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PDBsum entry 1hmh
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Ribozyme PDB id
1hmh

 

 

 

 

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Contents
DNA/RNA
PDB id:
1hmh
Name: Ribozyme
Title: Three-dimensional structure of a hammerhead ribozyme
Structure: Hammerhead ribozyme-RNA strand. Chain: a, c, e. Engineered: yes. Hammerhead ribozyme-DNA strand. Chain: b, d, f. Engineered: yes
Source: not given
Biol. unit: Dimer (from PQS)
Resolution:
2.60Å     R-factor:   0.257     R-free:   0.305
Authors: H.W.Pley,K.M.Flaherty,D.B.Mckay
Key ref: H.W.Pley et al. (1994). Three-dimensional structure of a hammerhead ribozyme. Nature, 372, 68-74. PubMed id: 7969422
Date:
06-Jun-95     Release date:   07-Dec-95    
 Headers
 References

DNA/RNA chains
  G-G-C-G-A-C-C-C-U-G-A-U-G-A-G-G-C-C-G-A-A-A-G-G-C-C-G-A-A-A-C-C-G-U 34 bases
  A-C-G-G-T-C-G-G-T-C-G-C-C 13 bases
  G-G-C-G-A-C-C-C-U-G-A-U-G-A-G-G-C-C-G-A-A-A-G-G-C-C-G-A-A-A-C-C-G-U 34 bases
  A-C-G-G-T-C-G-G-T-C-G-C-C 13 bases
  G-G-C-G-A-C-C-C-U-G-A-U-G-A-G-G-C-C-G-A-A-A-G-G-C-C-G-A-A-A-C-C-G-U 34 bases
  A-C-G-G-T-C-G-G-T-C-G-C-C 13 bases

 

 
Nature 372:68-74 (1994)
PubMed id: 7969422  
 
 
Three-dimensional structure of a hammerhead ribozyme.
H.W.Pley, K.M.Flaherty, D.B.McKay.
 
  ABSTRACT  
 
The hammerhead ribozyme is a small catalytic RNA motif made up of three base-paired stems and a core of highly conserved, non-complementary nucleotides essential for catalysis. The X-ray crystallographic structure of a hammerhead RNA-DNA ribozyme-inhibitor complex at 2.6 A resolution reveals that the base-paired stems are A-form helices and that the core has two structural domains. The first domain is formed by the sequence 5'-CUGA following stem I and is a sharp turn identical to the uridine turn of transfer RNA, whereas the second is a non-Watson-Crick three-base-pair duplex with a divalent-ion binding site. The phosphodiester backbone of the DNA inhibitor strand is splayed out at the phosphate 5' to the cleavage site. The structure indicates that the ribozyme may destabilize a substrate strand in order to facilitate twisting of the substrate to allow cleavage of the scissile bond.
 

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).
Functional complexity and regulation through RNA dynamics.
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21133351 B.Liu, J.M.Diamond, D.H.Mathews, and D.H.Turner (2011).
Fluorescence competition and optical melting measurements of RNA three-way multibranch loops provide a revised model for thermodynamic parameters.
  Biochemistry, 50, 640-653.  
21428954 D.M.Lilley (2011).
Catalysis by the nucleolytic ribozymes.
  Biochem Soc Trans, 39, 641-646.  
21169337 S.Blouin, R.Chinnappan, and D.A.Lafontaine (2011).
Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation.
  Nucleic Acids Res, 39, 3373-3387.  
20713730 A.H.El-Sagheer, and T.Brown (2010).
New strategy for the synthesis of chemically modified RNA constructs exemplified by hairpin and hammerhead ribozymes.
  Proc Natl Acad Sci U S A, 107, 15329-15334.  
20822574 A.R.Ferré-D'Amaré (2010).
The glmS ribozyme: use of a small molecule coenzyme by a gene-regulatory RNA.
  Q Rev Biophys, 43, 423-447.  
20935068 D.H.Burke, and S.S.Rhee (2010).
Assembly and activation of a kinase ribozyme.
  RNA, 16, 2349-2359.  
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.
  RNA, 16, 1597-1609.  
20204525 M.Giel-Pietraszuk, A.Fedoruk-Wyszomirska, and J.Barciszewski (2010).
Effect of high hydrostatic pressure on hydration and activity of ribozymes.
  Mol Biol Rep, 37, 3713-3719.  
20675355 Y.Nomura, S.Sugiyama, T.Sakamoto, S.Miyakawa, H.Adachi, K.Takano, S.Murakami, T.Inoue, Y.Mori, Y.Nakamura, and H.Matsumura (2010).
Conformational plasticity of RNA for target recognition as revealed by the 2.15 A crystal structure of a human IgG-aptamer complex.
  Nucleic Acids Res, 38, 7822-7829.
PDB code: 3agv
19879179 A.C.Rios, and Y.Tor (2009).
Model systems: how chemical biologists study RNA.
  Curr Opin Chem Biol, 13, 660-668.  
19638248 A.Rich (2009).
The era of RNA awakening: structural biology of RNA in the early years.
  Q Rev Biophys, 42, 117-137.  
19718544 C.Reymond, J.D.Beaudoin, and J.P.Perreault (2009).
Modulating RNA structure and catalysis: lessons from small cleaving ribozymes.
  Cell Mol Life Sci, 66, 3937-3950.  
20090924 I.Yildirim, H.A.Stern, J.Sponer, N.Spackova, and D.H.Turner (2009).
Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs.
  J Chem Theory Comput, 5, 2088-2100.  
19186984 J.L.Fiore, B.Kraemer, F.Koberling, R.Edmann, and D.J.Nesbitt (2009).
Enthalpy-driven RNA folding: single-molecule thermodynamics of tetraloop-receptor tertiary interaction.
  Biochemistry, 48, 2550-2558.  
19416070 M.J.Fedor (2009).
Comparative enzymology and structural biology of RNA self-cleavage.
  Annu Rev Biophys, 38, 271-299.  
19398008 P.Banás, P.Jurecka, N.G.Walter, J.Sponer, and M.Otyepka (2009).
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.
  Methods, 49, 202-216.  
