The detailed structure of tandem G-A mismatched base-pair motifs in RNA duplexes is context dependent

被引:56
作者
Heus, HA
Wijmenga, SS
Hoppe, H
Hilbers, CW
机构
[1] NSR Ctr. for Molec. Struct., D., Laboratory of Biophysical Chemistry, University of Nijmegen, Toernooiveld
[2] Dept. of Med. Biochem./Biophysics, University of Umeå
关键词
RNA structure; G-A base-pair; ribozymes; NMR;
D O I
10.1006/jmbi.1997.1158
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The solution structure of the RNA duplex (rGGGCUGAAGCCCU), containing tandem G.A mismatches has been determined by NMR spectroscopy and restrained molecular dynamics. A homonuclear 3D TOCSY-NOESY was used to derive 18 to 30 distance restraints per nucleotide, as well as all gamma torsion angles and sugar puckers for the central UGAA part of the molecule. Using these constraints, together with cross-strand distances, involving exchangeable imino protons, and essentially all other torsion angles that can accurately be determined (i.e. beta, epsilon) otherwise, the structure of the UGAA domain could be determined with high precision (r.m.s.d. 0.62 Angstrom), without the aid of isotopically enriched RNA. The G.A base-pairs are of the sheared pairing type, with both nucleotides in the anti conformation, and hydrogen bonds between the guanine 2-amino and the adenine N7 and between the guanine N3 and the adenine 6-amino. Surprisingly the sugar of the guanosine of the G.A mismatch adopts a 2'-endo sugar pucker conformation. Comparison with other RNA structures, in which two such G.A base-pairs are formed reveals that this detailed structure depends on the identity of the base 5' to the guanosine in the tandem G.A base-pairs. A geometrical model for the incorporation of sheared tandem G.A base-pairs in A-form helices is formulated, which explains the distinct different stacking properties and helical parameters in sequences containing tandem sheared G.A base-pairs. (C) 1997 Academic Press Limited.
引用
收藏
页码:147 / 158
页数:12
相关论文
共 49 条
  • [31] GAAA TETRALOOP AND CONSERVED BULGE STABILIZE TERTIARY STRUCTURE OF A GROUP-I INTRON DOMAIN
    MURPHY, FL
    CECH, TR
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1994, 236 (01) : 49 - 63
  • [32] A CALCULATION STRATEGY FOR THE STRUCTURE DETERMINATION OF SYMMETRICAL DIMERS BY H-1-NMR
    NILGES, M
    [J]. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1993, 17 (03): : 297 - 309
  • [33] EXCHANGEABLE PROTON NMR WITHOUT BASE-LINE DISTORTION, USING NEW STRONG-PULSE SEQUENCES
    PLATEAU, P
    GUERON, M
    [J]. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1982, 104 (25) : 7310 - 7311
  • [34] MODEL FOR AN RNA TERTIARY INTERACTION FRONT THE STRUCTURE OF AN INTERMOLECULAR COMPLEX BETWEEN A GAAA TETRALOOP AND AN RNA HELIX
    PLEY, HW
    FLAHERTY, KM
    MCKAY, DB
    [J]. NATURE, 1994, 372 (6501) : 111 - 113
  • [35] 3-DIMENSIONAL STRUCTURE OF A HAMMERHEAD RIBOZYME
    PLEY, HW
    FLAHERTY, KM
    MCKAY, DB
    [J]. NATURE, 1994, 372 (6501) : 68 - 74
  • [36] IMPROVED SPECTRAL RESOLUTION IN COSY H-1-NMR SPECTRA OF PROTEINS VIA DOUBLE QUANTUM FILTERING
    RANCE, M
    SORENSEN, OW
    BODENHAUSEN, G
    WAGNER, G
    ERNST, RR
    WUTHRICH, K
    [J]. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 1983, 117 (02) : 479 - 485
  • [37] SEQUENCE REQUIREMENTS OF THE HAMMERHEAD RNA SELF-CLEAVAGE REACTION
    RUFFNER, DE
    STORMO, GD
    UHLENBECK, OC
    [J]. BIOCHEMISTRY, 1990, 29 (47) : 10695 - 10702
  • [38] STRUCTURE OF (RGGC(GA)UNDER-BARGCC)2 IN SOLUTION FROM NMR AND RESTRAINED MOLECULAR-DYNAMICS
    SANTALUCIA, J
    TURNER, DH
    [J]. BIOCHEMISTRY, 1993, 32 (47) : 12612 - 12623
  • [39] THE CRYSTAL-STRUCTURE OF AN ALL-RNA HAMMERHEAD RIBOZYME - A PROPOSED MECHANISM FOR RNA CATALYTIC CLEAVAGE
    SCOTT, WG
    FINCH, JT
    KLUG, A
    [J]. CELL, 1995, 81 (07) : 991 - 1002
  • [40] ASSIGNMENT OF THE P-31 AND H-1 RESONANCES IN OLIGONUCLEOTIDES BY TWO-DIMENSIONAL NMR-SPECTROSCOPY
    SKLENAR, V
    MIYASHIRO, H
    ZON, G
    MILES, HT
    BAX, A
    [J]. FEBS LETTERS, 1986, 208 (01) : 94 - 98