Novel Conformation of an RNA Structural Switch (original) (raw)
Related papers
Biochemistry, 2010
Thermodynamic stabilities of 2 Â 2 nucleotide tandem AG internal loops in RNA range from -1.3 to þ3.4 kcal/mol at 37°C and are not predicted well with a hydrogen-bonding model. To provide structural information to facilitate development of more sophisticated models for the sequence dependence of stability, we report the NMR solution structures of five RNA duplexes: (rGACGAGCGUCA) 2 , (rGACU-AGAGUCA) 2 , (rGACAAGUGUCA) 2 , (rGGUAGGCCA) 2 , and (rGACGAGUGUCA) 2 . The structures of these duplexes are compared to that of the previously solved (rGGCAGGCC) 2 (Wu, M., SantaLucia, J., Jr., and Turner, D. H. (1997) Biochemistry 36, 4449-4460). For loops bounded by Watson-Crick pairs, the AG and Watson-Crick pairs are all head-to-head imino-paired (cis Watson-Crick/Watson-Crick). The structures suggest that the sequence-dependent stability may reflect non-hydrogen-bonding interactions. Of the two loops bounded by G-U pairs, only the 5 0 UAGG/3 0 GGAU loop adopts canonical UG wobble pairing (cis Watson-Crick/Watson-Crick), with AG pairs that are only weakly imino-paired. Strikingly, the 5 0 GAGU/3 0 UGAG loop has two distinct duplex conformations, the major of which has both guanosine residues (G4 and G6 in (rGACGAGUGUCA) 2 ) in a syn glycosidic bond conformation and forming a sheared GG pair (G4-G6*, GG trans Watson-Crick/Hoogsteen), both uracils (U7 and U7*) flipped out of the helix, and an AA pair (A5-A5*) in a dynamic or stacked conformation. These structures provide benchmarks for computational investigations into interactions responsible for the unexpected differences in loop free energies and structure.
Biochemistry, 2017
The prediction of RNA three-dimensional structure from sequence alone has been a long-standing goal. High-resolution, experimentally determined structures of simple noncanonical pairings and motifs are critical to the development of prediction programs. Here, we present the nuclear magnetic resonance structure of the (5'CCAGAAACGGAUGGA)2 duplex, which contains an 8 × 8 nucleotide internal loop flanked by three Watson-Crick pairs on each side. The loop is comprised of a central 5'AC/3'CA nearest neighbor flanked by two 3RRs motifs, a known stable motif consisting of three consecutive sheared GA pairs. Hydrogen bonding patterns between base pairs in the loop, the all-atom root-mean-square deviation for the loop, and the deformation index were used to compare the structure to automated predictions by MC-sym, RNA FARFAR, and RNAComposer.
Crystal structure of a 14 bp RNA duplex with non-symmetrical tandem GxU wobble base pairs
Nucleic Acids Research, 1999
Adjacent G·U wobble base pairs are frequently found in rRNA. Atomic structures of small RNA motifs help to provide a better understanding of the effects of various tandem mismatches on duplex structure and stability, thereby providing better rules for RNA structure prediction and validation. The crystal structure of an RNA duplex containing the sequence r(GGUAUUGC-GGUACC) 2 has been solved at 2.1 Å resolution using experimental phases. Novel refinement strategies were needed for building the correct solvent model. At present, this is the only short RNA duplex structure containing 5′-U-U-3′/3′-G-G-5′ non-symmetric tandem G·U wobble base pairs. In the 14mer duplex, the six central base pairs are all displaced away from the helix axis, yielding significant changes in local backbone conformation, helix parameters and charge distribution that may provide specific recognition sites for biologically relevant ligand binding. The greatest deviations from A-form helix occur where the guanine of a wobble base pair stacks over a purine from the opposite strand. In this vicinity, the intra-strand phosphate distances increase significantly, and the major groove width increases up to 3 Å. Structural comparisons with other short duplexes containing symmetrical tandem G·U or G·T wobble base pairs show that nearestneighbor sequence dependencies govern helical twist and the occurrence of cross-strand purine stacks.
Crystal structure of a 14 bp RNA duplex with non-symmetrical tandem G·U wobble base pairs
Nucleic Acids Research, 2000
Adjacent G·U wobble base pairs are frequently found in rRNA. Atomic structures of small RNA motifs help to provide a better understanding of the effects of various tandem mismatches on duplex structure and stability, thereby providing better rules for RNA structure prediction and validation. The crystal structure of an RNA duplex containing the sequence r(GGUAUUGC- GGUACC)2 has been solved at
Structure, 1994
Background: Non-Watson-Crick base pair associations contribute significantly to the stabilization of RNA tertiary structure. The conformation adopted by such pairs appears to be a function of both the sequence and the secondary structure of the RNA molecule. GA mispairs adopt G(anti)A(anti) configurations in some circumstances, such as the ends of helical regions of rRNAs, but in other circumstances probably adopt an unusual configuration in which the inter-base hydrogen bonds involve functional groups from other bases. We investigated the structure of GA pairs in a synthetic RNA dodecamer, r(CGCGAAUUAGCG), which forms a duplex containing two such mismatches. Results: The structure of the RNA duplex was determined by single crystal X-ray diffraction techniques to a resolution in the range 7.0-1.8A, and found to be an A-type helical structure with 10 Watson-Crick pairs and two GA mispairs. The mispairs adopt the G(anti) A(anti) conformation, held together by two obvious hydrogen bonds. Unlike analogous base pairs seen in a DNA duplex, they do not exhibit a high propeller twist and may therefore be further stabilized by weak, reverse, three-center hydrogen bonds. Conclusions: G(anti)A(anti) mispairs are held together by two hydrogen bonds between the 06 and N1 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.