19294348 Q.Wu, L.Huang, and Y.Zhang (2009).
The structure and function of catalytic RNAs.
  Sci China C Life Sci, 52, 232-244.  
20183593 W.Wang, J.Zhao, Q.Han, G.Wang, G.Yang, A.J.Shallop, J.Liu, B.L.Gaffney, and R.A.Jones (2009).
Modulation of RNA metal binding by flanking bases: 15N NMR evaluation of GC, tandem GU, and tandem GA sites.
  Nucleosides Nucleotides Nucleic Acids, 28, 424-434.  
18636557 A.Vourekas, V.Stamatopoulou, C.Toumpeki, M.Tsitlaidou, and D.Drainas (2008).
Insights into functional modulation of catalytic RNA activity.
  IUBMB Life, 60, 669-683.  
18755052 D.M.Lilley (2008).
Analysis of branched nucleic acid structure using comparative gel electrophoresis.
  Q Rev Biophys, 41, 1.  
17998291 J.A.Nelson, and O.C.Uhlenbeck (2008).
Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis.
  RNA, 14, 43-54.  
18287565 J.A.Nelson, and O.C.Uhlenbeck (2008).
Hammerhead redux: does the new structure fit the old biochemical data?
  RNA, 14, 605-615.  
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.
  RNA, 14, 2212-2222.  
18621836 J.L.Fiore, J.H.Hodak, O.Piestert, C.D.Downey, and D.J.Nesbitt (2008).
Monovalent and divalent promoted GAAA tetraloop-receptor tertiary interactions from freely diffusing single-molecule studies.
  Biophys J, 95, 3892-3905.  
18420140 M.Martick, T.S.Lee, D.M.York, and W.G.Scott (2008).
Solvent structure and hammerhead ribozyme catalysis.
  Chem Biol, 15, 332-342.
PDB code: 2oeu
18322526 M.Parisien, and F.Major (2008).
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data.
  Nature, 452, 51-55.  
18973652 T.Jorg, O.C.Martin, and A.Wagner (2008).
Neutral network sizes of biological RNA molecules can be computed and are not atypically small.
  BMC Bioinformatics, 9, 464.  
18802606 Y.Tanaka, and A.Ono (2008).
Nitrogen-15 NMR spectroscopy of N-metallated nucleic acids: insights into 15N NMR parameters and N-metal bonds.
  Dalton Trans, (), 4965-4974.  
18707751 Y.Zhao, J.L.Knee, and A.M.Baranger (2008).
Characterization of two adenosine analogs as fluorescence probes in RNA.
  Bioorg Chem, 36, 271-277.  
17806104 C.G.Hoogstraten, and M.Sumita (2007).
Structure-function relationships in RNA and RNP enzymes: recent advances.
  Biopolymers, 87, 317-328.  
17913750 D.J.Patel, A.T.Phan, and V.Kuryavyi (2007).
Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics.
  Nucleic Acids Res, 35, 7429-7455.  
17089350 E.Westhof (2007).
A tale in molecular recognition: the hammerhead ribozyme.
  J Mol Recognit, 20, 1-3.  
17688253 G.Todd, and K.Karbstein (2007).
RNA takes center stage.
  Biopolymers, 87, 275-278.  
17505105 J.Kondo, T.Sunami, and A.Takénaka (2007).
The structure of a d(gcGAACgc) duplex containing two consecutive bulged A residues in both strands suggests a molecular switch.
  Acta Crystallogr D Biol Crystallogr, 63, 673-681.
PDB code: 2got
17337436 J.Sefcikova, M.V.Krasovska, J.Sponer, and N.G.Walter (2007).
The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis.
  Nucleic Acids Res, 35, 1933-1946.  
17616553 K.J.Travers, N.Boyd, and D.Herschlag (2007).
Low specificity of metal ion binding in the metal ion core of a folded RNA.
  RNA, 13, 1205-1213.  
17363667 M.P.Robertson, and W.G.Scott (2007).
The structural basis of ribozyme-catalyzed RNA assembly.
  Science, 315, 1549-1553.
PDB code: 2oiu
17456566 M.Roychowdhury-Saha, and D.H.Burke (2007).
Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme.
  RNA, 13, 841-848.  
19404418 N.Kisseleva, S.Kraut, A.Jäschke, and O.Schiemann (2007).
Characterizing multiple metal ion binding sites within a ribozyme by cadmium-induced EPR silencing.
  HFSP J, 1, 127-136.  
17507661 R.Tyagi, and D.H.Mathews (2007).
Predicting helical coaxial stacking in RNA multibranch loops.
  RNA, 13, 939-951.  
17718616 T.Ikeda, M.Boero, and K.Terakura (2007).
Hydration properties of magnesium and calcium ions from constrained first principles molecular dynamics.
  J Chem Phys, 127, 074503.  
17570825 W.G.Scott (2007).
Morphing the minimal and full-length hammerhead ribozymes: implications for the cleavage mechanism.
  Biol Chem, 388, 727-735.  
17572081 W.G.Scott (2007).
Ribozymes.
  Curr Opin Struct Biol, 17, 280-286.  
17028097 A.Carbonell, M.De la Peña, R.Flores, and S.Gago (2006).
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.
  Nucleic Acids Res, 34, 5613-5622.  
16373494 A.Lescoute, and E.Westhof (2006).
Topology of three-way junctions in folded RNAs.
  RNA, 12, 83-93.  
16525552 B.Knobloch, H.Sigel, A.Okruszek, and R.K.Sigel (2006).
Acid-base properties of the nucleic-acid model 2'-deoxyguanylyl(5'-->3')-2'-deoxy-5'-guanylate, d(pGpG)3-, and of related guanine derivatives.
  Org Biomol Chem, 4, 1085-1090.  
16531589 C.Hsiao, S.Mohan, E.Hershkovitz, A.Tannenbaum, and L.D.Williams (2006).
Single nucleotide RNA choreography.
  Nucleic Acids Res, 34, 1481-1491.  
16741503 J.A.Daròs, S.F.Elena, and R.Flores (2006).
Viroids: an Ariadne's thread into the RNA labyrinth.
  EMBO Rep, 7, 593-598.  
