Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis

Gilbert, 1986, The RNA, world, Nature, 319, 618, 10.1038/319618a0 Scott, 1996, Molecular palaeontology: understanding catalytic mechanisms in the RNA world by excavating clues from a ribozyme three-dimensional structure, Biochem. Soc. Trans., 24, 604, 10.1042/bst0240604 Gesteland, 1999 Yarus, 1999, Boundaries for an RNA world, Curr. Opin. Chem. Biol., 3, 260, 10.1016/S1367-5931(99)80041-6 Chen, 2007, Ribozyme catalysis of metabolism in the RNA world, Chem. Biodivers., 4, 633, 10.1002/cbdv.200790055 Lilley, 2008, Ribozymes and RNA Catalysis, 66 Scott, 2007, Ribozymes, Curr. Opin. Struct. Biol., 13, 280, 10.1016/j.sbi.2007.05.003 Bartel, 2009, MicroRNAs: target recognition and regulatory functions, Cell, 136, 215, 10.1016/j.cell.2009.01.002 Montange, 2008, Riboswitches: emerging themes in RNA structure and function, Annu. Rev. Biophys., 37, 117, 10.1146/annurev.biophys.37.032807.130000 Shabalina, 2008, Origins and evolution of eukaryotic RNA interference, Trends Ecol. Evol., 23, 578, 10.1016/j.tree.2008.06.005 Sotiropoulou, 2009, Emerging roles of microRNAs as molecular switches in the integrated circuit of the cancer cell, RNA, 15, 1443, 10.1261/rna.1534709 Cech, 1981, In vitro splicing of the ribosomal RNA precursor of tetrahymena: involvement of a guanosine nucleotide in the excision of the intervening sequence, Cell, 27, 487, 10.1016/0092-8674(81)90390-1 Sharp, 2009, The centrality of RNA, Cell, 136, 577, 10.1016/j.cell.2009.02.007 Wilson, 2009, Biochemistry. The evolution of ribozyme chemistry, Science, 323, 1436, 10.1126/science.1169231 Rubenstein, 2004, A review of antisense oligonucleotides in the treatment of human disease, Drugs Future, 29, 893, 10.1358/dof.2004.029.09.854176 Vaish, 2002, Monitoring post-translation modification of proteins with allosteric ribozymes, Nat. Biotech., 20, 810, 10.1038/nbt719 Breaker, 2002, Engineered allosteric ribozymes as biosensor components, Curr. Opin. Biotechnol., 13, 31, 10.1016/S0958-1669(02)00281-1 Rasmussen, 2007, Hitting bacteria at the heart of the central dogma: sequence-specific inhibition, Microb. Cell Fact., 6, 24, 10.1186/1475-2859-6-24 Mackerell, 2008, Molecular dynamics simulations of nucleic acid-protein complexes, Curr. Opin. Struct. Biol., 18, 194, 10.1016/j.sbi.2007.12.012 McDowell, 2007, Molecular dynamics simulations of RNA: an in silico single molecule approach, Biopolymers, 85, 169, 10.1002/bip.20620 Norberg, 2002, Molecular dynamics applied to nucleic acids, Acc. Chem. Res., 35, 465, 10.1021/ar010026a Orozco, 2003, Theoretical methods for the simulation of nucleic acids, Chem. Soc. Rev., 32, 350, 10.1039/B207226M Sherwood, 2008, Multiscale methods for macromolecular simulations, Curr. Opin. Struct. Biol., 18, 630, 10.1016/j.sbi.2008.07.003 Ayton, 2007, Multiscale modeling of biomolecular systems: in serial and in parallel, Curr. Opin. Struct. Biol., 17, 192, 10.1016/j.sbi.2007.03.004 2009, Vol. 7 Gao, 1995, Methods and applications of combined quantum mechanical and molecular mechanical potentials, Rev Comput Chem., 7, 119 Hawkins, 1998, Universal solvation models, 209 Monard, 1999, Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems, Acc. Chem. Res., 32, 904, 10.1021/ar970218z