Nucleic acids from self-assembly to induced-fit recognition (original) (raw)
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Crystal Structure of a Bulged RNA Tetraplex at 1.1 Å Resolution
Structure, 2003
sequence d(GGGCGG) (Gralla et al., 1987; Oppenheim et al., 1992), and Saccharomyces cerevisiae telomere and Biochemistry Yale University repeat d(GGGT) (Zakian, 1989). These fragments may play an important role in biological processes. For in-New Haven, Connecticut stance, the auxiliary downstream element in SV40 liter pre-mRNA r(GGGGGAGGUGUGGG) (Bagga et al., 1995) is bound by hnRNA H/HЈ protein, and their interaction Summary may stimulate the polyadenylation of SV40 liter pre-mRNA (Bagga et al., 1998). Four consecutive guanines Bulges are an important structural motif in RNA and can form guanine tetraplex in both solution (Kim et al., can be used as recognition and interaction sites in 1991; Cheong and Moore, 1992) and crystalline state RNA-protein interaction and RNA-RNA interaction. (Laughlan et al., 1994; Phillips, et al., 1997; Deng et al., Here we report the first crystal structure of a bulged 2001a). Because pyrimidines are smaller than purines RNA tetraplex at 1.1 Å resolution. The hexamer r(U)( Br dG)
An eight-stranded helical fragment in RNA crystal structure: implications for tetraplex interaction
Structure (London, England : 1993), 2003
tetrads (Patel et al., 1999b; Pan et al., 2003) have been observed in both NMR and crystal structures. These 200 Johnston Lab 176 West 19th Avenue base tetrads show that hydrogen bond donors and acceptors are also exposed in the groove, and tetraplexes Columbus, Ohio 43210 2 Department of Molecular Biophysics are expected to have strong interactions in their groove. Recent research has been conducted on the interactions and Biochemistry Yale University of tetraplexes and the possible pharmaceutical applications to the tetraplexes (Kerwin, 2000; Neidle and Read, New Haven, Connecticut 06511 2001). However, we still have little structural information about the interaction.
A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair
Angewandte Chemie (International ed. in English), 2015
As one of its goals, synthetic biology seeks to increase the number of building blocks in nucleic acids. While efforts towards this goal are well advanced for DNA, they have hardly begun for RNA. Herein, we present a crystal structure for an RNA riboswitch where a stem C:G pair has been replaced by a pair between two components of an artificially expanded genetic-information system (AEGIS), Z and P, (6-amino-5-nitro-2(1H)-pyridone and 2-amino-imidazo[1,2-a]-1,3,5-triazin-4-(8H)-one). The structure shows that the Z:P pair does not greatly change the conformation of the RNA molecule nor the details of its interaction with a hypoxanthine ligand. This was confirmed in solution by in-line probing, which also measured a 3.7 nM affinity of the riboswitch for guanine. These data show that the Z:P pair mimics the natural Watson-Crick geometry in RNA in the first example of a crystal structure of an RNA molecule that contains an orthogonal added nucleobase pair.
An Eight-Stranded Helical Fragment in RNA Crystal Structure
Structure, 2003
Multistranded helical structures in nucleic acids play various functions in biological processes. Here we report the crystal structure of a hexamer, rU(BrdG)r(AGGU),at 1.5 Å resolution containing a structural complex of an alternating antiparallel eight-stranded helical fragment that is sandwiched in two tetraplexes. The octaplex is formed by groove binding interaction and base tetrad intercalation between two tetraplexes. Two different forms of octaplexes have been proposed, which display different properties in interaction with proteins and nucleic acids. Adenines form a base tetrad in the novel N6-H…N3 conformation and further interact with uridines to form an adenine-uridine octad in the reverse Hoogsteen pairing scheme. The conformational flexibility of adenine tetrad indicates that it can optimize its conformation in different interactions.
Crystallographic structure of an RNA helix: [U(UA)6A]2
Journal of Molecular Biology, 1989
The crystallographic structure of the synthetic oligoribonucleotide, U(UA),A, has been solved at 2.25 A resolution. The crystallographic refinement permitted the identification of 91 solvent molecules, with a final agreement factor of 13%. The molecule is a dimer of 14 base-pairs and shows the typical features of an A-type helix. However, the presence of two kinks causes a divergence from a straight helix. The observed deformation, which is stabilized by a few hydrogen bonds in the crystal packing, could be due to the relatively high (35°C) temperature of crystallization. The complete analysis of the structure is presented. It includes the stacking geometries, the backbone conformation and the solvation.