16937241 J.E.Johnson, K.R.Julien, and C.G.Hoogstraten (2006).
Alternate-site isotopic labeling of ribonucleotides for NMR studies of ribose conformational dynamics in RNA.
  J Biomol NMR, 35, 261-274.  
16452297 J.Kondo, A.Urzhumtsev, and E.Westhof (2006).
Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site.
  Nucleic Acids Res, 34, 676-685.
PDB code: 2fqn
16462950 J.P.García-Terán, O.Castillo, A.Luque, U.García-Couceiro, G.Beobide, and P.Román (2006).
Supramolecular architectures assembled by the interaction of purine nucleobases with metal-oxalato frameworks. Non-covalent stabilization of the 7H-adenine tautomer in the solid-state.
  Dalton Trans, (), 902-911.  
16381830 L.R.Stefan, R.Zhang, A.G.Levitan, D.K.Hendrix, S.E.Brenner, and S.R.Holbrook (2006).
MeRNA: a database of metal ion binding sites in RNA structures.
  Nucleic Acids Res, 34, D131-D134.  
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.
  RNA, 12, 797-806.  
16859740 M.Martick, and W.G.Scott (2006).
Tertiary contacts distant from the active site prime a ribozyme for catalysis.
  Cell, 126, 309-320.
PDB codes: 2goz 3zd5
16912216 M.Roychowdhury-Saha, and D.H.Burke (2006).
Extraordinary rates of transition metal ion-mediated ribozyme catalysis.
  RNA, 12, 1846-1852.  
16871639 M.Wieland, and J.S.Hartig (2006).
Turning inhibitors into activators: a hammerhead ribozyme controlled by a guanine quadruplex.
  Angew Chem Int Ed Engl, 45, 5875-5878.  
16894219 O.H.Gumbs, R.A.Padgett, and K.T.Dayie (2006).
Fluorescence and solution NMR study of the active site of a 160-kDa group II intron ribozyme.
  RNA, 12, 1693-1707.  
17006738 R.A.Beckman, D.Moreland, S.Louise-May, and C.Humblet (2006).
RNA unrestrained molecular dynamics ensemble improves agreement with experimental NMR data compared to single static structure: a test case.
  J Comput Aided Mol Des, 20, 263-279.  
16991176 R.Przybilski, and C.Hammann (2006).
The hammerhead ribozyme structure brought in line.
  Chembiochem, 7, 1641-1644.  
16675665 S.Thore, M.Leibundgut, and N.Ban (2006).
Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand.
  Science, 312, 1208-1211.
PDB code: 2cky
16963495 T.Ogawa, S.Inoue, S.Yajima, M.Hidaka, and H.Masaki (2006).
Sequence-specific recognition of colicin E5, a tRNA-targeting ribonuclease.
  Nucleic Acids Res, 34, 6065-6073.  
16272439 W.Zhang, and S.J.Chen (2006).
Exploring the complex folding kinetics of RNA hairpins: II. Effect of sequence, length, and misfolded states.
  Biophys J, 90, 778-787.  
15723077 A.Serganov, S.Keiper, L.Malinina, V.Tereshko, E.Skripkin, C.Höbartner, A.Polonskaia, A.T.Phan, R.Wombacher, R.Micura, Z.Dauter, A.Jäschke, and D.J.Patel (2005).
Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation.
  Nat Struct Mol Biol, 12, 218-224.
PDB codes: 1ykq 1ykv 1yls
16100266 A.W.Van Wynsberghe, and Q.Cui (2005).
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.
  Chembiochem, 6, 1506-1519.  
15870731 J.A.Doudna, and J.R.Lorsch (2005).
Ribozyme catalysis: not different, just worse.
  Nat Struct Mol Biol, 12, 395-402.  
16024731 J.H.Hodak, C.D.Downey, J.L.Fiore, A.Pardi, and D.J.Nesbitt (2005).
Docking kinetics and equilibrium of a GAAA tetraloop-receptor motif probed by single-molecule FRET.
  Proc Natl Acad Sci U S A, 102, 10505-10510.  
15869397 K.F.Blount, and O.C.Uhlenbeck (2005).
The structure-function dilemma of the hammerhead ribozyme.
  Annu Rev Biophys Biomol Struct, 34, 415-440.  
17191972 M.Gallo, R.Kretschmer-Kazemi Far, G.Sczakiel, and A.M.Iribarren (2005).
Activity and stability of hammerhead ribozymes containing 2'-C-methyluridine: a new RNA mimic.
  Chem Biodivers, 2, 198-204.  
15956979 M.J.Fedor, and J.R.Williamson (2005).
The catalytic diversity of RNAs.
  Nat Rev Mol Cell Biol, 6, 399-412.  
15611296 N.Kisseleva, A.Khvorova, E.Westhof, and O.Schiemann (2005).
Binding of manganese(II) to a tertiary stabilized hammerhead ribozyme as studied by electron paramagnetic resonance spectroscopy.
  RNA, 11, 1-6.  
15846405 Y.Tanaka, and K.Taira (2005).
Detection of RNA nucleobase metalation by NMR spectroscopy.
  Chem Commun (Camb), (), 2069-2079.  
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.
  Nucleic Acids Res, 32, 2017-2022.  
14681591 B.R.Linger, L.Kunovska, R.J.Kuhn, and B.L.Golden (2004).
Sindbis virus nucleocapsid assembly: RNA folding promotes capsid protein dimerization.
  RNA, 10, 128-138.  
14730013 D.M.Lilley (2004).
The Varkud satellite ribozyme.
  RNA, 10, 151-158.  
14691945 D.R.Hodgson, and H.Suga (2004).
Mechanistic studies on acyl-transferase ribozymes and beyond.
  Biopolymers, 73, 130-150.  
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.
  BMC Chem Biol, 4, 1.  
15134461 P.J.Mikulecky, J.C.Takach, and A.L.Feig (2004).
Entropy-driven folding of an RNA helical junction: an isothermal titration calorimetric analysis of the hammerhead ribozyme.
  Biochemistry, 43, 5870-5881.  
15121895 P.S.Klosterman, D.K.Hendrix, M.Tamura, S.R.Holbrook, and S.E.Brenner (2004).
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns.
