PDBsum entry 1mme

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Ribozyme PDB id
PDB id:
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)
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
09-Dec-95     Release date:   06-Feb-96    


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.
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

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20822574 A.R.Ferré-D'Amaré (2010).
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20935068 D.H.Burke, and S.S.Rhee (2010).
Assembly and activation of a kinase ribozyme.
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20581129 J.Ouellet, S.Melcher, A.Iqbal, Y.Ding, and D.M.Lilley (2010).
Structure of the three-way helical junction of the hepatitis C virus IRES element.
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18409029 B.Hatton, and D.Rickard (2008).
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18755052 D.M.Lilley (2008).
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18560149 F.Pavelcik, and B.Schneider (2008).
Building of RNA and DNA double helices into electron density.
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17998291 J.A.Nelson, and O.C.Uhlenbeck (2008).
Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis.
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18287565 J.A.Nelson, and O.C.Uhlenbeck (2008).
Hammerhead redux: does the new structure fit the old biochemical data?
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18755844 J.L.Boots, M.D.Canny, E.Azimi, and A.Pardi (2008).
Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme.
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18566509 M.P.Robertson, and W.G.Scott (2008).
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Structural principles from large RNAs.
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18658118 W.Rypniewski, D.A.Adamiak, J.Milecki, and R.W.Adamiak (2008).
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PDB codes: 3czw 3d0m
18802606 Y.Tanaka, and A.Ono (2008).
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17089350 E.Westhof (2007).
A tale in molecular recognition: the hammerhead ribozyme.
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Molecular dynamics simulations of RNA: an in silico single molecule approach.
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Morphing the minimal and full-length hammerhead ribozymes: implications for the cleavage mechanism.
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The 1.3 A resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): metal ion binding correlates with base unstacking and groove contraction.
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PDB codes: 2r1s 2r20
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Effects of the trinucleotide preceding the self-cleavage site on eggplant latent viroid hammerheads: differences in co- and post-transcriptional self-cleavage may explain the lack of trinucleotide AUC in most natural hammerheads.
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Viroids: an Ariadne's thread into the RNA labyrinth.
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Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site.
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MeRNA: a database of metal ion binding sites in RNA structures.
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16556935 L.Yen, M.Magnier, R.Weissleder, B.R.Stockwell, and R.C.Mulligan (2006).
Identification of inhibitors of ribozyme self-cleavage in mammalian cells via high-throughput screening of chemical libraries.
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Tertiary contacts distant from the active site prime a ribozyme for catalysis.
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Extraordinary rates of transition metal ion-mediated ribozyme catalysis.
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Turning inhibitors into activators: a hammerhead ribozyme controlled by a guanine quadruplex.
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RNA unrestrained molecular dynamics ensemble improves agreement with experimental NMR data compared to single static structure: a test case.
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16991176 R.Przybilski, and C.Hammann (2006).
The hammerhead ribozyme structure brought in line.
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16427014 R.Rashid, B.Liang, D.L.Baker, O.A.Youssef, Y.He, K.Phipps, R.M.Terns, M.P.Terns, and H.Li (2006).
Crystal structure of a Cbf5-Nop10-Gar1 complex and implications in RNA-guided pseudouridylation and dyskeratosis congenita.
  Mol Cell, 21, 249-260.
PDB code: 2ey4
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Comparison of mode analyses at different resolutions applied to nucleic acid systems.
  Biophys J, 89, 2939-2949.  
15659358 E.M.Osborne, J.E.Schaak, and V.J.Derose (2005).
Characterization of a native hammerhead ribozyme derived from schistosomes.
  RNA, 11, 187-196.  
16141058 H.F.Noller (2005).
RNA structure: reading the ribosome.
  Science, 309, 1508-1514.  
16138302 H.M.Al-Hashimi (2005).
Dynamics-based amplification of RNA function and its characterization by using NMR spectroscopy.
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15870731 J.A.Doudna, and J.R.Lorsch (2005).
Ribozyme catalysis: not different, just worse.
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15869397 K.F.Blount, and O.C.Uhlenbeck (2005).
The structure-function dilemma of the hammerhead ribozyme.
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15956979 M.J.Fedor, and J.R.Williamson (2005).
The catalytic diversity of RNAs.
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16100381 M.Xiao, T.Li, X.Yuan, Y.Shang, F.Wang, S.Chen, and Y.Zhang (2005).
A peripheral element assembles the compact core structure essential for group I intron self-splicing.
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Detection of RNA nucleobase metalation by NMR spectroscopy.
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15064361 A.P.Massey, and S.T.Sigurdsson (2004).
Chemical syntheses of inhibitory substrates of the RNA-RNA ligation reaction catalyzed by the hairpin ribozyme.
