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PDBsum entry 1mme

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Ribozyme PDB id
1mme
Jmol
Contents
DNA/RNA
PDB id:
1mme
Name: Ribozyme
Title: The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage
Structure: RNA hammerhead ribozyme. Chain: a, c. Engineered: yes. RNA hammerhead ribozyme. Chain: b, d. Engineered: yes
Source: Synthetic: yes. Synthetic: yes
Biol. unit: Dimer (from PQS)
Resolution:
3.10Å     R-factor:   0.251     R-free:   0.293
Authors: W.G.Scott,J.T.Finch,A.Klug
Key ref:
W.G.Scott et al. (1995). The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell, 81, 991. PubMed id: 7541315 DOI: 10.1016/S0092-8674(05)80004-2
Date:
09-Dec-95     Release date:   06-Feb-96    
 Headers
 References

 

 
DOI no: 10.1016/S0092-8674(05)80004-2 Cell 81:991 (1995)
PubMed id: 7541315  
 
 
The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage.
W.G.Scott, J.T.Finch, A.Klug.
 
  ABSTRACT  
 
We have solved the crystal structure of an all-RNA hammerhead ribozyme having a single 2'-O-methyl cytosine incorporated at the active site to prevent cleavage. The conditions used differ from those in another recent solution in four significant ways: first, it is an all-RNA ribozyme rather than a DNA-RNA hybrid; second, the connectivity of the ribozyme backbone strands is different; third, the crystals were grown in the presence of a much lower concentration of salt; and fourth, the crystal packing scheme is very different. Nevertheless, the three-dimensional structure of the all-RNA hammerhead ribozyme is similar to the previous structure. Five potential Mg(II)-binding sites are identified, including one positioned near the ribozyme catalytic pocket. Upon this basis, as well as upon comparisons with the metal-binding sites in the structurally homologous uridine turn of tRNAPhe, we propose a mechanism for RNA catalytic cleavage.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Crystal Structure of the Hammerhead Ribozyme
(a) The noncrystallographic symmetry-averaged and solvent-flattened MIRAS 3.1/~. resolution Fourier electron density map is shown superimposed on the refined structure of the hammerhead RNA. The enzyme strand is shown in red, and the substrate strand is shown in yellow. Before symmetry averaging, most of the electron density for the individual base pairs was not visible. (b) Illustration of the 5' to 5' and 3' to 3' packing scheme of the dimer of hammerhead ribozymes in an asymmetric unit of the crystal. The enzyme strands of molecule one and molecule two are shown in red and magenta, respectively, and the substrate strands are likewise shown in yellow and green. (c) A schematic diagram that shows the structural architecture of the hammerhead RNA. Again the enzyme strand is shown in red and the substrate strand in yellow with the active site cytosine at position 17 highlighted in green. Nonconserved bases are shown as solid letters, and conserved bases are set off as shadowed letters as in Figure la. Stems I, II, and III as well as the catalytic pocket formed by the uridine turn and C17 are labeled, as is the augmented stem II helix, as described in the text. Note that the augmented stem II helix stacks directly upon stem III, forming a pseudocontinuous long helix. The phosphate backbone then diverges, as depicted by the yellow strand crossing over the red strand, resulting in C17 being brought into close proximity to the conserved CUGA turn. Watson-Crick and reversed-Hoogste~n bases are denoted by white ovals. Single hydrogen bonds between non-Watson-Crick bases are shown as white broken lines. Single hydrogen bonds between bases and backbone riboses are shown as pink broken lines, and the two aromatic stabilization interactions between C17 and the uridine turn of the catalytic pocket are shown as green broken lines. The scissile bond between C17 and A1.1 is marked with an arrow. (d) The same view of the refined hammerhead ribozyme as shown in (a) now shows the conserved bases of stem III as well as the 3 bp augmenting helix that joins stem II (top left) to stem-loop III (bottom) highlighted in cyan, the CUGA uridine turn highlighted in white, and the active site cytosine (at position 17) in green. The other helical residues are all shown in red to deemphasize the arbitrary distinction between enzyme and substrate strands, as described in the text.
Figure 4.
Figure 4. The Hammerhead Ribozyme Catalytic Pocket and Metal-Binding Sites
(a) A stereo view of the hammerhead ribozyme catalytic pocket and flanking regions found in the first molecule in the asymmetric unit of our crystal is shown. The uridine turn (C3-U4-G5-A6) and the active site cytosine (C17) are shown as a color-coded stick model (yellow, carbon; white, phosphorous; red, oxygen; blue, nitrogen). The flanking stem I base pair (A1.1-U2.1) is shown in magenta, and the two flanking non-Watson- Crick base pairs of stem III and the augmented stem II helix are shown in dark and light blue, respectively. Hydrogen bonds and the U4-C17 interaction are marked with distances in angstroms in red. Note that aromatic stabilization interactions occur between the furanose oxygen of C17 and the base of A6 and between the exocyclic oxygen of U4 and the base of C17. (b) Stereo diagram illustrating the five potential magnesium-binding sites. The enzyme and substrate analog strands are shown in red and yellow, respectively, with the active site base shown in green. Five solvent difference Fourier peaks that cannot be assigned as water sites are shown in magenta, contoured at 2.8 m These have been assigned as hydrated Mg(H20)n ~+ complex ion sites as described in the text, according to stereochemical criteria that are summarized there and in Table 2. Site 1 is located on stem I; site 2 is on stem II and is essentially the same as the Mn(ll) site observed in the previous hammerhead structure. Site 3 is the only solvent peak near the active site base and the catalytic pocket, and sites 4 and 5 are associated with stem III. The refined positions of the five Mg(ll) cations are indicated by light blue spheres.
 
  The above figures are reprinted by permission from Cell Press: Cell (1995, 81, 991-0) copyright 1995.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22337051 E.A.Dethoff, J.Chugh, A.M.Mustoe, and H.M.Al-Hashimi (2012).
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  Nature, 482, 322-330.  
  21469161 E.J.Denning, U.D.Priyakumar, L.Nilsson, and A.D.Mackerell (2011).
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  J Comput Chem, 32, 1929-1943.  
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  Methods, 52, 159-167.  
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  20948783 S.P.Ryder (2010).
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  F1000 Biol Rep, 2, 0.  
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  Curr Opin Chem Biol, 13, 660-668.  
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  RNA, 9, 355-363.
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  Nat Struct Biol, 10, 672-673.  
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  FEMS Microbiol Rev, 27, 75-97.  