  Nucleic Acids Res, 32, 2342-2352.  
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.
  RNA, 10, 254-264.  
14744982 T.M.Coleman, G.Wang, and F.Huang (2004).
Superior 5' homogeneity of RNA from ATP-initiated transcription under the T7 phi 2.5 promoter.
  Nucleic Acids Res, 32, e14.  
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
12756321 A.S.Krasilnikov, and A.Mondragón (2003).
On the occurrence of the T-loop RNA folding motif in large RNA molecules.
  RNA, 9, 640-643.  
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.
  Proc Natl Acad Sci U S A, 100, 7003-7008.
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.
  RNA, 9, 355-363.
PDB code: 1msy
12756325 C.D.Cilley, and J.R.Williamson (2003).
Structural mimicry in the phage phi21 N peptide-boxB RNA complex.
  RNA, 9, 663-676.
PDB code: 1nyb
12604517 C.Parolin, B.Gatto, C.Del Vecchio, T.Pecere, E.Tramontano, V.Cecchetti, A.Fravolini, S.Masiero, M.Palumbo, and G.Palù (2003).
New anti-human immunodeficiency virus type 1 6-aminoquinolones: mechanism of action.
  Antimicrob Agents Chemother, 47, 889-896.  
12942136 D.M.Lilley (2003).
Ribozymes--a snip too far?
  Nat Struct Biol, 10, 672-673.  
12736309 E.J.Borda, J.C.Markley, and S.T.Sigurdsson (2003).
Zinc-dependent cleavage in the catalytic core of the hammerhead ribozyme: evidence for a pH-dependent conformational change.
  Nucleic Acids Res, 31, 2595-2600.  
12697343 E.Puerta-Fernández, C.Romero-López, A.Barroso-delJesus, and A.Berzal-Herranz (2003).
Ribozymes: recent advances in the development of RNA tools.
  FEMS Microbiol Rev, 27, 75-97.  
14610908 F.F.Poordad, T.Tran, and P.Martin (2003).
Developments in hepatitis C therapy during 2000-2002.
  Expert Opin Emerg Drugs, 8, 9.  
12829496 G.Villescas-Diaz, and M.Zacharias (2003).
Sequence context dependence of tandem guanine:adenine mismatch conformations in RNA: a continuum solvent analysis.
  Biophys J, 85, 416-425.  
12824344 H.Yang, F.Jossinet, N.Leontis, L.Chen, J.Westbrook, H.Berman, and E.Westhof (2003).
Tools for the automatic identification and classification of RNA base pairs.
  Nucleic Acids Res, 31, 3450-3460.  
12777762 J.Deng, Y.Xiong, B.Pan, and M.Sundaralingam (2003).
Structure of an RNA dodecamer containing a fragment from SRP domain IV of Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 59, 1004-1011.
PDB code: 1lnt
14645041 J.Sarzynska, L.Nilsson, and T.Kulinski (2003).
Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations.
  Biophys J, 85, 3445-3459.  
14517358 K.Chandrasekhar, and R.Malathhi (2003).
Non-Watson Crick base pairs might stabilize RNA structural motifs in ribozymes -- a comparative study of group-I intron structures.
  J Biosci, 28, 547-555.  
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.
  J Biol Chem, 278, 47987-47996.  
14532128 M.De la Peña, S.Gago, and R.Flores (2003).
Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity.
  EMBO J, 22, 5561-5570.  
12831880 N.B.Leontis, and E.Westhof (2003).
Analysis of RNA motifs.
  Curr Opin Struct Biol, 13, 300-308.  
14623996 O.C.Uhlenbeck (2003).
Less isn't always more.
  RNA, 9, 1415-1417.  
14523924 O.Schiemann, J.Fritscher, N.Kisseleva, S.T.Sigurdsson, and T.F.Prisner (2003).
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12772587 Y.Tanaka (2003).
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New modalities in oncology: ribozymes.
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The global structure of the VS ribozyme.
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12384614 D.Ferrari, and A.Peracchi (2002).
A continuous kinetic assay for RNA-cleaving deoxyribozymes, exploiting ethidium bromide as an extrinsic fluorescent probe.
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12444967 F.Nishikawa, M.Shirai, and S.Nishikawa (2002).
Site-specific modification of functional groups in genomic hepatitis delta virus (HDV) ribozyme.
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11867514 G.J.Farrar, P.F.Kenna, and P.Humphries (2002).
On the genetics of retinitis pigmentosa and on mutation-independent approaches to therapeutic intervention.
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11929999 H.D.Kim, G.U.Nienhaus, T.Ha, J.W.Orr, J.R.Williamson, and S.Chu (2002).
Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules.
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12087167 I.Amarantos, I.K.Zarkadis, and D.L.Kalpaxis (2002).
The identification of spermine binding sites in 16S rRNA allows interpretation of the spermine effect on ribosomal 30S subunit functions.
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12110898 J.A.Doudna, and T.R.Cech (2002).
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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.
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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.
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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.
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12198171 S.L.Hiley, V.D.Sood, J.Fan, and R.A.Collins (2002).
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12119023 Y.Komatsu, K.Nobuoka, N.Karino-Abe, A.Matsuda, and E.Ohtsuka (2002).
In vitro selection of hairpin ribozymes activated with short oligonucleotides.
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11170470 C.Hammann, A.Cooper, and D.M.Lilley (2001).
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11331743 C.Hammann, D.G.Norman, and D.M.Lilley (2001).
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11214174 D.J.Battle, and J.A.Doudna (2001).
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11441810 E.A.Doherty, and J.A.Doudna (2001).
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11345431 G.A.Soukup, E.C.DeRose, M.Koizumi, and R.R.Breaker (2001).
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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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11296237 J.Swisher, C.M.Duarte, L.J.Su, and A.M.Pyle (2001).
Visualizing the solvent-inaccessible core of a group II intron ribozyme.
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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).
Chemical and enzymatic synthesis of tRNAs for high-throughput crystallization.
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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).
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).
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11170437 N.L.Greenbaum, C.Mundoma, and D.R.Peterman (2001).
