A dimeric DNA interface stabilized by stacked A·(G·G·G·G)·A hexads and coordinated monovalent cations

Journal of Molecular Biology

Volumn 297, Issue 3, 2000, Pages 627-644

  Kettani, Abdelali ^a   Gorin, Andrey ^a   Majumdar, Ananya ^a   Hermann, Thomas ^a   Skripkin, Eugene ^a   Zhao, Hong ^b   Jones, Roger ^b   Patel, Dinshaw J ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

A (G G G G) A hexad formation; G quadruplex recognition; G (A G) triads; Sheared G A mismatch formation; Uniform 13C, 15N labeled DNA

Indexed keywords

DOUBLE STRANDED DNA; OLIGODEOXYNUCLEOTIDE; POTASSIUM ION; SODIUM ION;

ARTICLE; BASE MISPAIRING; BASE PAIRING; CONTROLLED STUDY; DNA SEQUENCE; DNA STRAND; DNA STRUCTURE; METAL BINDING; MOLECULAR RECOGNITION; MOLECULAR STABILITY; NONHUMAN; PRIORITY JOURNAL; STOICHIOMETRY;

ALISMATACEAE;

EID: 0034737307     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2000.3524     Document Type: Article

References (72)

1. 4T) in the presence of sodium ions by NMR spectroscopy
2. 4
3. Attenuation of gene expression by a trinucleotide repeat-rich tract from the terminal exon of the rat hepatic polymeric immunoglobulin receptor gene
4. Fluorescent dyes specific for quadruplex DNA
5. Preparation of isotopically enriched RNAs for heteronuclear NMR
6. + cation dependent conformational switch within a loop spanning segment of a DNA quadruplex containing G-G-G-C repeats
7. Solution structure of P22 transcriptional antitermination N-peptide-boxB RNA complex
8. RNA tertiary structure mediation by adenosine platforms
9. Spectroscopic recognition of guanine dimeric hairpin quadruplexes by a carbocyanine dye
10. Modified crush and soak method for recovering oligodeoxynucleotides from polyacrylamide gels
11. Solution structure of an unusually stable RNA tetraplex containing G- and U-quartet structures
12. Hairpin loops consisting of single adenine residues closed by a sheared A·A and G·G pairs formed by the DNA triplets AAA and GAG: Solution structure of the d(GTACAAAGTAC)
13. Sheared purine·purine pairing in biology
14. Crystal structure of a conserved ribosomal protein-RNA complex
15. A second generation force field for the simulation of proteins, nucleic acids and organic molecules
16. 2J(NN) couplings
17. Molecular recognition in the FMN-internal loop RNA aptamer complex
18. NMR-based model of a telomerase-inhibiting compound bound to G-quadruplex DNA
19. 15N-labeled RNA using HCCNH-TOCSY experiment
20. 4
21. Intercalative G-tetraplex stabilization of telomeric DNA by a cation porphyrin
22. 3GCG)
23. Repeat arrays in cellular DNA related to the Epstein-Barr virus IR3 repeat
24. Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations
25. Molecular dynamics investigations of hammerhead ribozyme RNA
26. Structural features that give rise to unusual stability of RNA hairpins containing GNRA loops
27. Most compact hairpin turn structure exerted by a short DNA fragment d(GCGAAGC) in solution: An extraordinarily stable structure resistant to nucleases and heat
28. Ammonium ion as an NMR probe for monovalent cation coordination sites of DNA quadruplexes
29. Structural features of the binding site for ribosomal protein S8 in E. coli 16 S rRNA defined using NMR spectroscopy
30. Crystal structure of four-stranded Oxytricha telomeric DNA
31. Bombyx mori single repeat telomeric DNA sequence forms a G-quadruplex capped by base triads
32. + cation stabilized DNA quadruplex containing G·G·G·G and G·C·G·C tetrads formed by G-G-G-C repeats observed in adeno-associated viral DNA
33. Interlocked mismatch-aligned arrowhead DNA motifs
34. Discordant expression and variable numbers of neigboring GGA- and GAA-rich triplet repeats in the 3'-untranslated regions of two groups of messenger RNAs encoded by the rat polymorphic immunoglobulin receptor gene
35. Triad DNA: A model for trinucleotide repeats
36. Triangular complementarity of the triad-DNA duplex
37. A diamond-shaped zipper-like DNA architecture containing triads sandwiched between mismatches and tetrads
38. The high resolution crystal structure of a parallel-stranded guanine tetraplex
39. NMR structure of the bacteriophage λ N peptide/boxB RNA complex: Recognition of a GNRA fold by an arginine rich motif
40. Acid multimers of oligocytidine strands: Stoichiometry, base-pair characterization and proton exchange properties
41. NMR and molecular evidence for a G·A mismatch base-pair in a purine-rich DNA duplex
42. Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: Distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP
43. Formation of an amino acid-binding pocket through adaptive zippering-up of a large DNA hairpin loop
44. Biological applications of electrostatic calculations and Brownian dynamics simulations
45. 15N nuclei with widely separaterd chemical shifts
46. Observation of internucleotide N-H··N hydrogen bonds in the absence of directly detectable protons
47. Pairing of DNA fragments containing (GGA:TTC)(n) repeats and promotion by high mobility group protein 1 and histone H1
48. Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE cross peaks and disulfide connectivities
49. Relaxation matrix alignment of the solution structure of squash trypsin inhibitor
50. Right-handed and left-handed DNA: Studies of B-DNA and Z-DNA by using proton nuclear Overhauser effect and phosphorus NMR
51. Structures of guanine-rich and cytosine-rich quadruplexes formed in vitro by telomeric, centromeric and triplet repeat disease sequences
52. Human telomerase inhibitors by regioisomeric disubstituted amidoanthracene-9,10-diones
53. NMR scalar couplings across Watson-Crick base pair hydrogen bonds in DNA observed by transverse relaxation-optimized spectroscopy
54. Telomere structure and function
55. A zipper-like duplex in DNA: The crystal structure of d(GCGAAAGCT) at 2.1 Å resolution
56. 15N-labeled RNA with an HNC-TOCSY-CH experiment
57. 15N-labeled RNA via heteronuclear TOCSY
58. 15N-labeled DNA for NMR studies
59. Quadruplex structure of Oxytricha telomeric DNA oligonucleotides
60. The conformation of the sarcin/ricin loop from 28 S ribosomal RNA
61. Molecular structure of a left-handed DNA fragment at atomic resolution
62. Solution structure of a parallel-stranded G-quadruplex formed by d(TTGGGGT)
63. + cation stabilized complex formed by d(G-G-T-T-T-T-C-G-G) in solution: Implications for G-tetrad structures
64. Cationic porphyrins as telomerase inhibitors: The interaction of tetra-(N-methyl-4-pyridyl)-porphine with quadruplex DNA
65. The conformation of loop E of eukaryotic 5 S ribosomal RNA
66. A detailed view of a ribosomal active site: The structure of the L11-RNA complex
67. GNA trinucleotide loop sequences producing extraordinarily stable DNA minihairpins
68. Structure of a single-cytidine hairpin loop formed by the DNA triplet GCA
69. 15N-labeled DNA oligonucleotides
70. Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA aptamer