An eight-stranded helical fragment in RNA crystal structure: Implications for tetraplex interaction

Structure

Volumn 11, Issue 7, 2003, Pages 825-831

  Pan, Baocheng ^a   Xiong, Yong ^b   Shi, Ke ^a   Sundaralingam, Muttaiya ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; NUCLEIC ACID; PROTEIN; URIDINE;

ARTICLE; BINDING AFFINITY; CONFORMATION; CRYSTAL STRUCTURE; MOLECULAR INTERACTION; PRIORITY JOURNAL; RNA BINDING; RNA STRUCTURE;

EID: 0037970596     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(03)00108-4     Document Type: Article

References (36)

1. Ahmed S., Kintanar A., Henderson E. Human telomeric C-strand tetraplexes. Nat. Struct. Biol. 1:1994;83-88.
2. Bassi G.S., Mollegaard N.E., Murchie A.I., von Kitzing E., Lilley D.M. Ionic interactions and the global conformations of the hammerhead ribozyme. Nat. Struct. Biol. 2:1995;45-55.
3. Berger I., Kang C.H., Fredian A., Ratliff R., Moyzis R., Rich A. Extension of the four-stranded intercalated cytosine motif by adenine.adenine base pairing in the crystal structure of d(CCCAAT). Nat. Struct. Biol. 2:1995;416-425.
4. Berman H.M., Olson W.K., Beveridge D.L., Westbrook J., Gelbin A., Demeny T., Hsieh S.-H., Srinivasan A.R., Schneider B. The Nucleic Acid Database. a comprehensive relational data base of three-dimensional structure of nucleic acids Biophys. J. 63:1992;751-759.
5. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S.et al. Crystallography and NMR System. a new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54:1998;905-921.
6. Chen L., Cai L., Zhang X., Rich A. Crystal structure of a four-stranded intercalated DNA. d(C4) Biochemistry. 33:1994;13540-13546.
7. Cheong C., Moore P.B. Solution structure of an unusually stable RNA tetraplex containing G and U-quartet structures. Biochemistry. 36:1992;8406-8414.
8. 2+ ions at subatomic resolution (0.61 Å). Proc. Natl. Acad. Sci. USA. 98:2001;13665-13670.
9. Drew R.H., Dickerson R.E. Structure of a B-DNA dodecamer III. Geometry of hydration. J. Mol. Biol. 151:1981;535-556.
10. Gehring K., Leroy J.L., Gueron M. A tetrameric DNA-structure with protonated cytosine·cytosine base-pairs. Nature. 363:1993;561-565.
11. Gonzalez R.L. Jr., Tinoco I. Jr. Solution structure and thermodynamics of a divalent metal ion binding site in an RNA pseudoknot. J. Mol. Biol. 289:1999;1267-1282.
12. Haider S., Parkinson G.N., Neidle S. Crystal structure of the potassium form of an Oxytricha nova G-quaruplex. J. Mol. Biol. 320:2002;189-200.
13. Haschemeyer A.E.V., Rich A. Nucleoside conformations. an analysis of steric barriers to rotation about the glycosidic bond J. Mol. Biol. 27:1967;369-384.
14. Horton T.E., DeRose V.J. Cobalt haxammine inhibition of the hammerhead ribozyme. Biochemistry. 39:2000;11408-11416.
15. Kang C.H., Zhang X., Ratliff R., Moyzis R., Rich A. Crystal structure of four-stranded Oxytricha telomeric DNA. Nature. 356:1992;126-131.
16. Kang C.H., Berger I., Lockshin C., Ratliff R., Moyzis R., Rich A. Crystal structure of intercalated four-stranded d(C3T) at 1.4 Å resolution. Proc. Natl. Acad. Sci. USA. 91:1994;11636-11640.
17. Kang C.H., Berger I., Lockshin C., Ratliff R., Moyzis R., Rich A. Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere. Proc. Natl. Acad. Sci. USA. 92:1995;3874-3878.
18. Kerwin S.M. G-quadruplex DNA as a target for drug design. Curr. Pharm. Des. 6:2000;441-471.
19. Kettani A., Gorin A., Majumdar A., Hermann T., Skripkin E., Zhao H., Jones R., Patel D.J. A dimeric DNA interface stabilized stacked A-(G-G-G-G)-A hexads and coordinated monovalent cations. J. Mol. Biol. 297:2000;627-644.
20. Kieft J.S., Tinoco I. Jr. Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt(III) hexamine. Structure. 5:1997;713-721.
21. Laughlan G., Murchie A.I.H., Norman D.G., Moore M.H., Moody P.C.E., Lilley D.M.J., Luisi B. The high-resolution crystal structure of a parallel-stranded guanine tetraplex. Science. 265:1994;520-524.
22. Matsugami A., Ouhashi K., Kanagawa M., Liu H., Kanagawa S., Uesugi S., Katahira M. An intramolecular quadruplex of (GGA)4 triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction. J. Mol. Biol. 313:2001;255-269.
23. Mohanty D., Bansal M. Conformational polymorphism in G-tetraplex structures. strand reversal by base flipover or sugar flipover Nucleic Acids Res. 21:1993;1767-1774.
24. Neidle S., Read M.A. G-quadruplexes as therapeutic targets. Biopolymers. 56:2001;195-208.
25. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
26. Pan B.C., Xiong Y., Shi K., Deng J.P., Sundaralingam M. Crystal structure of an RNA purine-rich tetraplex containing adenine tetrads. implications for specific binding in RNA tetraplexes Structure. 11:2003;815-823. this issue,
27. Parkinson G.N., Lee M.P.H., Neidle S. Crystal structure of parallel quadruplexes from human telomeric DNA. Nature. 417:2002;876-880.
28. Patel D.J., Bouaziz S., Kettani A., Wang Y. Structures of guanine-rich and cytosine-rich quadruplexes formed in vitro by telomeric, centromeric, and triplet repeat disease DNA sequences. Neidle S. Oxford Handbook of Nucleic Acid Structure. 1999;Oxford University Press, Oxford. a 389-453.pp.
29. Patel P.K., Koti A.S.R., Hosur R.V. NMR studies on truncated sequences of human telomeric DNA. observation of a novel A-tetrad Nucleic Acids Res. 27:1999;3836-3843. b.
30. Phillips K., Dauter Z., Murchie A.I.H., Lilley D.M.J., Luisi B. The crystal structure of a parallel-stranded guanine tetraplex at 0.95 Å resolution. J. Mol. Biol. 273:1997;171.
31. Rüdisser S., Tinoco I. Jr. Solution structure of cobalt(III)hexammine complexed to the GAAA tetraloop and metal-ion binding to G-A mismatches. J. Mol. Biol. 295:2000;1211-1223.
32. Sack J., Quiocho F.A. CHAIN - Crystallographic Modelling Program. 1992;Baylor College of Medicine, Houston, TX.
33. Tavale S.S., Sobell H.M. Crystal and molecular structure of 8-bromoguanosine and 8-bromoadenosine, two purine nucleotides in the syn conformation. J. Mol. Biol. 48:1970;109-123.
34. Terwilliger T. SOLVE/RESOLVE Manual. 2001;Los Alamos National Laboratory, Los Alamos, NM.
35. Wang E., Feigon J. Structures of nucleic acid triplexes. Neidle S. Oxford Handbook of Nucleic Acid Structure. 1999;Oxford University Press, Oxford. 355-388.pp.
36. Wemmer D.E., Dervan P.B. Targeting the minor groove of DNA. Curr. Opin. Struct. Biol. 7:1997;355-361.