Probing of metal-binding domains of RNA hairpin loops by laser-induced lanthanide(III) luminescence.
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  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.
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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.
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PDB codes: 1i2x 1i2y
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.
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10882132 A.A.Andersen, and R.A.Collins (2000).
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10933815 C.G.Hoogstraten, J.R.Wank, and A.Pardi (2000).
Active site dynamics in the lead-dependent ribozyme.
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11142372 D.Drygin, and R.A.Zimmermann (2000).
Magnesium ions mediate contacts between phosphoryl oxygens at positions 2122 and 2176 of the 23S rRNA and ribosomal protein L1.
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10828955 D.J.Earnshaw, M.L.Hamm, J.A.Piccirilli, A.Karpeisky, L.Beigelman, B.S.Ross, M.Manoharan, and M.J.Gait (2000).
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11006537 D.M.Lilley, and T.J.Wilson (2000).
Fluorescence resonance energy transfer as a structural tool for nucleic acids.
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10966470 E.A.Doherty, and J.A.Doudna (2000).
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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.
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PDB code: 1g2j
10736151 G.Minasov, M.Teplova, P.Nielsen, J.Wengel, and M.Egli (2000).
Structural basis of cleavage by RNase H of hybrids of arabinonucleic acids and RNA.
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PDB code: 1ei4
11060723 H.A.James (2000).
Therapeutic potential of ribozymes in haematological disorders.
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10943889 H.Shi, and P.B.Moore (2000).
The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited.
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PDB code: 1ehz
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
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Comparative sequence analysis and patterns of covariation in RNA secondary structures.
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10968986 J.Sarzynska, T.Kulinski, and L.Nilsson (2000).
Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge.
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  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.
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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.
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PDB code: 1duh
10704214 M.A.Engelhardt, E.A.Doherty, D.S.Knitt, J.A.Doudna, and D.Herschlag (2000).
The P5abc peripheral element facilitates preorganization of the tetrahymena group I ribozyme for catalysis.
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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.
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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.
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11071929 M.Menger, F.Eckstein, and D.Porschke (2000).
Multiple conformational states of the hammerhead ribozyme, broad time range of relaxation and topology of dynamics.
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10785397 M.Nashimoto (2000).
Correct folding of a ribozyme induced by nonspecific macromolecules.
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10985772 N.Sugimoto, M.Nakano, and S.Nakano (2000).
Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes.
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10694382 S.E.Butcher, F.H.Allain, and J.Feigon (2000).
Determination of metal ion binding sites within the hairpin ribozyme domains by NMR.
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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.
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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.
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10786851 T.Dale, R.Smith, and M.J.Serra (2000).
A test of the model to predict unusually stable RNA hairpin loop stability.
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10985786 T.E.Horton, and V.J.DeRose (2000).
Cobalt hexammine inhibition of the hammerhead ribozyme.
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10744992 T.Franch, and K.Gerdes (2000).
U-turns and regulatory RNAs.
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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.
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10773088 Y.Xiong, and M.Sundaralingam (2000).
Crystal structure of a DNA.RNA hybrid duplex with a polypurine RNA r(gaagaagag) and a complementary polypyrimidine DNA d(CTCTTCTTC).
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PDB code: 479d
10393536 A.Loria, and T.Pan (1999).
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10410795 A.R.Ferré-D'Amaré, and J.A.Doudna (1999).
RNA folds: insights from recent crystal structures.
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10021931 B.Llano-Sotelo, and C.S.Chow (1999).
RNA-aminoglycoside antibiotic interactions: fluorescence detection of binding and conformational change.
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10385001 C.Bravo, A.Woisard, J.L.Fourrey, P.Laugâa, and A.Favre (1999).
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10361084 D.M.Lilley (1999).
Structure, folding and catalysis of the small nucleolytic ribozymes.
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10449422 D.Scarabino, A.Crisari, S.Lorenzini, K.Williams, and G.P.Tocchini-Valentini (1999).
tRNA prefers to kiss.
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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.
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11169382 F.Eckstein, and B.Bramlage (1999).
The hammerhead ribozyme.
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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.  
10024177 J.A.Holland, M.R.Hansen, Z.Du, and D.W.Hoffman (1999).
An examination of coaxial stacking of helical stems in a pseudoknot motif: the gene 32 messenger RNA pseudoknot of bacteriophage T2.
  RNA, 5, 257-271.
PDB code: 2tpk
10089439 J.C.Nix, A.R.Newhoff, and C.Wilson (1999).
Preliminary crystallographic characterization of an in vitro evolved biotin-binding RNA pseudoknot.
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10021422 J.J.Rossi (1999).
Ribozymes, genomics and therapeutics.
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10573125 K.K.Singh, R.Parwaresch, and G.Krupp (1999).
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  RNA, 5, 1348-1356.  
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.  
10872451 P.B.Moore (1999).
Structural motifs in RNA.
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10580471 P.Babin, M.Dolan, P.Wollenzien, and R.R.Gutell (1999).
Identity and geometry of a base triple in 16S rRNA determined by comparative sequence analysis and molecular modeling.
  RNA, 5, 1430-1439.  
10737860 P.J.Beuning, and K.Musier-Forsyth (1999).
Transfer RNA recognition by aminoacyl-tRNA synthetases.
  Biopolymers, 52, 1.  
  10355818 R.Levitz, Y.Dong, J.Y.Wang, S.W.Jeng, C.R.Chen, J.W.Wang, X.Zhao, J.Zhou, T.Lu, and K.Drlica (1999).
Cytotoxic hammerhead ribozymes.
  Antisense Nucleic Acid Drug Dev, 9, 117-123.  
10580468 S.Basu, and S.A.Strobel (1999).
Thiophilic metal ion rescue of phosphorothioate interference within the Tetrahymena ribozyme P4-P6 domain.
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10393544 S.K.Silverman, and T.R.Cech (1999).
Energetics and cooperativity of tertiary hydrogen bonds in RNA structure.
  Biochemistry, 38, 8691-8702.  
10199567 S.S.Ashraf, G.Ansari, R.Guenther, E.Sochacka, A.Malkiewicz, and P.F.Agris (1999).
The uridine in "U-turn": contributions to tRNA-ribosomal binding.