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  J Biol Chem, 278, 47987-47996.  
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  EMBO J, 22, 5561-5570.  
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  RNA, 9, 1415-1417.  
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  Chembiochem, 4, 1057-1065.  
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  Yakugaku Zasshi, 123, 305-313.  
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  J Biol Chem, 277, 40617-40622.  
11170470 C.Hammann, A.Cooper, and D.M.Lilley (2001).
Thermodynamics of ion-induced RNA folding in the hammerhead ribozyme: an isothermal titration calorimetric study.
  Biochemistry, 40, 1423-1429.  
11331743 C.Hammann, D.G.Norman, and D.M.Lilley (2001).
Dissection of the ion-induced folding of the hammerhead ribozyme using 19F NMR.
  Proc Natl Acad Sci U S A, 98, 5503-5508.  
11250907 D.A.Lafontaine, D.G.Norman, and D.M.Lilley (2001).
Structure, folding and activity of the VS ribozyme: importance of the 2-3-6 helical junction.
  EMBO J, 20, 1415-1424.  
11214179 D.J.Williams, J.L.Boots, and K.B.Hall (2001).
Thermodynamics of 2'-ribose substitutions in UUCG tetraloops.
  RNA, 7, 44-53.  
11441810 E.A.Doherty, and J.A.Doudna (2001).
Ribozyme structures and mechanisms.
  Annu Rev Biophys Biomol Struct, 30, 457-475.  
11173496 E.Ennifar, P.Walter, and P.Dumas (2001).
An efficient method for solving RNA structures: MAD phasing by replacing magnesium with zinc.
  Acta Crystallogr D Biol Crystallogr, 57, 330-332.  
11345432 J.L.O'Rear, S.Wang, A.L.Feig, L.Beigelman, O.C.Uhlenbeck, and D.Herschlag (2001).
Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations.
  RNA, 7, 537-545.  
11389613 J.M.Diamond, D.H.Turner, and D.H.Mathews (2001).
Thermodynamics of three-way multibranch loops in RNA.
  Biochemistry, 40, 6971-6981.  
11286889 K.Juneau, E.Podell, D.J.Harrington, and T.R.Cech (2001).
Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA--solvent interactions.
  Structure, 9, 221-231.
PDB code: 1hr2
  11720294 L.D.Sherlin, T.L.Bullock, T.A.Nissan, J.J.Perona, F.J.Lariviere, O.C.Uhlenbeck, and S.A.Scaringe (2001).
Chemical and enzymatic synthesis of tRNAs for high-throughput crystallization.
  RNA, 7, 1671-1678.  
11531997 M.Hertweck, and M.W.Mueller (2001).
Mapping divalent metal ion binding sites in a group II intron by Mn(2+)- and Zn(2+)-induced site-specific RNA cleavage.
  Eur J Biochem, 268, 4610-4620.  
11173467 M.Perbandt, M.Vallazza, C.Lippmann, C.Betzel, and V.A.Erdmann (2001).
Structure of an RNA duplex with an unusual G.C pair in wobble-like conformation at 1.6 A resolution.
  Acta Crystallogr D Biol Crystallogr, 57, 219-224.
PDB code: 439d
11422386 M.Szyrach, F.E.Münchberg, H.Riehle, A.Nordheim, J.Krauter, S.Nagel, G.Heil, and O.Heidenreich (2001).
Cleavage of AML1/MTG8 by asymmetric hammerhead ribozymes.
  Eur J Biochem, 268, 3550-3557.  
11258939 S.L.Larsson, and O.Nygård (2001).
Proposed secondary structure of eukaryote specific expansion segment 15 in 28S rRNA from mice, rats, and rabbits.
  Biochemistry, 40, 3222-3231.  
  11680848 S.T.Nonekowski, and G.A.Garcia (2001).
tRNA recognition by tRNA-guanine transglycosylase from Escherichia coli: the role of U33 in U-G-U sequence recognition.
  RNA, 7, 1432-1441.  
11573091 T.K.Stage-Zimmermann, and O.C.Uhlenbeck (2001).
A covalent crosslink converts the hammerhead ribozyme from a ribonuclease to an RNA ligase.
  Nat Struct Biol, 8, 863-867.  
11375501 U.Das, S.Chen, M.Fuxreiter, A.A.Vaguine, J.Richelle, H.M.Berman, and S.J.Wodak (2001).
Checking nucleic acid crystal structures.
  Acta Crystallogr D Biol Crystallogr, 57, 813-828.  
11222771 V.Tereshko, C.J.Wilds, G.Minasov, T.P.Prakash, M.A.Maier, A.Howard, Z.Wawrzak, M.Manoharan, and M.Egli (2001).
Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments.
  Nucleic Acids Res, 29, 1208-1215.
PDB codes: 1i0f 1i0g 1i0j 1i0k 1i0m 1i0n 1i0o 1i0p 1i0q 1i0t
11333021 V.Tereshko, S.T.Wallace, N.Usman, F.E.Wincott, and M.Egli (2001).
X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid.
  RNA, 7, 405-420.
PDB codes: 1i2x 1i2y
11685244 X.Yang, T.Gérczei, L.T.Glover, and C.C.Correll (2001).
Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping.
  Nat Struct Biol, 8, 968-973.
PDB codes: 1jbr 1jbs 1jbt
11328865 Y.Takagi, M.Warashina, W.J.Stec, K.Yoshinari, and K.Taira (2001).
Recent advances in the elucidation of the mechanisms of action of ribozymes.
  Nucleic Acids Res, 29, 1815-1834.  
10882132 A.A.Andersen, and R.A.Collins (2000).
Rearrangement of a stable RNA secondary structure during VS ribozyme catalysis.
  Mol Cell, 5, 469-478.  
10933815 C.G.Hoogstraten, J.R.Wank, and A.Pardi (2000).
Active site dynamics in the lead-dependent ribozyme.
  Biochemistry, 39, 9951-9958.  
10828955 D.J.Earnshaw, M.L.Hamm, J.A.Piccirilli, A.Karpeisky, L.Beigelman, B.S.Ross, M.Manoharan, and M.J.Gait (2000).
Investigation of the proposed interdomain ribose zipper in hairpin ribozyme cleavage using 2'-modified nucleosides.
  Biochemistry, 39, 6410-6421.  
11006537 D.M.Lilley, and T.J.Wilson (2000).
Fluorescence resonance energy transfer as a structural tool for nucleic acids.
