Crystal and molecular structure of r(CGCGAAUUAGCG): an RNA duplex containing two G(anti)· A(anti) base pairs

Abstract

G(anti).A(anti) mispairs are held together by two hydrogen of guanine and the N6 and N1 of adenine. If the mispairs do not exhibit high propeller twist they may be further stabilized by inter-base reverse three-centre hydrogen bonds. These interactions, and other hydrogen bonds seen in our study, may be important in modelling the structure of RNA molecules and their interactions with other molecules.

The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited

“…The dependence of the position of nucleotide D16 on solvent divalent cation composition discussed above correlates with differences in the way the three divalent cations in question bind to site M2+ When the metal in that site is Mg 2ϩ , the only inner shell interaction between the metal and the RNA involves G19O2P (Fig+ 7A)+ The remaining cation-RNA interactions, which involve D17O1P, G20N7, G20O6, and G59O4, are all mediated by water molecules+ When Co 2ϩ binds to M2, the geometry changes (Fig+ 7C)+ The G19O2P interaction becomes an outer shell interaction, but the G20N7 interaction becomes inner shell+ Everything else remains the same+ The position assumed by the Co 2ϩ is about 1+5 Å away from the position where Mg 2ϩ binds, and this shift enables D16 to swing around and pair with U59+ When M2 is filled with Mn 2ϩ (Fig+ 7B), the effect is intermediate+ D16O29, which is not a ligand for either Mg 2ϩ or Co 2ϩ , becomes an inner shell ligand, which also pulls D16 towards U59, but not quite as far+ Water-binding sites 120 water molecules were detected in this study that do not interact with metal ions+ Most of them are in the molecule's major grooves and around its elbow region, which has a higher concentration of tightly bound water molecules than anywhere else in the molecule+ The waters fall into three categories+ Thirteen percent of the bound waters bridge sequentially adjacent phosphate oxygens+ Bridging occurs not only in helical regions, as has been reported in the past (Kennard et al+, 1986;Saenger et al+, 1986;Leonard et al+, 1994), but also in loops+ Figure 6A shows the chain of water molecules that bridges phosphate groups in the T⌿C loop+ In helical regions, bridging waters tend to be closer to the phosphate oxygen on the 59 side than to the phosphate 297 (5) 166 (6) 55 (1) 79 (2) 203 (2) 295 (4) 208 (1) G71 280 (5) 174 (3) 62 (4) 80 (2) 213 (7) 291 (4) 196 (1) C72 288 (4) 175 (5) 64 (5) 83 (1) 203 (1) 297 (4) 199 (1) CCA end A73 289 (3) 182 (1) 54 (2) 82 (1) 212 (1) 295 (3) 192 (2)...…”

Crystal structures of nucleic acids and their drug complexes

“…The G·U mismatch is stabilised by a solvent molecule in the minor groove which also interacts with the ribose hydroxy group. The structure of r(CGCGAAUUA GCG) 88 has two separated G·A mismatches within the dodecamer duplex structure. The structure of r(GGCCGAA AGGCC) 89 has an internal loop with G·A and A·A mismatches.…”

1.76 Å Structure of a Pyrimidine Start Alternating A-RNA Hexamer r(CGUAC)dG

“…During the past decade other RNA crystal structures have been unravelled: the hammerhead ribozyme (Pley et al, 1994;Scott et al, 1995Scott et al, , 1996, the P4±P6 domain of group I intron (Cate et al, 1996) after the model of the entire intron was proposed by Michel & Westhof (1990), complexes of RNA with proteins (Rould et al, 1989;Ruff et al, 1991;Biou et al, 1994;Arnez & Steitz, 1994;Oubridge et al, 1994;Valegard et al, 1994) and duplex RNA (Dock-Bregeon et al, 1988Holbrook et al, 1991;Leonard et al, 1994;Betzel et al, 1994;Cruse et al, 1994;Portmann et al, 1995;Schindelin et al, 1995;Baeyens et al, 1995;. Complex RNA's, like tRNA, rRNA, ribozyme, have double helical stems, loops and other tertiary structures, while DNA's are commonly composed of duplexes.…”