  RNA, 5, 503-511.  
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.  
  9630244 A.Ioudovitch, and S.V.Steinberg (1998).
Modeling the tertiary interactions in the eukaryotic selenocysteine tRNA.
  RNA, 4, 365-373.  
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.
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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.
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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.  
9818266 B.L.Stoddard (1998).
New results using Laue diffraction and time-resolved crystallography.
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Visualizing metal-ion-binding sites in group I introns by iron(II)-mediated Fenton reactions.
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Crystal structure of the ribosomal RNA domain essential for binding elongation factors.
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PDB code: 430d
11180044 D.M.Lilley (1998).
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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9551555 D.R.Tomchick, R.J.Turner, R.L.Switzer, and J.L.Smith (1998).
Adaptation of an enzyme to regulatory function: structure of Bacillus subtilis PyrR, a pyr RNA-binding attenuation protein and uracil phosphoribosyltransferase.
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PDB codes: 1a3c 1a4x
9666322 G.L.Conn, and D.E.Draper (1998).
RNA structure.
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Possible involvement of Escherichia coli 23S ribosomal RNA in peptide bond formation.
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9663384 J.A.Doudna (1998).
Ribozymes: the hammerhead swings into action.
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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.
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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.
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PDB code: 379d
9646875 J.E.Wedekind, and D.B.McKay (1998).
Crystallographic structures of the hammerhead ribozyme: relationship to ribozyme folding and catalysis.
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9724958 J.J.Rossi (1998).
Ribozymes to the rescue: repairing genetically defective mRNAs.
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9503589 J.Kjems, and J.Egebjerg (1998).
Modern methods for probing RNA structure.
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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.
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9685477 J.P.Rife, C.S.Cheng, P.B.Moore, and S.A.Strobel (1998).
N 2-methylguanosine is iso-energetic with guanosine in RNA duplexes and GNRA tetraloops.
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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.  
9586987 M.A.Weiss (1998).
RNA-mediated signaling in transcription.
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10333744 M.A.Weiss, and N.Narayana (1998).
RNA recognition by arginine-rich peptide motifs.
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9649622 M.Araki, Y.Okuno, Y.Hara, and Y.Sugiura (1998).
Allosteric regulation of a ribozyme activity through ligand-induced conformational change.
  Nucleic Acids Res, 26, 3379-3384.  
9722650 M.Gerstein, and W.Krebs (1998).
A database of macromolecular motions.
  Nucleic Acids Res, 26, 4280-4290.  
9454601 M.R.Giese, K.Betschart, T.Dale, C.K.Riley, C.Rowan, K.J.Sprouse, and M.J.Serra (1998).
Stability of RNA hairpins closed by wobble base pairs.
  Biochemistry, 37, 1094-1100.  
9482855 N.K.Vaish, P.A.Heaton, O.Fedorova, and F.Eckstein (1998).
In vitro selection of a purine nucleotide-specific hammerheadlike ribozyme.
  Proc Natl Acad Sci U S A, 95, 2158-2162.  
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.  
9485366 P.Zheng, C.J.Burrows, and S.E.Rokita (1998).
Nickel- and cobalt-dependent reagents identify structural features of RNA that are not detected by dimethyl sulfate or RNase T1.
  Biochemistry, 37, 2207-2214.  
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.  
9493396 S.Neidle, and C.M.Nunn (1998).
Crystal structures of nucleic acids and their drug complexes.
  Nat Prod Rep, 15, 1.  
9759484 S.Verma, and F.Eckstein (1998).
Modified oligonucleotides: synthesis and strategy for users.
  Annu Rev Biochem, 67, 99.  
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.  
9724510 U.Mueller, G.Maier, A.Mochi Onori, L.Cellai, H.Heumann, and U.Heinemann (1998).
Crystal structure of an eight-base pair duplex containing the 3'-DNA-RNA-5' junction formed during initiation of minus-strand synthesis of HIV replication.
  Biochemistry, 37, 12005-12011.
PDB code: 398d
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.  
9687367 W.Shepard, W.B.Cruse, R.Fourme, E.de la Fortelle, and T.Prangé (1998).
A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution.
  Structure, 6, 849-861.
PDB code: 376d
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.  
9327395 A.Menke, and G.Hobom (1997).
Antiviral ribozymes. New jobs for ancient molecules.
  Mol Biotechnol, 8, 17-33.  
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.  
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.  
9326597 B.Navarro, and R.Flores (1997).
Chrysanthemum chlorotic mottle viroid: unusual structural properties of a subgroup of self-cleaving viroids with hammerhead ribozymes.
  Proc Natl Acad Sci U S A, 94, 11262-11267.  
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 373d
9155037 C.H.Kim, D.E.Ryan, T.Marciniec, and J.Abelson (1997).
Site-specific deoxynucleotide substitutions in yeast U6 snRNA block splicing of pre-mRNA in vitro.
  EMBO J, 16, 2119-2129.  
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.  
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.  
9369470 C.Sich, O.Ohlenschläger, R.Ramachandran, M.Görlach, and L.R.Brown (1997).
Structure of an RNA hairpin loop with a 5'-CGUUUCG-3' loop motif by heteronuclear NMR spectroscopy and distance geometry.
  Biochemistry, 36, 13989-14002.
PDB code: 1uuu
9358171 D.A.Adamiak, J.Milecki, M.Popenda, R.W.Adamiak, Z.Dauter, and W.R.Rypniewski (1997).
Crystal structure of 2'-O-Me(CGCGCG)2, an RNA duplex at 1.30 A resolution. Hydration pattern of 2'-O-methylated RNA.
  Nucleic Acids Res, 25, 4599-4607.
PDB code: 310d
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.  
9228948 J.H.Cate, R.L.Hanna, and J.A.Doudna (1997).
A magnesium ion core at the heart of a ribozyme domain.
  Nat Struct Biol, 4, 553-558.  
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.  
  9303537 L.Su, J.T.Radek, L.A.Labeots, K.Hallenga, P.Hermanto, H.Chen, S.Nakagawa, M.Zhao, S.Kates, and M.A.Weiss (1997).
An RNA enhancer in a phage transcriptional antitermination complex functions as a structural switch.