  Curr Opin Chem Biol, 4, 507-517.  
10966470 E.A.Doherty, and J.A.Doudna (2000).
Ribozyme structures and mechanisms.
  Annu Rev Biochem, 69, 597-615.  
10745012 E.Westhof, and V.Fritsch (2000).
RNA folding: beyond Watson-Crick pairs.
  Structure, 8, R55-R65.  
10899150 G.Ferbeyre, V.Bourdeau, M.Pageau, P.Miramontes, and R.Cedergren (2000).
Distribution of hammerhead and hammerhead-like RNA motifs through the GenBank.
  Genome Res, 10, 1011-1019.  
11105752 G.Minasov, J.Matulic-Adamic, C.J.Wilds, P.Haeberli, N.Usman, L.Beigelman, and M.Egli (2000).
Crystal structure of an RNA duplex containing phenyl-ribonucleotides, hydrophobic isosteres of the natural pyrimidines.
  RNA, 6, 1516-1528.
PDB code: 1g2j
10882069 J.B.Murray, H.Szöke, A.Szöke, and W.G.Scott (2000).
Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction.
  Mol Cell, 5, 279-287.
PDB code: 488d
10606646 J.Li, W.Zheng, A.H.Kwon, and Y.Lu (2000).
In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme.
  Nucleic Acids Res, 28, 481-488.  
  10655240 J.Parsch, J.M.Braverman, and W.Stephan (2000).
Comparative sequence analysis and patterns of covariation in RNA secondary structures.
  Genetics, 154, 909-921.  
  10805160 K.W.Lazowski, and L.Kaczmarek (2000).
Highly sensitive detection of hybridization of oligonucleotides to specific sequences of nucleic acids by application of fluorescence resonance energy transfer.
  Antisense Nucleic Acid Drug Dev, 10, 97.  
10734192 K.Yoshinari, and K.Taira (2000).
A further investigation and reappraisal of the thio effect in the cleavage reaction catalyzed by a hammerhead ribozyme.
  Nucleic Acids Res, 28, 1730-1742.  
10801497 L.Jovine, T.Hainzl, C.Oubridge, W.G.Scott, J.Li, T.K.Sixma, A.Wonacott, T.Skarzynski, and K.Nagai (2000).
Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA.
  Structure, 8, 527-540.
PDB code: 1duh
11015188 M.Maderia, L.M.Hunsicker, and V.J.DeRose (2000).
Metal-phosphate interactions in the hammerhead ribozyme observed by 31P NMR and phosphorothioate substitutions.
  Biochemistry, 39, 12113-12120.  
10889026 M.Maderia, T.E.Horton, and V.J.DeRose (2000).
Metal interactions with a GAAA RNA tetraloop characterized by (31)P NMR and phosphorothioate substitutions.
  Biochemistry, 39, 8193-8200.  
10757999 M.Menger, F.Eckstein, and D.Porschke (2000).
Dynamics of the RNA hairpin GNRA tetraloop.
  Biochemistry, 39, 4500-4507.  
10785397 M.Nashimoto (2000).
Correct folding of a ribozyme induced by nonspecific macromolecules.
  Eur J Biochem, 267, 2738-2745.  
11142381 P.J.Michiels, C.H.Schouten, C.W.Hilbers, and H.A.Heus (2000).
Structure of the ribozyme substrate hairpin of Neurospora VS RNA: a close look at the cleavage site.
  RNA, 6, 1821-1832.
PDB code: 1e4p
10694382 S.E.Butcher, F.H.Allain, and J.Feigon (2000).
Determination of metal ion binding sites within the hairpin ribozyme domains by NMR.
  Biochemistry, 39, 2174-2182.  
11015228 S.K.Silverman, M.L.Deras, S.A.Woodson, S.A.Scaringe, and T.R.Cech (2000).
Multiple folding pathways for the P4-P6 RNA domain.
  Biochemistry, 39, 12465-12475.  
11058117 T.C.Kuo, and D.L.Herrin (2000).
Quantitative studies of Mn(2+)-promoted specific and non-specific cleavages of a large RNA: Mn(2+)-GAAA ribozymes and the evolution of small ribozymes.
  Nucleic Acids Res, 28, 4197-4206.  
10786851 T.Dale, R.Smith, and M.J.Serra (2000).
A test of the model to predict unusually stable RNA hairpin loop stability.
  RNA, 6, 608-615.  
10985786 T.E.Horton, and V.J.DeRose (2000).
Cobalt hexammine inhibition of the hammerhead ribozyme.
  Biochemistry, 39, 11408-11416.  
10947846 Y.Nakamatsu, M.Warashina, T.Kuwabara, Y.Tanaka, K.Yoshinari, and K.Taira (2000).
Significant activity of a modified ribozyme with N7-deazaguanine at g10.1: the double-metal-ion mechanism of catalysis in reactions catalysed by hammerhead ribozymes.
  Genes Cells, 5, 603-612.  
10393536 A.Loria, and T.Pan (1999).
The cleavage step of ribonuclease P catalysis is determined by ribozyme-substrate interactions both distal and proximal to the cleavage site.
  Biochemistry, 38, 8612-8620.  
10410795 A.R.Ferré-D'Amaré, and J.A.Doudna (1999).
RNA folds: insights from recent crystal structures.
  Annu Rev Biophys Biomol Struct, 28, 57-73.  
10021931 B.Llano-Sotelo, and C.S.Chow (1999).
RNA-aminoglycoside antibiotic interactions: fluorescence detection of binding and conformational change.
  Bioorg Med Chem Lett, 9, 213-216.  
10385001 C.Bravo, A.Woisard, J.L.Fourrey, P.Laugâa, and A.Favre (1999).
A Y form of hammerhead ribozyme trapped by photo-cross-links retains full cleavage activity.
  Biochimie, 81, 201-212.  
10361084 D.M.Lilley (1999).
Structure, folding and catalysis of the small nucleolytic ribozymes.
  Curr Opin Struct Biol, 9, 330-338.  
10449422 D.Scarabino, A.Crisari, S.Lorenzini, K.Williams, and G.P.Tocchini-Valentini (1999).
tRNA prefers to kiss.
  EMBO J, 18, 4571-4578.  
10089440 D.Sussman, D.Greensides, K.Reilly, and C.Wilson (1999).
Preliminary characterization of crystals of an in vitro evolved cyanocobalamin (vitamin B12) binding RNA.
  Acta Crystallogr D Biol Crystallogr, 55, 326-328.  