Solution Structure of an RNA Duplex Including a C−U Base Pair † , ‡
Biochemistry, 2000
The formation of the C-U base pair in a duplex was observed in solution by means of the temperature profile of 15 N chemical shifts, and the precise geometry of the C-U base pair was also determined by NOE-based structure calculation. From the solution structure of the RNA oligomer, r[CGACUCAGG]‚r[CCUGCGUCG], it was found that a single C-U mismatch preferred being stacked in the duplex rather than being flipped-out even in solution. Moreover, it adopts an irregular geometry, where the amino nitrogen (N4) of the cytidine and keto-oxygen (O4) of the uridine are within hydrogenbonding distance, as seen in crystals. To further prove the presence of a hydrogen bond in the C-U pair, we employed a point-labeled cytidine at the exocyclic amino nitrogen of the cytidine in the C-U pair. The temperature profile of its 15 N chemical shift showed a sigmoidal transition curve, indicating the presence of a hydrogen bond in the C-U pair in the duplex.
Structure of an RNA duplex r(GGCG Br UGCGCU) 2 with terminal and internal tandem G·U base pairs
Acta Crystallographica Section D Biological Crystallography, 2006
The crystal structure of a self-complementary RNA duplex r(GGCG Br UGCGCU) 2 with terminal GÁU and internal tandem GÁU base pairs has been determined at 2.1 Å resolution. The crystals belong to the tetragonal space group P4 3 , with unit-cell parameters a = b = 37.69, c = 96.28 Å and two duplexes in the asymmetric unit. The two strands of each duplex are related by a pseudodyad axis. The structure was refined to final R work and R free values of 20.9 and 25.3%, respectively. The duplexes stack in an end-to-end manner, forming infinite columns along the c axis. This is the first structural study of an RNA duplex containing GÁU pairs at the termini. The stacking overlaps of the terminal GÁU base pairs with their adjacent Watson-Crick base pairs are larger than those of Watson-Crick base pairs of the 5 0-YR-3 0 /3 0-RY-5 0 type. The terminal GÁU base pairs of neighbouring duplexes are also stacked with each other. An alternating underwoundoverwound pattern of the twist angles is seen at each step along the duplex. This observation is typical for internal tandem GÁU pairs, while the terminal GÁU base pairs exhibit high twist angles with the adjacent Watson-Crick pairs. The 3 0-side of U of the internal GÁU base pair, which is unstacked, appears to be stabilized by-cation interaction with an Mg 2+ ion.
Structure of a 16-mer RNA duplex r(GCAGACUUAAAUCUGC)2 with wobble C·A+ mismatches
Journal of Molecular Biology, 1998
The crystal structure of a 16-mer, the longest known RNA duplex, has been determined at 2.5 A Ê resolution. The hexadecamer r(GCAGA-CUUAAAUCUGC) contains isolated C ÁA/A ÁC mismatches with two hydrogen bonds. The two hydrogen bonds in the mismatches suggests that N1 of A is protonated even though the crystallization was done at neutral pH. Therefore, the C Á A mismatch is a C ÁA wobble similar to the G ÁU wobble. The two C Á A pairs are isolated by four Watson-Crick pairs and¯anked by ®ve Watson-Crick base-pairs on either sides. Kinks/ bends of 20 are observed at the wobble sites. The Watson-Crick basepair A5 ÁU26 on the 5 H -side of the ®rst C6 Á A27 wobble has a twist angle of 27 compared to the 3 H -side U7 ÁA28 pair of 36 . The twist angles are reversed (37 and 26 ) in the second A11 ÁC22 wobble because of the approximate dyad in the molecule, the¯anking base-pair sequences are A ÁU pairs. The wobbles expand the major groove to 7.1 A Ê /7.3 A Ê . The duplexes form helical columns and are tightly packed around the 3 1 -screw axis. The minor grooves of adjacent columns in juxtaposition interact through the O2 H atoms and the anionic phosphate oxygen atoms.
Structures and Energetics of Four Adjacent G·U Pairs That Stabilize an RNA Helix
The Journal of Physical Chemistry B, 2015
Consecutive G•U base pairs inside RNA helices can be destabilizing while those at the ends of helices are thermodynamically stabilizing. To determine if this paradox could be explained by differences in base stacking, we determined the high-resolution (1.32 Å) crystal structure of (5'-GGUGGCUGUU-3') 2 and studied three sequences with four consecutive terminal G•U pairs by NMR spectroscopy. In the crystal structure of (5'-GGUGGCUGUU-3') 2 , the helix is overwound but retains the overall features of A-form RNA. The penultimate base steps at each end of the helix have high base overlap and contribute to the unexpectedly favorable energetic contribution for the 5'-GU-3'/3'-UG-5' motif in this helix position. The balance of base stacking and helical twist contributes to the positional dependence of G•U pair stabilities. The energetic stabilities and similarity to A-form RNA helices suggest that consecutive G•U pairs would be recognized by RNA helix binding proteins, such as Dicer and Ago. Thus, these results will aid future searches for target sites of small RNAs in gene regulation.
Journal of Molecular Biology, 1997
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 A), 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.