  Genes Dev, 11, 2214-2226.  
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.  
  9303183 P.L.Fell, A.J.Hudson, M.A.Reynolds, N.Usman, and S.Akhtar (1997).
Cellular uptake properties of a 2'-amino/2'-O-methyl-modified chimeric hammerhead ribozyme targeted to the epidermal growth factor receptor mRNA.
  Antisense Nucleic Acid Drug Dev, 7, 319-326.  
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.  
9125492 P.Z.Qin, and A.M.Pyle (1997).
Stopped-flow fluorescence spectroscopy of a group II intron ribozyme reveals that domain 1 is an independent folding unit with a requirement for specific Mg2+ ions in the tertiary structure.
  Biochemistry, 36, 4718-4730.  
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
  9094703 S.López de Quinto, and E.Martínez-Salas (1997).
Conserved structural motifs located in distal loops of aphthovirus internal ribosome entry site domain 3 are required for internal initiation of translation.
  J Virol, 71, 4171-4175.  
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.  
9396806 T.B.Campbell, C.K.McDonald, and M.Hagen (1997).
The effect of structure in a long target RNA on ribozyme cleavage efficiency.
  Nucleic Acids Res, 25, 4985-4993.  
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.  
  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.  
8804835 D.P.Millar (1996).
Fluorescence studies of DNA and RNA structure and dynamics.
  Curr Opin Struct Biol, 6, 322-326.  
8952482 E.Jankowsky, and B.Schwenzer (1996).
Efficient improvement of hammerhead ribozyme mediated cleavage of long substrates by oligonucleotide facilitators.
  Biochemistry, 35, 15313-15321.  
  8551640 E.Martínez-Salas, M.P.Regalado, and E.Domingo (1996).
Identification of an essential region for internal initiation of translation in the aphthovirus internal ribosome entry site and implications for viral evolution.
  J Virol, 70, 992-998.  
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.  
8918806 J.E.Kanyo, J.Duhamel, and P.Lu (1996).
Secondary structure of the r(CUUCGG) tetraloop.
  Nucleic Acids Res, 24, 4015-4022.  
8939748 J.H.Cate, and J.A.Doudna (1996).
Metal-binding sites in the major groove of a large ribozyme domain.
  Structure, 4, 1221-1229.  
8710489 J.Hamm (1996).
Characterisation of antibody-binding RNAs selected from structurally constrained libraries.
  Nucleic Acids Res, 24, 2220-2227.  
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.  
  8626292 J.Y.Wang, L.Qiu, E.D.Wu, and K.Drlica (1996).
RNases involved in ribozyme degradation in Escherichia coli.
  J Bacteriol, 178, 1640-1645.  
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.  
8948629 M.Homann, W.Nedbal, and G.Sczakiel (1996).
Dissociation of long-chain duplex RNA can occur via strand displacement in vitro: biological implications.
  Nucleic Acids Res, 24, 4395-4400.  
8876152 M.J.Corey, and E.Corey (1996).
On the failure of de novo-designed peptides as biocatalysts.
  Proc Natl Acad Sci U S A, 93, 11428-11434.  
8942631 M.Menger, T.Tuschl, F.Eckstein, and D.Porschke (1996).
Mg(2+)-dependent conformational changes in the hammerhead ribozyme.
  Biochemistry, 35, 14710-14716.  
8805553 N.L.Greenbaum, I.Radhakrishnan, D.J.Patel, and D.Hirsh (1996).
Solution structure of the donor site of a trans-splicing RNA.
  Structure, 4, 725-733.
PDB codes: 1slo 1slp
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.  
8980476 P.Klaff, D.Riesner, and G.Steger (1996).
RNA structure and the regulation of gene expression.
  Plant Mol Biol, 32, 89.  
8599806 P.L.Coletta, E.J.Cartwright, and A.F.Markham (1996).
Transgenic models and cancer treatment.
  Cancer Treat Rev, 21, 565-576.  
8672458 P.Y.Shi, M.A.Brinton, J.M.Veal, Y.Y.Zhong, and W.D.Wilson (1996).
Evidence for the existence of a pseudoknot structure at the 3' terminus of the flavivirus genomic RNA.
  Biochemistry, 35, 4222-4230.  
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.  
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.  
  8816503 S.C.Boulanger, P.H.Faix, H.Yang, J.Zhuo, J.S.Franzen, C.L.Peebles, and P.S.Perlman (1996).
Length changes in the joining segment between domains 5 and 6 of a group II intron inhibit self-splicing and alter 3' splice site selection.
  Mol Cell Biol, 16, 5896-5904.  
  8654381 S.Cusack, A.Yaremchuk, and M.Tukalo (1996).
The crystal structure of the ternary complex of T.thermophilus seryl-tRNA synthetase with tRNA(Ser) and a seryl-adenylate analogue reveals a conformational switch in the active site.
  EMBO J, 15, 2834-2842.  
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.  
9000010 V.Lehnert, L.Jaeger, F.Michel, and E.Westhof (1996).
New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme.
  Chem Biol, 3, 993.  
8626495 V.N.Gladyshev, J.C.Boyington, S.V.Khangulov, D.A.Grahame, T.C.Stadtman, and P.D.Sun (1996).
Characterization of crystalline formate dehydrogenase H from Escherichia coli. Stabilization, EPR spectroscopy, and preliminary crystallographic analysis.
  J Biol Chem, 271, 8095-8100.  
8703955 Y.Komatsu, I.Kanzaki, and E.Ohtsuka (1996).
Enhanced folding of hairpin ribozymes with replaced domains.
  Biochemistry, 35, 9815-9820.  
9080546 Y.Timsit, and D.Moras (1996).
Cruciform structures and functions.
  Q Rev Biophys, 29, 279-307.  
8758993 Y.X.Wang, S.Huang, and D.E.Draper (1996).
Structure of a U.U pair within a conserved ribosomal RNA hairpin.
  Nucleic Acids Res, 24, 2666-2672.  
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.  
  8722002 A.A.Bogdanov, O.A.Dontsova, S.S.Dokudovskaya, and I.N.Lavrik (1995).
Structure and function of 5S rRNA in the ribosome.