Warshel, 2002, Molecular dynamics simulations of biological reactions, Acc. Chem. Res., 35, 385, 10.1021/ar010033z Warshel, 2003, Computer simulations of enzyme catalysis: methods, progress, and insights, Annu. Rev. Biophys. Biomol. Struct., 32, 425, 10.1146/annurev.biophys.32.110601.141807 Senn, 2007, QM/MM studies of enzymes, Curr. Opin. Chem. Biol., 11, 182, 10.1016/j.cbpa.2007.01.684 Orozco, 2008, Recent advances in the study of nucleic acid flexibility by molecular dynamics, Curr. Opin. Struct. Biol., 18, 185, 10.1016/j.sbi.2008.01.005 Auffinger, 2007, Nucleic acid solvation: from outside to insight, Curr. Opin. Struct. Biol., 17, 325, 10.1016/j.sbi.2007.05.008 Cheatham, 2004, Simulation and modeling of nucleic acid structure, dynamics and interactions, Curr. Opin. Struct. Biol., 14, 360, 10.1016/j.sbi.2004.05.001 Chen, 2008, RNA folding: conformational statistics, folding kinetics, and ion electrostatics, Annu. Rev. Biophys., 37, 197, 10.1146/annurev.biophys.37.032807.125957 Hashem, 2009, A short guide for molecular dynamics simulations of RNA systems, Methods, 47, 187, 10.1016/j.ymeth.2008.09.020 Forster, 1987, Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites, Cell, 49, 211, 10.1016/0092-8674(87)90562-9 Scott, 1999, Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme, Q. Rev. Biophys., 32, 241, 10.1017/S003358350000353X Blount, 2002, The hammerhead ribozyme, Biochem. Soc. Trans., 30, 1119, 10.1042/bst0301119 Scott, 1998, RNA catalysis, Curr. Opin. Struct. Biol., 8, 720, 10.1016/S0959-440X(98)80091-2 Scott, 2007, Ribozymes, Curr. Opin. Struct. Biol., 17, 280, 10.1016/j.sbi.2007.05.003 Doherty, 2001, Ribozyme structures and mechanisms, Annu. Rev. Biophys. Biomol. Struct., 30, 457, 10.1146/annurev.biophys.30.1.457 Rios, 2009, Model systems: how chemical biologists study RNA, Curr. Opin. Chem. Biol., 13, 660, 10.1016/j.cbpa.2009.09.028 Cochrane, 2008, Catalytic strategies of self-cleaving ribozymes, Acc. Chem. Res., 41, 1027, 10.1021/ar800050c Bevilacqua, 2006, Nucleobase catalysis in ribozyme mechanism, Curr. Opin. Chem. Biol., 10, 455, 10.1016/j.cbpa.2006.08.014 Sarver, 1990, Ribozymes as potential anti-HIV-1 therapeutic agents, Science, 247, 1222, 10.1126/science.2107573 Michienzi, 2000, Ribozyme-mediated inhibition of HIV 1 suggests nucleolar trafficking of HIV-1 RNA, Proc. Natl. Acad. Sci. USA., 97, 8955, 10.1073/pnas.97.16.8955 Nazari, 2008, Inhibition of human immunodeficiency virus-1 entry using vectors expressing a multimeric hammerhead ribozyme targeting the CCR5 mRNA, J. Gen. Virol., 89, 2252, 10.1099/vir.0.2008/001222-0 Unwalla, 2008, Use of a U16 snoRNA-containing ribozyme library to identify ribozyme targets in HIV-1, Mol. Ther., 16, 1113, 10.1038/mt.2008.54 Snyder, 1993, Ribozyme-mediated inhibition of bcr-abl gene expression in a Philadelphia chromosome-positive cell line, Blood, 82, 600, 10.1182/blood.V82.2.600.600 Feng, 2001, Intracellular inhibition of the replication of hepatitis B virus by hammerhead ribozymes, J. Gastroenterol. Hepatol., 16, 1125, 10.1046/j.1440-1746.2001.02548.x Weinberg, 2000, Hammerhead ribozyme-mediated inhibition of hepatitis B virus X gene expression in cultured cells, J. Hepatol., 33, 142, 10.1016/S0168-8278(00)80171-3 Sano, 