Structures of non-canonical tandem base pairs in RNA helices: Review

Nucleosides, Nucleotides and Nucleic Acids

Volumn 22, Issue 5-8, 2003, Pages 559-571

  Heus, Hans A ^a   Hilbers, Cornelis W ^a  

^a RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

Author keywords

Non canonical tandem base pairs; RNA; RNA geometry; Structure

Indexed keywords

ANALYTIC METHOD; BASE PAIRING; CATALYSIS; CONFERENCE PAPER; DNA FLANKING REGION; HYDROGEN BOND; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN MOTIF; RNA ANALYSIS; STRUCTURE ANALYSIS; TANDEM REPEAT; THERMODYNAMICS;

BASE PAIRING; BASE SEQUENCE; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; OLIGORIBONUCLEOTIDES; RNA;

EID: 0141537265     PISSN: 15257770     EISSN: None     Source Type: Journal    
DOI: 10.1081/NCN-120021955     Document Type: Conference Paper

References (32)

1. Ban, N.; Nissen, P.; Hansen, J.; Moore, P.B.; Steitz, T.A. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 2000, 289, 905-920.
2. Biswas, R.; Wahl, M.C.; Ban, C.; Sundaralingam, M. Crystal structure of an alternating octamer r(GUAUGUA)dC with adjacent G x U wobble pairs. J. Mol. Biol. 1997, 267, 1149-1156.
3. Biswas, R.; Sundaralingam, M. Crystal structure of r(GUGUGUA)dC with tandem G x U/U x G wobble pairs with strand slippage. J. Mol. Biol. 1997, 270, 511-519.
4. Cate, J.H.; Gooding, A.R.; Podell, E.; Zhou, K.; Golden, B.L.; Kundrot, C.E.; Cech, T.E.; Doudna, J.A. Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 1996, 273, 1678-1685.
5. Chen, X.; McDowell, J.A.; Kierzek, R.; Krugh, T.R.; Turner, D.H. Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U pairs: one hydrogen bond for each G.U pair in r(GGCGUGCC)2 and two for each G.U pair in r(GAGUGCUC)2. Biochemistry 2000, 39, 8970-8982.
6. Gautheret, D.; Konings, D.; Gutell, R.R. A major family of motifs involving G.A mismatches in ribosomal RNA. J Mol Biol. 1994, 242, 1-8.
7. Gautheret, D.; Konings, D.; Gutell, R.R. G.U base pairing motifs in ribosomal RNA. RNA 1995, 1, 807-814.
8. Heus, H.A.; Pardi, A. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science 1991, 253, 191-194.
9. Heus, H.A.; Wijmenga, S.S.; Hoppe, H.; Hilbers, C.W. The detailed structure of tandem G.A mismatched base-pair motifs in RNA duplexes is context dependent. J. Mol. Biol. 1997, 271, 147-158.
10. Holbrook, S.R.; Cheong, C.; Tinoco, I. Jr.; Kim, S.H. Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs. Nature 1991, 353, 579-581.
11. Jang, S.B.; Hung, L.W.; Chi, Y.I.; Holbrook, E.L.; Carter, R.J.; Holbrook, S.R. Structure of an RNA internal loop consisting of tandem C-A+ base pairs. Biochemistry 1998, 37, 11,726-11,731.
12. Kierzek, R.; Burkard, M.E.; Turner, D.H. Thermodynamics of single mismatches in RNA duplexes. Biochemistry 1999, 38, 14,214-14,223.
13. Kuglstatter, A.; Oubridge, C.; Nagai, K. Induced structural changes of 7SL RNA during the assembly of human signal recognition particle. Nat Struct Biol. 2002, 9, 740-744.
14. Leontis, N.B.; Westhof, E. The 5S rRNA loop E: Chemical probing and phylogenetic data versus crystal structure. RNA 1998a, 4, 1134-1153.
15. Leontis, N.B.; Westhof, E. Conserved geometrical base-pairing patterns in RNA. Q Rev Biophys. 1998b, 31, 399-455.
16. Leontis, N.B.; Westhof, E. Geometric nomenclature and classification of RNA base pairs. RNA 2001, 7, 499-512.
17. Leontis, N.B.; Stombaugh, J.; Westhof, E. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res. 2002, 30, 3497-3531.
18. Lescrinier, E.M.H.P.; Tessari, M.; van Kuppeveld, F.J.M.; Melchers, W.J.G.; Hilbers, C.W.; Heus, H.A. Structure of the pyrimidine rich internal loop in the poliovirus 3′-UTR. The importance of maintaining pseudodyad symmetry in RNA helices containing two adjacent non-canonical base pairs.
19. Lietzke, S.E.; Barnes, C.L.; Berglund, J.A.; Kundrot, C.E. The structure of an RNA dodecamer shows how tandem U-U base pairs increase the range of stable RNA structures and the diversity of recognition sites. Structure 1996, 4, 917-930.
20. Masquida, B.; Westhof, E. On the wobble GoU and related pairs. RNA 2000, 6, 9-15.
21. McDowell, J.A.; Turner, D.H. Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: Solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing. Biochemistry 1996, 35, 14,077-14,089.
22. McDowell, J.A.; He, L.; Chen, X.; Turner, D.H. Investigation of the structural basis for thermodynamic stabilities of tandem GU wobble pairs: NMR structures of (rGGAGUUCC)2 and (rGGAUGUCC)2. Biochemistry 1997, 36, 8030-8038.
23. Mckay, D.B. Structure and function of the hammerhead ribozyme: An unfinished story. RNA 1996, 2, 395-403.
24. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1984.
25. 2 in solution from NMR and restrained molecular dynamics. Biochemistry 1993, 32, 6026-6036.
26. Traub, W.; Sussman, J.L. Adenine-guanine base pairing ribosomal RNA. Nucleic Acids Res. 1982, 10, 2701-2708.
27. Trikha, J.; Filman, D.J.; Hogle, J.M. Crystal structure of a 14 bp RNA duplex with non-symmetrical tandem G x U wobble base pairs. Nucleic Acids Res. 1999, 27, 1728-1739.
28. van Knippenberg, P.H.; Formenoy, L.J.; Heus, H.A. Is there a special function for U.G basepairs in ribosomal RNA?. Biochim Biophys Acta. 1990, 1050 14-17.
29. Wu, M.; McDowell, J.A.; Turner, D.H. A periodic table of symmetric tandem mismatches in RNA. Biochemistry 1995, 34, 3204-3211.
30. Wu, M.; Turner, D.H. Solution structure of r(GCGGACGC)2 by two-dimensional NMR and the iterative relaxation matrix approach. Biochemistry 1996, 35, 9677-9689.
31. 2 by two-dimensional NMR and the iterative relaxation matrix approach. Biochemistry 1997, 36, 4449-4460.
32. Xia, T.; McDowell, J.A.; Turner, D.H. Thermodynamics of nonsymmetric tandem mismatches adjacent to G.C base pairs in RNA. Biochemistry 1997, 36, 12,486-12,497.