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.
RNA, 2001
The RNA strand in an RNA/DNA duplex with unpaired ribonucleotides can undergo self-cleavage at bulge sites in the presence of a variety of divalent metal ions (Hüsken et al., Biochemistry, 1996, 35:16591-16600). Transesterification proceeds via an in-line mechanism, with the 29-OH of the bulged nucleotide attacking the 39-adjacent phosphate group. The site-specificity of the reaction is most likely a consequence of the greater local conformational freedom of the RNA backbone in the bulge region. A standard A-form backbone geometry prohibits formation of an in-line arrangement between 29-oxygen and phosphate. However, the backbone in the region of an unpaired nucleotide appears to be conducive to an in-line approach. Therefore, the bulge-mediated phosphoryl transfer reaction represents one of the simplest RNA self-cleavage systems. Here we focus on the conformational features of the RNA that underlie site-specific cleavage. The structures of an RNA/DNA duplex with single ribo-adenosyl bulges were analyzed in two crystal forms, permitting observation of 10 individual conformations of the RNA bulge moiety. The bulge geometries cover a range of relative arrangements between the 29-oxygen of the bulged nucleotide and the P-O59 bond (including adjacent and near in-line) and give a detailed picture of the conformational changes necessary to line up the 29-OH nucleophile and scissile bond. Although metal ions are of crucial importance in the catalysis of analogous cleavage reactions by ribozymes, it is clear that local strain or conformational flexibility in the RNA also affect cleavage selectivity and rate (Soukup & Breaker, RNA, 1999, 5:1308-1325). The geometries of the RNA bulges frozen out in the crystals provide snapshots along the reaction pathway prior to the transition state of the phosphoryl transfer reaction.
Cation-Specific Structural Accommodation within a Catalytic RNA
Biochemistry, 2006
Metal ions facilitate the folding of the hairpin ribozyme, but do not participate directly in catalysis. The metal complex cobalt (III) hexaammine supports folding and activity of the ribozyme and also mediates specific internucleotide photocrosslinks, several of which retain catalytic ability. These crosslinks imply that the active core structure organized by [Co(NH 3) 6 ] 3+ is different from that organized by Mg 2+ and that revealed in the crystal structure (1). Residues U+2 and C+3 of the substrate, in particular, adopt different conformations in [Co(NH 3) 6 ] 3+. U+2 is bulged out of loop A and stacked on residue G36, whereas the nucleotide at position +3 is stacked on G8, a nucleobase crucial for catalysis. Cleavage kinetics performed with +2 variants and a C+3 U variant correlate with the crosslinking observations. Variants that decreased cleavage rates in magnesium up to 70fold showed only subtle decreases or even increases in observed rates when assayed in [Co (NH 3) 6 ] 3+. Here, we propose a model of the [Co(NH 3) 6 ] 3+-mediated catalytic core generated by MC-SYM that is consistent with these data. Interactions between cations and RNA molecules are critical for the biological activity of RNA, in that metal ions promote RNA folding events and RNA-catalyzed reactions, including RNA processing reactions and peptide bond formation (2). In the hairpin and hammerhead ribozymes, cations function to facilitate folding into the active conformations, but play little or no direct role in catalysis (3-6). Folding and cleavage activity of the hairpin ribozyme can be supported by high concentrations (>1 M) of monovalent ions (4), moderate concentrations (2 to 20 mM) of magnesium and some other divalent ions (7), or by low concentrations (~1 mM) of the trivalent complex [Co(NH 3) 6 ] 3+.. This complex serves as an analogue of hexahydrated magnesium, in that it cannot make inner-sphere binding interactions with RNA (3). Catalysis by the hairpin ribozyme is preceded by a major conformational change, in which the two domains of the ribozyme-substrate complex come into close association with one another. This docking step is accompanied by changes in the orientation of the Watson-Crick helical elements within the complex, which can be monitored by biochemical and biophysical methods, including FRET, electrophoretic mobility, transient electric birefringence, and hydroxyl radical footprinting (8-10). Concomitantly, extensive interactions between the two major non-helical regions are formed, and result in the positioning of the likely catalytic bases, G8 and A38, at the scissile phosphodiester linkage. These latter conformational changes can be monitored by the photocrosslinking and fluorescence behavior of the affected nucleobases (11). The scope of overall conformational change can be visualized by comparing the NMR