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Sindbis virus nucleocapsid assembly: RNA folding promotes capsid protein dimerization.
  RNA, 10, 128-138.  
14730013 D.M.Lilley (2004).
The Varkud satellite ribozyme.
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15100442 J.C.Penedo, T.J.Wilson, S.D.Jayasena, A.Khvorova, and D.M.Lilley (2004).
Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements.
  RNA, 10, 880-888.  
15588292 P.Hendry, M.J.McCall, T.S.Stewart, and T.J.Lockett (2004).
Redesigned and chemically-modified hammerhead ribozymes with improved activity and serum stability.
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Entropy-driven folding of an RNA helical junction: an isothermal titration calorimetric analysis of the hammerhead ribozyme.
  Biochemistry, 43, 5870-5881.  
15103128 S.B.Jang, K.Baeyens, M.S.Jeong, J.SantaLucia, D.Turner, and S.R.Holbrook (2004).
Structures of two RNA octamers containing tandem G.A base pairs.
  Acta Crystallogr D Biol Crystallogr, 60, 829-835.
PDB codes: 1sa9 1saq
14730024 T.A.Goody, S.E.Melcher, D.G.Norman, and D.M.Lilley (2004).
The kink-turn motif in RNA is dimorphic, and metal ion-dependent.
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14993665 T.Sunami, J.Kondo, I.Hirao, K.Watanabe, K.Miura, and A.Takénaka (2004).
Structures of d(GCGAAGC) and d(GCGAAAGC) (tetragonal form): a switching of partners of the sheared G.A pairs to form a functional G.AxA.G crossing.
  Acta Crystallogr D Biol Crystallogr, 60, 422-431.
PDB codes: 1ub8 1ue4
12881719 A.Khvorova, A.Lescoute, E.Westhof, and S.D.Jayasena (2003).
Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity.
  Nat Struct Biol, 10, 708-712.
PDB code: 1p66
12782785 B.Hoffmann, G.T.Mitchell, P.Gendron, F.Major, A.A.Andersen, R.A.Collins, and P.Legault (2003).
NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site.
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PDB code: 1ow9
12592009 C.C.Correll, and K.Swinger (2003).
Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution.
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PDB code: 1msy
12756325 C.D.Cilley, and J.R.Williamson (2003).
Structural mimicry in the phage phi21 N peptide-boxB RNA complex.
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PDB code: 1nyb
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Ribozymes--a snip too far?
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12697343 E.Puerta-Fernández, C.Romero-López, A.Barroso-delJesus, and A.Berzal-Herranz (2003).
Ribozymes: recent advances in the development of RNA tools.
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12952967 M.Cieslak, J.Szymanski, R.W.Adamiak, and C.S.Cierniewski (2003).
Structural rearrangements of the 10-23 DNAzyme to beta 3 integrin subunit mRNA induced by cations and their relations to the catalytic activity.
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14532128 M.De la Peña, S.Gago, and R.Flores (2003).
Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity.
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14623996 O.C.Uhlenbeck (2003).
Less isn't always more.
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14523924 O.Schiemann, J.Fritscher, N.Kisseleva, S.T.Sigurdsson, and T.F.Prisner (2003).
Structural investigation of a high-affinity MnII binding site in the hammerhead ribozyme by EPR spectroscopy and DFT calculations. Effects of neomycin B on metal-ion binding.
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12772587 Y.Tanaka (2003).
[Spectroscopic analyses of the interaction between hammerhead ribozymes and metal ions]
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12409449 A.Kertsburg, and G.A.Soukup (2002).
A versatile communication module for controlling RNA folding and catalysis.
  Nucleic Acids Res, 30, 4599-4606.  
12006498 D.A.Lafontaine, D.G.Norman, and D.M.Lilley (2002).
The global structure of the VS ribozyme.
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12136136 E.Ennifar, P.Carpentier, J.L.Ferrer, P.Walter, and P.Dumas (2002).
X-ray-induced debromination of nucleic acids at the Br K absorption edge and implications for MAD phasing.
  Acta Crystallogr D Biol Crystallogr, 58, 1262-1268.  
12110898 J.A.Doudna, and T.R.Cech (2002).
The chemical repertoire of natural ribozymes.
  Nature, 418, 222-228.  
11751899 J.Kurreck, B.Bieber, R.Jahnel, and V.A.Erdmann (2002).
Comparative study of DNA enzymes and ribozymes against the same full-length messenger RNA of the vanilloid receptor subtype I.
  J Biol Chem, 277, 7099-7107.  
12022888 K.F.Blount, and O.C.Uhlenbeck (2002).
Internal equilibrium of the hammerhead ribozyme is altered by the length of certain covalent cross-links.