11169382 F.Eckstein, and B.Bramlage (1999).
The hammerhead ribozyme.
  Biopolymers, 52, 147-154.  
10573122 G.A.Soukup, and R.R.Breaker (1999).
Relationship between internucleotide linkage geometry and the stability of RNA.
  RNA, 5, 1308-1325.  
10425680 G.A.Soukup, and R.R.Breaker (1999).
Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization.
  Structure, 7, 783-791.  
10079078 G.S.Bassi, N.E.Møllegaard, A.I.Murchie, and D.M.Lilley (1999).
RNA folding and misfolding of the hammerhead ribozyme.
  Biochemistry, 38, 3345-3354.  
10021422 J.J.Rossi (1999).
Ribozymes, genomics and therapeutics.
  Chem Biol, 6, R33-R37.  
10573125 K.K.Singh, R.Parwaresch, and G.Krupp (1999).
Rapid kinetic characterization of hammerhead ribozymes by real-time monitoring of fluorescence resonance energy transfer (FRET).
  RNA, 5, 1348-1356.  
10573119 M.B.Elliott, P.A.Gottlieb, and P.Gollnick (1999).
Probing the TRAP-RNA interaction with nucleoside analogs.
  RNA, 5, 1277-1289.  
10201848 M.Dunkel, and V.Reither (1999).
Synthesis of 2'-C-alpha-difluoromethylarauridine and its 3'-O-phosphoramidite incorporation into a hammerhead ribozyme.
  Bioorg Med Chem Lett, 9, 787-792.  
10445883 M.R.Hansen, J.P.Simorre, P.Hanson, V.Mokler, L.Bellon, L.Beigelman, and A.Pardi (1999).
Identification and characterization of a novel high affinity metal-binding site in the hammerhead ribozyme.
  RNA, 5, 1099-1104.  
10334335 M.Sohail, S.Akhtar, and E.M.Southern (1999).
The folding of large RNAs studied by hybridization to arrays of complementary oligonucleotides.
  RNA, 5, 646-655.  
10872451 P.B.Moore (1999).
Structural motifs in RNA.
  Annu Rev Biochem, 68, 287-300.  
10572011 S.Wang, K.Karbstein, A.Peracchi, L.Beigelman, and D.Herschlag (1999).
Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate.
  Biochemistry, 38, 14363-14378.  
10376872 T.S.Wadkins, A.T.Perrotta, A.R.Ferré-D'Amaré, J.A.Doudna, and M.D.Been (1999).
A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes.
  RNA, 5, 720-727.  
10600106 Y.G.Gao, H.Robinson, R.Sanishvili, A.Joachimiak, and A.H.Wang (1999).
Structure and recognition of sheared tandem G x A base pairs associated with human centromere DNA sequence at atomic resolution.
  Biochemistry, 38, 16452-16460.
PDB codes: 1d8x 1d9r 1dcr
9660970 A.I.Murchie, J.B.Thomson, F.Walter, and D.M.Lilley (1998).
Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops.
  Mol Cell, 1, 873-881.  
9769099 A.L.Feig, G.E.Ammons, and O.C.Uhlenbeck (1998).
Cryoenzymology of the hammerhead ribozyme.
  RNA, 4, 1251-1258.  
9417029 A.L.Feig, W.G.Scott, and O.C.Uhlenbeck (1998).
Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb.
  Science, 279, 81-84.
PDB code: 359d
9778351 A.Peracchi, A.Karpeisky, L.Maloney, L.Beigelman, and D.Herschlag (1998).
A core folding model for catalysis by the hammerhead ribozyme accounts for its extraordinary sensitivity to abasic mutations.
  Biochemistry, 37, 14765-14775.  
9814755 A.Peracchi, J.Matulic-Adamic, S.Wang, L.Beigelman, and D.Herschlag (1998).
Structure-function relationships in the hammerhead ribozyme probed by base rescue.
  RNA, 4, 1332-1346.  
9722629 A.R.Kore, N.K.Vaish, U.Kutzke, and F.Eckstein (1998).
Sequence specificity of the hammerhead ribozyme revisited; the NHH rule.
  Nucleic Acids Res, 26, 4116-4120.  
9701285 A.V.Kazantsev, and N.R.Pace (1998).
Identification by modification-interference of purine N-7 and ribose 2'-OH groups critical for catalysis by bacterial ribonuclease P.
  RNA, 4, 937-947.  
9818266 B.L.Stoddard (1998).
New results using Laue diffraction and time-resolved crystallography.
  Curr Opin Struct Biol, 8, 612-618.  
9811818 C.C.Correll, A.Munishkin, Y.L.Chan, Z.Ren, I.G.Wool, and T.A.Steitz (1998).
Crystal structure of the ribosomal RNA domain essential for binding elongation factors.
  Proc Natl Acad Sci U S A, 95, 13436-13441.
PDB code: 430d
11180044 D.M.Lilley (1998).
Folding of branched RNA species.
  Biopolymers, 48, 101-112.  
9759486 D.N.Frank, and N.R.Pace (1998).
Ribonuclease P: unity and diversity in a tRNA processing ribozyme.
  Annu Rev Biochem, 67, 153-180.  
9461461 F.Seela, H.Debelak, N.Usman, A.Burgin, and L.Beigelman (1998).
1-Deazaadenosine: synthesis and activity of base-modified hammerhead ribozymes.
  Nucleic Acids Res, 26, 1010-1018.  
9666322 G.L.Conn, and D.E.Draper (1998).
RNA structure.
  Curr Opin Struct Biol, 8, 278-285.  
10089485 H.M.Berman, C.Zardecki, and J.Westbrook (1998).
The Nucleic Acid Database: A resource for nucleic acid science.
  Acta Crystallogr D Biol Crystallogr, 54, 1095-1104.  
9663384 J.A.Doudna (1998).
Ribozymes: the hammerhead swings into action.
  Curr Biol, 8, R495-R497.  
9818150 J.B.Murray, A.A.Seyhan, N.G.Walter, J.M.Burke, and W.G.Scott (1998).
The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone.
  Chem Biol, 5, 587-595.  
9506521 J.B.Murray, D.P.Terwey, L.Maloney, A.Karpeisky, N.Usman, L.Beigelman, and W.G.Scott (1998).
The structural basis of hammerhead ribozyme self-cleavage.
  Cell, 92, 665-673.
PDB code: 379d
9646875 J.E.Wedekind, and D.B.McKay (1998).
Crystallographic structures of the hammerhead ribozyme: relationship to ribozyme folding and catalysis.