2007, Hammerhead ribozyme-based target discovery, Methods Mol. Biol., 360, 143 Weinberg, 2007, Effective anti-hepatitis B virus hammerhead ribozymes derived from multimeric precursors, Oligonucleotides, 17, 104, 10.1089/oli.2006.0049 Ferbeyre, 2000, Distribution of hammerhead and hammerhead-like RNA motifs through the GenBank, Genome Res., 10, 1011, 10.1101/gr.10.7.1011 Martick, 2008, A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA, Nature, 454, 899, 10.1038/nature07117 Takagi, 2004, Ribozyme mechanisms, Top. Curr. Chem., 232, 213, 10.1007/b13783 Shepotinovskaya, 2008, Catalytic diversity of extended hammerhead ribozymes, Biochemistry, 47, 7034, 10.1021/bi7025358 Thomas, 2008, Probing general base catalysis in the hammerhead ribozyme, J. Am. Chem. Soc., 130, 15467, 10.1021/ja804496z Thomas, 2009, Probing general acid catalysis in the hammerhead ribozyme, J. Am. Chem. Soc., 131, 1135, 10.1021/ja807790e Blount, 2005, The structure-function dilemma of the hammerhead ribozyme, Annu. Rev. Biophys. Biomol. Struct., 34, 415, 10.1146/annurev.biophys.34.122004.184428 Suzumura, 2004, NMR-based reappraisal of the coordination of a metal ion at the pro- Rp oxygen of the A9/G10.1 site in a hammerhead ribozyme, J. Am. Chem. Soc., 126, 15504, 10.1021/ja0472937 Wang, 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, 10.1021/bi9913202 Tanaka, 2004, Nature of the chemical bond formed with the structural metal ion at the A9/G10.1 motif derived from hammerhead ribozymes, J. Am. Chem. Soc., 126, 744, 10.1021/ja036826t Tanaka, 2005, NMR spectroscopic analyses of functional nucleic acids-metal interaction and their solution structure analyses, Nucleic Acids Symp. Ser. (Oxf), 49, 51, 10.1093/nass/49.1.51 Vogt, 2006, Coordination environment of a site-bound metal ion in the hammerhead ribozyme determined by 15N and 2H ESEEM spectroscopy, J. Am. Chem. Soc., 128, 16764, 10.1021/ja057035p Przybilski, 2007, The tolerance to exchanges of the Watson Crick base pair in the hammerhead ribozyme core is determined by surrounding elements, RNA, 13, 1625, 10.1261/rna.631207 Nelson, 2008, Hammerhead redux: does the new structure fit the old biochemical data?, RNA, 14, 605, 10.1261/rna.912608 Sheldon, 1989, Mutagenesis analysis of a self-cleaving RNA, Nucleic Acids Res., 17, 5679, 10.1093/nar/17.14.5679 Scott, 1996, Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme, Science, 274, 2065, 10.1126/science.274.5295.2065 Murray, 1998, The structural basis of hammerhead ribozyme self-cleavage, Cell, 92, 665, 10.1016/S0092-8674(00)81134-4 Murray, 2000, Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and x-Ray holographic reconstruction, Mol. Cell, 5, 279, 10.1016/S1097-2765(00)80423-2 Martick, 2006, Tertiary contacts distant from the active site prime a ribozyme for catalysis, Cell, 126, 309, 10.1016/j.cell.2006.06.036 Martick, 2008, Solvent structure and hammerhead ribozyme catalysis, Chem. Biol., 15, 332, 10.1016/j.chembiol.2008.03.010 Lee, 2007, Insight into the role of Mg2+ in hammerhead ribozyme catalysis from x-ray crystallography and molecular dynamics simulation, J. Chem. Theory Comput., 3, 325, 10.1021/ct6003142 Lee, 2008, Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation, J. Am. Chem. Soc., 130, 3053, 