  Biochem Cell Biol, 73, 869-876.  
7583628 A.M.Pyle, and J.B.Green (1995).
RNA folding.
  Curr Opin Struct Biol, 5, 303-310.  
7542858 A.Rich, and A.Rich (1995).
The nucleic acids. A backward glance.
  Ann N Y Acad Sci, 758, 97.  
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.  
7567466 B.Lustig, N.H.Lin, S.M.Smith, R.L.Jernigan, and K.T.Jeang (1995).
A small modified hammerhead ribozyme and its conformational characteristics determined by mutagenesis and lattice calculation.
  Nucleic Acids Res, 23, 3531-3538.  
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.  
7629188 C.Sturchler-Pierrat, N.Hubert, T.Totsuka, T.Mizutani, P.Carbon, and A.Krol (1995).
Selenocysteylation in eukaryotes necessitates the uniquely long aminoacyl acceptor stem of selenocysteine tRNA(Sec).
  J Biol Chem, 270, 18570-18574.  
7885828 F.H.Allain, and G.Varani (1995).
Divalent metal ion binding to a conserved wobble pair defining the upstream site of cleavage of group I self-splicing introns.
  Nucleic Acids Res, 23, 341-350.  
7719853 G.S.Bassi, N.E.Møllegaard, A.I.Murchie, E.von Kitzing, and D.M.Lilley (1995).
Ionic interactions and the global conformations of the hammerhead ribozyme.
  Nat Struct Biol, 2, 45-55.  
  7489515 J.Ciesiolka, J.Gorski, and M.Yarus (1995).
Selection of an RNA domain that binds Zn2+.
  RNA, 1, 538-550.  
  8846773 K.Harada, and A.D.Frankel (1995).
Identification of two novel arginine binding DNAs.
  EMBO J, 14, 5798-5811.  
7501467 L.Beigelman, A.Karpeisky, J.Matulic-Adamic, P.Haeberli, D.Sweedler, and N.Usman (1995).
Synthesis of 2'-modified nucleotides and their incorporation into hammerhead ribozymes.
  Nucleic Acids Res, 23, 4434-4442.  
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.  
  7493319 L.P.Yap, and K.Musier-Forsyth (1995).
Transfer RNA aminoacylation: identification of a critical ribose 2'-hydroxyl-base interaction.
  RNA, 1, 418-424.  
7583626 M.C.Wahl, and M.Sundaralingam (1995).
New crystal structures of nucleic acids and their complexes.
  Curr Opin Struct Biol, 5, 282-295.  
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.  
7723502 M.Kiehntopf, E.L.Esquivel, M.A.Brach, and F.Herrmann (1995).
Clinical applications of ribozymes.
  Lancet, 345, 1027-1031.  
7583631 M.Kochoyan, and J.L.Leroy (1995).
Hydration and solution structure of nucleic acids.
  Curr Opin Struct Biol, 5, 329-333.  
7610038 M.Werner, and O.C.Uhlenbeck (1995).
The effect of base mismatches in the substrate recognition helices of hammerhead ribozymes on binding and catalysis.
  Nucleic Acids Res, 23, 2092-2096.  
7552719 O.C.Uhlenbeck (1995).
Hammerhead: Part 2.
  Nat Struct Biol, 2, 610-614.  
7479037 P.Hendry, M.J.McCall, F.S.Santiago, and P.A.Jennings (1995).
In vitro activity of minimised hammerhead ribozymes.
  Nucleic Acids Res, 23, 3922-3927.  
8524666 P.Sandusky, E.W.Wooten, A.V.Kurochkin, T.Kavanaugh, W.Mandecki, and E.R.Zuiderweg (1995).
Occurrence, solution structure and stability of DNA hairpins stabilized by a GA/CG helix unit.
  Nucleic Acids Res, 23, 4717-4725.  
7585055 S.Akhtar, H.James, and I.Gibson (1995).
Molecular DIY with hairpins and hammerheads.
  Nat Med, 1, 300-302.  
8574700 S.E.Lietzke, C.L.Barnes, and C.E.Kundrot (1995).
Crystallization and structure determination of RNA.
  Curr Opin Struct Biol, 5, 645-649.  
  7489712 S.P.Lyngstadaas, S.Risnes, B.S.Sproat, P.S.Thrane, and H.P.Prydz (1995).
A synthetic, chemically modified ribozyme eliminates amelogenin, the major translation product in developing mouse enamel in vivo.
  EMBO J, 14, 5224-5229.  
7662303 S.T.Sigurdsson, and F.Eckstein (1995).
Structure-function relationships of hammerhead ribozymes: from understanding to applications.
  Trends Biotechnol, 13, 286-289.  
7753865 T.L.Beattie, J.E.Olive, and R.A.Collins (1995).
A secondary-structure model for the self-cleaving region of Neurospora VS RNA.
  Proc Natl Acad Sci U S A, 92, 4686-4690.  
  7588614 T.M.Nakamura, Y.H.Wang, A.J.Zaug, J.D.Griffith, and T.R.Cech (1995).
Relative orientation of RNA helices in a group 1 ribozyme determined by helix extension electron microscopy.
  EMBO J, 14, 4849-4859.  
7583627 T.Tuschl, J.B.Thomson, and F.Eckstein (1995).
RNA cleavage by small catalytic RNAs.
  Curr Opin Struct Biol, 5, 296-302.  
7541315 W.G.Scott, J.T.Finch, and A.Klug (1995).
The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage.
  Cell, 81, 991.
PDB code: 1mme
8527670 Y.G.Gao, H.Robinson, J.H.van Boom, and A.H.Wang (1995).
Influence of counter-ions on the crystal structures of DNA decamers: binding of [Co(NH3)6]3+ and Ba2+ to A-DNA.
  Biophys J, 69, 559-568.
PDB codes: 212d 220d 221d 222d
7773770 A.Pardi (1994).
Ribozyme revealed.
  Nat Struct Biol, 1, 846-849.  
7704535 J.A.Doudna (1994).
Hammering out the shape of a ribozyme.
  Structure, 2, 1271-1272.  
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 code is shown on the right.

 

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