  Annu Rev Biophys Biomol Struct, 27, 475-502.  
9724958 J.J.Rossi (1998).
Ribozymes to the rescue: repairing genetically defective mRNAs.
  Trends Genet, 14, 295-298.  
9503589 J.Kjems, and J.Egebjerg (1998).
Modern methods for probing RNA structure.
  Curr Opin Biotechnol, 9, 59-65.  
9671051 J.Kufel, and L.A.Kirsebom (1998).
The P15-loop of Escherichia coli RNase P RNA is an autonomous divalent metal ion binding domain.
  RNA, 4, 777-788.  
9521724 J.P.Simorre, P.Legault, N.Baidya, O.C.Uhlenbeck, L.Maloney, F.Wincott, N.Usman, L.Beigelman, and A.Pardi (1998).
Structural variation induced by different nucleotides at the cleavage site of the hammerhead ribozyme.
  Biochemistry, 37, 4034-4044.  
9722642 J.Tang, and R.R.Breaker (1998).
Mechanism for allosteric inhibition of an ATP-sensitive ribozyme.
  Nucleic Acids Res, 26, 4214-4221.  
9836592 K.J.Hertel, T.K.Stage-Zimmermann, G.Ammons, and O.C.Uhlenbeck (1998).
Thermodynamic dissection of the substrate-ribozyme interaction in the hammerhead ribozyme.
  Biochemistry, 37, 16983-16988.  
9722650 M.Gerstein, and W.Krebs (1998).
A database of macromolecular motions.
  Nucleic Acids Res, 26, 4280-4290.  
9769102 N.Polacek, and A.Barta (1998).
Metal ion probing of rRNAs: evidence for evolutionarily conserved divalent cation binding pockets.
  RNA, 4, 1282-1294.  
9631298 P.Auffinger, and E.Westhof (1998).
Simulations of the molecular dynamics of nucleic acids.
  Curr Opin Struct Biol, 8, 227-236.  
9568720 P.Legault, J.Li, J.Mogridge, L.E.Kay, and J.Greenblatt (1998).
NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif.
  Cell, 93, 289-299.  
9736692 R.A.Torres, and T.C.Bruice (1998).
Molecular dynamics study displays near in-line attack conformations in the hammerhead ribozyme self-cleavage reaction.
  Proc Natl Acad Sci U S A, 95, 11077-11082.  
9701289 R.T.Batey, and J.R.Williamson (1998).
Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15.
  RNA, 4, 984-997.  
  9436910 R.Walczak, P.Carbon, and A.Krol (1998).
An essential non-Watson-Crick base pair motif in 3'UTR to mediate selenoprotein translation.
  RNA, 4, 74-84.  
9518479 S.Ambrós, and R.Flores (1998).
In vitro and in vivo self-cleavage of a viroid RNA with a mutation in the hammerhead catalytic pocket.
  Nucleic Acids Res, 26, 1877-1883.  
9628915 S.G.Chaulk, and A.M.MacMillan (1998).
Caged RNA: photo-control of a ribozyme reaction.
  Nucleic Acids Res, 26, 3173-3178.  
9741924 S.Koseki, J.Ohkawa, R.Yamamoto, Y.Takebe, and K.Taira (1998).
A simple assay system for examination of the inhibitory potential in vivo of decoy RNAs, ribozymes and other drugs by measuring the Tat-mediated transcription of a fusion gene composed of the long terminal repeat of HIV-1 and a gene for luciferase.
  J Control Release, 53, 159-173.  
9671048 S.Lemieux, P.Chartrand, R.Cedergren, and F.Major (1998).
Modeling active RNA structures using the intersection of conformational space: application to the lead-activated ribozyme.
  RNA, 4, 739-749.  
9493396 S.Neidle, and C.M.Nunn (1998).
Crystal structures of nucleic acids and their drug complexes.
  Nat Prod Rep, 15, 1.  
9808042 S.Rowsell, N.J.Stonehouse, M.A.Convery, C.J.Adams, A.D.Ellington, I.Hirao, D.S.Peabody, P.G.Stockley, and S.E.Phillips (1998).
Crystal structures of a series of RNA aptamers complexed to the same protein target.
  Nat Struct Biol, 5, 970-975.
PDB code: 5msf
9759484 S.Verma, and F.Eckstein (1998).
Modified oligonucleotides: synthesis and strategy for users.
  Annu Rev Biochem, 67, 99.  
9765233 S.Xirasagar, M.B.Elliott, W.Bartolini, P.Gollnick, and P.A.Gottlieb (1998).
RNA structure inhibits the TRAP (trp RNA-binding attenuation protein)-RNA interaction.
  J Biol Chem, 273, 27146-27153.  
9922178 T.E.Horton, D.R.Clardy, and V.J.DeRose (1998).
Electron paramagnetic resonance spectroscopic measurement of Mn2+ binding affinities to the hammerhead ribozyme and correlation with cleavage activity.
  Biochemistry, 37, 18094-18101.  
9503590 T.Hermann, and E.Westhof (1998).
RNA as a drug target: chemical, modelling, and evolutionary tools.
  Curr Opin Biotechnol, 9, 66-73.  
9782053 T.Hermann, and E.Westhof (1998).
Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations.
  Structure, 6, 1303-1314.  
9649320 T.K.Stage-Zimmermann, and O.C.Uhlenbeck (1998).
Circular substrates of the hammerhead ribozyme shift the internal equilibrium further toward cleavage.
  Biochemistry, 37, 9386-9393.  
9701280 T.K.Stage-Zimmermann, and O.C.Uhlenbeck (1998).
Hammerhead ribozyme kinetics.
  RNA, 4, 875-889.  
9788354 T.Kuwabara, M.Warashina, M.Orita, S.Koseki, J.Ohkawa, and K.Taira (1998).
Formation of a catalytically active dimer by tRNA(Val)-driven short ribozymes.
  Nat Biotechnol, 16, 961-965.  
10333741 V.K.Misra, and D.E.Draper (1998).
On the role of magnesium ions in RNA stability.
  Biopolymers, 48, 113-135.  
9435228 W.B.Lott, B.W.Pontius, and P.H.von Hippel (1998).
A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate.
  Proc Natl Acad Sci U S A, 95, 542-547.  
9914252 W.G.Scott (1998).
RNA catalysis.
  Curr Opin Struct Biol, 8, 720-726.  