  Biochemistry, 41, 6834-6841.  
12466547 M.Escaffre, J.C.Chottard, and S.Bombard (2002).
Rearrangement of a 1,3-trans-[Pt(NH3)2[(GXG)-N7G,N7G]] intrastrand cross-link into interstrand cross-links within RNA duplexes.
  Nucleic Acids Res, 30, 5222-5228.  
12177293 N.B.Leontis, J.Stombaugh, and E.Westhof (2002).
The non-Watson-Crick base pairs and their associated isostericity matrices.
  Nucleic Acids Res, 30, 3497-3531.  
11752346 P.S.Klosterman, M.Tamura, S.R.Holbrook, and S.E.Brenner (2002).
SCOR: a Structural Classification of RNA database.
  Nucleic Acids Res, 30, 392-394.  
12403463 P.T.Sekella, D.Rueda, and N.G.Walter (2002).
A biosensor for theophylline based on fluorescence detection of ligand-induced hammerhead ribozyme cleavage.
  RNA, 8, 1242-1252.  
12192010 Z.Zaborowska, J.P.Fürste, V.A.Erdmann, and J.Kurreck (2002).
Sequence requirements in the catalytic core of the "10-23" DNA enzyme.
  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).
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11250907 D.A.Lafontaine, D.G.Norman, and D.M.Lilley (2001).
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11214179 D.J.Williams, J.L.Boots, and K.B.Hall (2001).
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11441810 E.A.Doherty, and J.A.Doudna (2001).
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11173496 E.Ennifar, P.Walter, and P.Dumas (2001).
An efficient method for solving RNA structures: MAD phasing by replacing magnesium with zinc.
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11345432 J.L.O'Rear, S.Wang, A.L.Feig, L.Beigelman, O.C.Uhlenbeck, and D.Herschlag (2001).
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11389613 J.M.Diamond, D.H.Turner, and D.H.Mathews (2001).
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11286889 K.Juneau, E.Podell, D.J.Harrington, and T.R.Cech (2001).
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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).
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11531997 M.Hertweck, and M.W.Mueller (2001).
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11173467 M.Perbandt, M.Vallazza, C.Lippmann, C.Betzel, and V.A.Erdmann (2001).
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  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).
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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.
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11573091 T.K.Stage-Zimmermann, and O.C.Uhlenbeck (2001).
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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.
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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.
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PDB codes: 1i0f 1i0g 1i0j 1i0k 1i0m 1i0n 1i0o 1i0p 1i0q 1i0t
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PDB codes: 1i2x 1i2y
11685244 X.Yang, T.Gérczei, L.T.Glover, and C.C.Correll (2001).
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Probing the TRAP-RNA interaction with nucleoside analogs.
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10201848 M.Dunkel, and V.Reither (1999).
Synthesis of 2'-C-alpha-difluoromethylarauridine and its 3'-O-phosphoramidite incorporation into a hammerhead ribozyme.
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10445883 M.R.Hansen, J.P.Simorre, P.Hanson, V.Mokler, L.Bellon, L.Beigelman, and A.Pardi (1999).
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10334335 M.Sohail, S.Akhtar, and E.M.Southern (1999).
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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.
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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.
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PDB codes: 1d8x 1d9r 1dcr
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9417029 A.L.Feig, W.G.Scott, and O.C.Uhlenbeck (1998).
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A core folding model for catalysis by the hammerhead ribozyme accounts for its extraordinary sensitivity to abasic mutations.
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Sequence specificity of the hammerhead ribozyme revisited; the NHH rule.
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9701285 A.V.Kazantsev, and N.R.Pace (1998).
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New results using Laue diffraction and time-resolved crystallography.
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Crystal structure of the ribosomal RNA domain essential for binding elongation factors.
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Folding of branched RNA species.
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9759486 D.N.Frank, and N.R.Pace (1998).
Ribonuclease P: unity and diversity in a tRNA processing ribozyme.
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9461461 F.Seela, H.Debelak, N.Usman, A.Burgin, and L.Beigelman (1998).
1-Deazaadenosine: synthesis and activity of base-modified hammerhead ribozymes.
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Crystallographic structures of the hammerhead ribozyme: relationship to ribozyme folding and catalysis.
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9722650 M.Gerstein, and W.Krebs (1998).
A database of macromolecular motions.
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NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif.
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An essential non-Watson-Crick base pair motif in 3'UTR to mediate selenoprotein translation.
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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.
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Crystal structures of nucleic acids and their drug complexes.
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On the role of magnesium ions in RNA stability.
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RNA catalysis.
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Ribozyme-mediated cancer gene therapy.
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Ribozyme therapeutics.
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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.  
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