the influence of ions:A new packing of d(CGCGAATTCGCG)
33. Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing
34. Conformational flexibility of poly(dG-m5dC) under very low salt conditions
35. Structural analysis of DNA-chlorophyll complexes by fourier transform infrared difference spectroscopy
36. New parameters for the refinement of nmucleic acid containing structures
37. Crystal structures of oligodeoxyribonucleotides containing 6'-α-methyl and 6'-α-hydroxy carbocyclic thymidines
38. Helix geometry, hydration, and G-A mismatch in a B-DNA decamer
39. Structure of the B-DNA decamer CCAACGTTGG and comparison with isomorphous decamers CCAAGATTGG and CCAGGCCTGG
40. Molecular electrostatic potential of the nucleic acids
41. The structure of a B-DNA decamer with a central T-A step: CGATTAATCG
42. Ion-induced stabilization of the G-DNA quadruplex: Free energy perturbation studies
43. The bi-loop, a new general four-stranded DNA motif
44. X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract dependent curvature
45. SHELX-97: High resolution refinement
46. 5): Effects of sequence polarity on DNA curvature
47. The B-DNA dodecamer at high resolution reveals a spine of water on sodium
48. Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations
49. Effects of neutralization pattern and stereochemistry on DNA bending by methylphosphonate substitutions
50. The DICK-ERSON-DREW B-DNA dodecamer revisited - At atomic resolution
51. A 'Hydrat-ion spine' in a B-DNA minor groove
52. 2+ and other transition metals at low concentration induce the right-to-left helical transformation of poly[d(G-C)]
53. B-DNA at atomic resolution reveals extended hydration patterns
54. Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn
55. Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes
56. Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets
57. Alternative structures for alternating poly(dA-dT) tracts: The structure of the B-DNA decamer CGATATATCG
58. Conditions which cause the right-handed to left-handed DNA conformational transitions. Evidence for several types of left-handed DNA structures in solution