9831530 Y.Tor, T.Hermann, and E.Westhof (1998).
Deciphering RNA recognition: aminoglycoside binding to the hammerhead ribozyme.
  Chem Biol, 5, R277-R283.  
9256319 A.Irie, D.Y.Bouffard, and K.J.Scanlon (1997).
Ribozyme-mediated cancer gene therapy.
  Int J Urol, 4, 329-337.  
9341112 A.Peracchi, L.Beigelman, E.C.Scott, O.C.Uhlenbeck, and D.Herschlag (1997).
Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation.
  J Biol Chem, 272, 26822-26826.  
9306412 A.Persidis (1997).
Ribozyme therapeutics.
  Nat Biotechnol, 15, 921-922.  
9204272 A.Ramos, C.C.Gubser, and G.Varani (1997).
Recent solution structures of RNA and its complexes with drugs, peptides and proteins.
  Curr Opin Struct Biol, 7, 317-323.  
9254134 B.Clouet-d'Orval, and O.C.Uhlenbeck (1997).
Hammerhead ribozymes with a faster cleavage rate.
  Biochemistry, 36, 9087-9092.  
9222495 B.Masquida, B.Felden, and E.Westhof (1997).
Context dependent RNA-RNA recognition in a three-dimensional model of the 16S rRNA core.
  Bioorg Med Chem, 5, 1021-1035.  
9122187 B.W.Pontius, W.B.Lott, and P.H.von Hippel (1997).
Observations on catalysis by hammerhead ribozymes are consistent with a two-divalent-metal-ion mechanism.
  Proc Natl Acad Sci U S A, 94, 2290-2294.  
9393863 C.C.Correll, B.Freeborn, P.B.Moore, and T.A.Steitz (1997).
Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain.
  Cell, 91, 705-712.
PDB codes: 354d 356d 357d 364d
9365249 C.Hammann, R.Hormes, G.Sczakiel, and M.Tabler (1997).
A spermidine-induced conformational change of long-armed hammerhead ribozymes: ionic requirements for fast cleavage kinetics.
  Nucleic Acids Res, 25, 4715-4722.  
9281526 C.R.Geyer, and D.Sen (1997).
Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme.
  Chem Biol, 4, 579-593.  
9201943 C.S.Hamann, and Y.M.Hou (1997).
An RNA structural determinant for tRNA recognition.
  Biochemistry, 36, 7967-7972.  
9222494 C.S.Hamann, and Y.M.Hou (1997).
A strategy of tRNA recognition that includes determinants of RNA structure.
  Bioorg Med Chem, 5, 1011-1019.  
9405614 D.M.Zhou, L.H.Zhang, and K.Taira (1997).
Explanation by the double-metal-ion mechanism of catalysis for the differential metal ion effects on the cleavage rates of 5'-oxy and 5'-thio substrates by a hammerhead ribozyme.
  Proc Natl Acad Sci U S A, 94, 14343-14348.  
17029905 D.R.Duckett, A.I.Murchie, R.M.Clegg, G.S.Bassi, M.J.Giraud-Panis, and D.M.Lilley (1997).
Nucleic acid structure and recognition.
  Biophys Chem, 68, 53-62.  
9241244 E.J.Maglott, and G.D.Glick (1997).
A new method to monitor the rate of conformational transitions in RNA.
  Nucleic Acids Res, 25, 3297-3301.  
9416417 F.Burlina, A.Favre, and J.L.Fourrey (1997).
Chemical engineering of RNase resistant and catalytically active hammerhead ribozymes.
  Bioorg Med Chem, 5, 1999-2010.  
9242901 G.J.Narlikar, and D.Herschlag (1997).
Mechanistic aspects of enzymatic catalysis: lessons from comparison of RNA and protein enzymes.
  Annu Rev Biochem, 66, 19-59.  
9253414 G.R.Zimmermann, R.D.Jenison, C.L.Wick, J.P.Simorre, and A.Pardi (1997).
Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA.
  Nat Struct Biol, 4, 644-649.
PDB code: 1eht
9405376 G.S.Bassi, A.I.Murchie, F.Walter, R.M.Clegg, and D.M.Lilley (1997).
Ion-induced folding of the hammerhead ribozyme: a fluorescence resonance energy transfer study.
  EMBO J, 16, 7481-7489.  
9253403 H.A.Heus (1997).
RNA aptamers.
  Nat Struct Biol, 4, 597-600.  
9228937 I.Tinoco, and J.S.Kieft (1997).
The ion core in RNA folding.
  Nat Struct Biol, 4, 509-512.  
9204271 J.A.Doudna, and J.H.Cate (1997).
RNA structure: crystal clear?
  Curr Opin Struct Biol, 7, 310-316.  
9012667 J.P.Simorre, P.Legault, A.B.Hangar, P.Michiels, and A.Pardi (1997).
A conformational change in the catalytic core of the hammerhead ribozyme upon cleavage of an RNA substrate.
  Biochemistry, 36, 518-525.  
9195889 J.S.Kieft, and I.Tinoco (1997).
Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine.
  Structure, 5, 713-721.
PDB code: 1ajf
9238005 K.J.Hertel, A.Peracchi, O.C.Uhlenbeck, and D.Herschlag (1997).
Use of intrinsic binding energy for catalysis by an RNA enzyme.
  Proc Natl Acad Sci U S A, 94, 8497-8502.  
9128718 K.R.Birikh, P.A.Heaton, and F.Eckstein (1997).
The structure, function and application of the hammerhead ribozyme.
  Eur J Biochem, 245, 1.  
9336468 L.Wang, and D.E.Ruffner (1997).
An ultraviolet crosslink in the hammerhead ribozyme dependent on 2-thiocytidine or 4-thiouridine substitution.
  Nucleic Acids Res, 25, 4355-4361.  
9125504 M.J.Serra, T.W.Barnes, K.Betschart, M.J.Gutierrez, K.J.Sprouse, C.K.Riley, L.Stewart, and R.E.Temel (1997).
Improved parameters for the prediction of RNA hairpin stability.
  Biochemistry, 36, 4844-4851.  
9109652 M.Wu, J.SantaLucia, and D.H.Turner (1997).
Solution structure of (rGGCAGGCC)2 by two-dimensional NMR and the iterative relaxation matrix approach.
  Biochemistry, 36, 4449-4460.
PDB code: 1mwg
9033401 N.Baidya, and O.C.Uhlenbeck (1997).
A kinetic and thermodynamic analysis of cleavage site mutations in the hammerhead ribozyme.
  Biochemistry, 36, 1108-1114.  
9255788 N.Delihas, S.E.Rokita, and P.Zheng (1997).
Natural antisense RNA/target RNA interactions: possible models for antisense oligonucleotide drug design.
  Nat Biotechnol, 15, 751-753.  
9174367 N.K.Vaish, P.A.Heaton, and F.Eckstein (1997).
Isolation of hammerhead ribozymes with altered core sequences by in vitro selection.
  Biochemistry, 36, 6495-6501.  
9153320 O.Mitrasinovic, and L.M.Epstein (1997).
Differences in the phosphate oxygen requirements for self-cleavage by the extended and prototypical hammerhead forms.
  Nucleic Acids Res, 25, 2189-2196.  
9241415 P.Brion, and E.Westhof (1997).
Hierarchy and dynamics of RNA folding.
  Annu Rev Biophys Biomol Struct, 26, 113-137.  
9094330 P.Schuster, P.F.Stadler, and A.Renner (1997).
RNA structures and folding: from conventional to new issues in structure predictions.
  Curr Opin Struct Biol, 7, 229-235.  
9222498 R.G.Kuimelis, and L.W.McLaughlin (1997).
Application of a 5'-bridging phosphorothioate to probe divalent metal and hammerhead ribozyme mediated RNA cleavage.
  Bioorg Med Chem, 5, 1051-1061.  
9207012 R.H.Symons (1997).
Plant pathogenic RNAs and RNA catalysis.
  Nucleic Acids Res, 25, 2683-2689.  
9321667 R.J.Carter, K.J.Baeyens, J.SantaLucia, D.H.Turner, and S.R.Holbrook (1997).
The crystal structure of an RNA oligomer incorporating tandem adenosine-inosine mismatches.
  Nucleic Acids Res, 25, 4117-4122.
PDB code: 333d
9255068 S.A.Strobel, and J.A.Doudna (1997).
RNA seeing double: close-packing of helices in RNA tertiary structure.
  Trends Biochem Sci, 22, 262-266.  
9405377 S.E.Butcher, T.Dieckmann, and J.Feigon (1997).
Solution structure of a GAAA tetraloop receptor RNA.
  EMBO J, 16, 7490-7499.
PDB code: 1tlr
9097731 S.R.Holbrook, and S.H.Kim (1997).
RNA crystallography.
  Biopolymers, 44, 3.  
9667883 S.Verma, N.K.Vaish, and F.Eckstein (1997).
Structure-function studies of the hammerhead ribozyme.
  Curr Opin Chem Biol, 1, 532-536.  
9254698 T.Hermann, P.Auffinger, W.G.Scott, and E.Westhof (1997).
Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme.
  Nucleic Acids Res, 25, 3421-3427.  
9224607 T.Kuwabara, M.Warashina, T.Tanabe, K.Tani, S.Asano, and K.Taira (1997).
Comparison of the specificities and catalytic activities of hammerhead ribozymes and DNA enzymes with respect to the cleavage of BCR-ABL chimeric L6 (b2a2) mRNA.
  Nucleic Acids Res, 25, 3074-3081.  
9132001 T.Ohmichi, and N.Sugimoto (1997).
Role of Nd3+ and Pb2+ on the RNA cleavage reaction by a small ribozyme.
  Biochemistry, 36, 3514-3521.  
9222499 Y.Komatsu, M.Shirai, S.Yamashita, and E.Ohtsuka (1997).
Construction of hairpin ribozymes with a three-way junction.
  Bioorg Med Chem, 5, 1063-1069.  
9287156 Y.Li, and D.H.Turner (1997).
Effects of Mg2+ and the 2' OH of guanosine on steps required for substrate binding and reactivity with the Tetrahymena ribozyme reveal several local folding transitions.
  Biochemistry, 36, 11131-11139.  
8916894 A.B.Burgin, C.Gonzalez, J.Matulic-Adamic, A.M.Karpeisky, N.Usman, J.A.McSwiggen, and L.Beigelman (1996).
Chemically modified hammerhead ribozymes with improved catalytic rates.
  Biochemistry, 35, 14090-14097.  
8876168 A.Peracchi, L.Beigelman, N.Usman, and D.Herschlag (1996).
Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases.
  Proc Natl Acad Sci U S A, 93, 11522-11527.  
  8608444 B.Felden, C.Florentz, R.Giegé, and E.Westhof (1996).
A central pseudoknotted three-way junction imposes tRNA-like mimicry and the orientation of three 5' upstream pseudoknots in the 3' terminus of tobacco mosaic virus RNA.
  RNA, 2, 201-212.  
  8665863 B.Streicher, E.Westhof, and R.Schroeder (1996).
The environment of two metal ions surrounding the splice site of a group I intron.
  EMBO J, 15, 2556-2564.  
8614641 C.Bravo, F.Lescure, P.Laugâa, J.L.Fourrey, and A.Favre (1996).
Folding of the HDV antigenomic ribozyme pseudoknot structure deduced from long-range photocrosslinks.
  Nucleic Acids Res, 24, 1351-1359.  
8701472 D.E.Draper (1996).
Strategies for RNA folding.
  Trends Biochem Sci, 21, 145-149.  
8987994 D.Hüsken, G.Goodall, M.J.Blommers, W.Jahnke, J.Hall, R.Häner, and H.E.Moser (1996).
Creating RNA bulges: cleavage of RNA in RNA/DNA duplexes by metal ion catalysis.
  Biochemistry, 35, 16591-16600.  
8952482 E.Jankowsky, and B.Schwenzer (1996).
Efficient improvement of hammerhead ribozyme mediated cleavage of long substrates by oligonucleotide facilitators.
  Biochemistry, 35, 15313-15321.  
8913682 H.S.Pappa, A.E.Stewart, and N.Q.McDonald (1996).
Incorporating anomalous scattering centres into macromolecules.
  Curr Opin Struct Biol, 6, 611-616.  
8790355 H.Wang, R.J.Di Gate, and N.C.Seeman (1996).
An RNA topoisomerase.
  Proc Natl Acad Sci U S A, 93, 9477-9482.  
8901542 I.Berger, M.Egli, and A.Rich (1996).
Inter-strand C-H...O hydrogen bonds stabilizing four-stranded intercalated molecules: stereoelectronic effects of O4' in cytosine-rich DNA.
  Proc Natl Acad Sci U S A, 93, 12116-12121.  
8939599 I.Tinoco (1996).
RNA enzymes: putting together a large ribozyme.
  Curr Biol, 6, 1374-1376.  
8948630 J.B.Thomson, S.T.Sigurdsson, A.Zeuch, and F.Eckstein (1996).
In vitro selection of hammerhead ribozymes containing a bulged nucleotide in stem II.
  Nucleic Acids Res, 24, 4401-4406.  
8555235 J.Caceres-Cortes, and A.H.Wang (1996).
Binding of the antitumor drug nogalamycin to bulged DNA structures.
  Biochemistry, 35, 616-625.  
8901517 J.Kim, A.E.Walter, and D.H.Turner (1996).
Thermodynamics of coaxially stacked helixes with GA and CC mismatches.
  Biochemistry, 35, 13753-13761.  
8611561 J.Nowakowski, and I.Tinoco (1996).
Conformation of an RNA molecule that models the P4/P6 junction for group I introns.
  Biochemistry, 35, 2577-2585.  
8652564 J.Tao, and A.D.Frankel (1996).
Arginine-binding RNAs resembling TAR identified by in vitro selection.
  Biochemistry, 35, 2229-2238.  
8917508 K.J.Baeyens, H.L.De Bondt, A.Pardi, and S.R.Holbrook (1996).
A curved RNA helix incorporating an internal loop with G.A and A.A non-Watson-Crick base pairing.
  Proc Natl Acad Sci U S A, 93, 12851-12855.
PDB code: 283d
  8915500 K.K.Singh, P.Schluff, L.Lehnert, and G.Krupp (1996).
Design of hammerhead ribozymes to distinguish single base changes in substrate RNA.
  Antisense Nucleic Acid Drug Dev, 6, 165-168.  
8639602 M.A.Fountain, M.J.Serra, T.R.Krugh, and D.H.Turner (1996).
Structural features of a six-nucleotide RNA hairpin loop found in ribosomal RNA.
  Biochemistry, 35, 6539-6548.  
8548450 M.C.Wahl, S.T.Rao, and M.Sundaralingam (1996).
The structure of r(UUCGCG) has a 5'-UU-overhang exhibiting Hoogsteen-like trans U.U base pairs.
  Nat Struct Biol, 3, 24-31.
PDB code: 1osu
8692701 M.Grüne, J.P.Fürste, S.Klussmann, V.A.Erdmann, and L.R.Brown (1996).
Detection of multiple conformations of the E-domain of 5S rRNA from Escherichia coli in solution and in crystals by NMR spectroscopy.
  Nucleic Acids Res, 24, 2592-2596.  
8942631 M.Menger, T.Tuschl, F.Eckstein, and D.Porschke (1996).
Mg(2+)-dependent conformational changes in the hammerhead ribozyme.
  Biochemistry, 35, 14710-14716.  
8842234 P.Auffinger, and E.Westhof (1996).
H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations.
  Biophys J, 71, 940-954.  
8758995 P.Hendry, and M.McCall (1996).
Unexpected anisotropy in substrate cleavage rates by asymmetric hammerhead ribozymes.
  Nucleic Acids Res, 24, 2679-2684.  
8804834 P.J.Hagerman, and K.M.Amiri (1996).
Hammering away at RNA global structure.
  Curr Opin Struct Biol, 6, 317-321.  
8611518 R.G.Kuimelis, and L.W.McLaughlin (1996).
Ribozyme-mediated cleavage of a substrate analogue containing an internucleotide-bridging 5'-phosphorothioate: evidence for the single-metal model.
  Biochemistry, 35, 5308-5317.  
8768905 R.R.Breaker (1996).
Are engineered proteins getting competition from RNA?
  Curr Opin Biotechnol, 7, 442-448.  
8639595 S.Bevers, G.Xiang, and L.W.McLaughlin (1996).
Importance of specific adenosine N3-nitrogens for efficient cleavage by a hammerhead ribozyme.
  Biochemistry, 35, 6483-6490.  
8807843 S.Portmann, S.Grimm, C.Workman, N.Usman, and M.Egli (1996).
Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage.
  Chem Biol, 3, 173-184.
PDB codes: 247d 248d
8939747 S.Price, and K.Nagai (1996).
Secrets of RNA folding revealed.
  Structure, 4, 1129-1132.  
8604296 S.Schmidt, L.Beigelman, A.Karpeisky, N.Usman, U.S.Sorensen, and M.J.Gait (1996).
Base and sugar requirements for RNA cleavage of essential nucleoside residues in internal loop B of the hairpin ribozyme: implications for secondary structure.
  Nucleic Acids Res, 24, 573-581.  
  8654379 T.Rastogi, T.L.Beattie, J.E.Olive, and R.A.Collins (1996).
A long-range pseudoknot is required for activity of the Neurospora VS ribozyme.
  EMBO J, 15, 2820-2825.  
8703955 Y.Komatsu, I.Kanzaki, and E.Ohtsuka (1996).
Enhanced folding of hairpin ribozymes with replaced domains.
  Biochemistry, 35, 9815-9820.  
8634244 Z.Cai, and I.Tinoco (1996).
Solution structure of loop A from the hairpin ribozyme from tobacco ringspot virus satellite.
  Biochemistry, 35, 6026-6036.  
9383468 B.E.Eaton, L.Gold, and D.A.Zichi (1995).
Let's get specific: the relationship between specificity and affinity.
  Chem Biol, 2, 633-638.  
9383473 C.R.Allerson, and G.L.Verdine (1995).
Synthesis and biochemical evaluation of RNA containing an intrahelical disulfide crosslink.
  Chem Biol, 2, 667-675.  
7592749 L.Beigelman, J.A.McSwiggen, K.G.Draper, C.Gonzalez, K.Jensen, A.M.Karpeisky, A.S.Modak, J.Matulic-Adamic, A.B.DiRenzo, and P.Haeberli (1995).
Chemical modification of hammerhead ribozymes. Catalytic activity and nuclease resistance.
  J Biol Chem, 270, 25702-25708.  
8901497 M.E.Harris, and N.R.Pace (1995).
Analysis of the tertiary structure of bacterial RNase P RNA.
  Mol Biol Rep, 22, 115-123.  
7552719 O.C.Uhlenbeck (1995).
Hammerhead: Part 2.
  Nat Struct Biol, 2, 610-614.  
8901505 W.D.Hardt, J.M.Warnecke, and R.K.Hartmann (1995).
Recent approaches to probe functional groups in ribonuclease P RNA by modification interference.
  Mol Biol Rep, 22, 161-169.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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