10.1021/ja076529e Lee, 2008, Origin of mutational effects at the C3 and G8 positions on hammerhead ribozyme catalysis from molecular dynamics simulations, J. Am. Chem. Soc., 130, 7168, 10.1021/ja711242b Lee, 2009, Unraveling the mechanisms of ribozyme catalysis with multi-scale simulations Wong, 2011, Active participation of Mg2+ ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme, J. Chem. Theory Comput., 7, 1, 10.1021/ct100467t Scott, 2007, Morphing the minimal and full-length hammerhead ribozymes: implications for the cleavage mechanism, Biol. Chem., 388, 727, 10.1515/BC.2007.087 Haseloff, 1988, Simple RNA enzymes with new and highly specific endoribonuclease activities, Nature, 334, 585, 10.1038/334585a0 Birikh, 1997, The structure, function and application of the hammerhead ribozyme, Eur. J. Biochem., 245, 1, 10.1111/j.1432-1033.1997.t01-3-00001.x Ruffner, 1990, Sequence requirements of the hammerhead RNA self-cleavage reaction, Biochemistry, 29, 10695, 10.1021/bi00499a018 Khvorova, 2003, Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity, Nat. Struct. Biol., 10, 708, 10.1038/nsb959 Canny, 2007, Efficient ligation of the Schistosoma hammerhead ribozyme, Biochemistry, 46, 3826, 10.1021/bi062077r Canny, 2004, Fast cleavage kinetics of a natural hammerhead ribozyme, J. Am. Chem. Soc., 126, 10848, 10.1021/ja046848v Pley, 1994, Three-dimensional structure of a hammerhead ribozyme, Nature, 372, 68, 10.1038/372068a0 Scott, 1995, The crystal structure of an All-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage, Cell, 81, 991, 10.1016/S0092-8674(05)80004-2 Uhlenbeck, 2003, Less isn't always more, RNA, 9, 1415, 10.1261/rna.5155903 McKay, 1996, Structure and function of the hammerhead ribozyme: an unfinished story, RNA, 2, 395 Ruffner, 1990, Thiophosphate interference experiments locate phosphates important for the hammerhead RNA self-cleavage reaction, Nucleic Acids Res., 18, 6025, 10.1093/nar/18.20.6025 Peracchi, 1997, Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation, J. Biol. Chem., 272, 26822, 10.1074/jbc.272.43.26822 Murray, 2000, Does a single metal ion bridge the A-9 and scissile phosphate groups in the catalytically active hammerhead ribozyme structure?, J. Mol. Biol., 296, 33, 10.1006/jmbi.1999.3428 Tuschl, 1993, Importance of exocyclic base functional groups of central core guanosines for hammerhead ribozyme activity, Biochemistry, 32, 11658, 10.1021/bi00094a023 Peracchi, 1996, Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases, Proc. Natl. Acad. Sci., 93, 11522, 10.1073/pnas.93.21.11522 Han, 2005, Model for general acid–base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site, Biochemistry, 44, 7864, 10.1021/bi047941z Simorre, 1997, A conformational change in the catalytic core of the hammerhead ribozyme upon cleavage of an RNA substrate, Biochemistry, 36, 518, 10.1021/bi9620520 Beigelman, 1995, Chemical modification of hammerhead ribozymes, J. Biol. Chem., 270, 25702, 10.1074/jbc.270.43.25702 Nelson, 2006, When to believe what you see, Mol. Cell, 23, 447, 10.1016/j.molcel.2006.08.001 Przybilski, 2006, The hammerhead ribozyme structure brought in line, Chem. Biol. Chem., 7, 1641, 10.1002/cbic.200600312 Westhof, 2007, A tale in molecular recognition: the hammerhead ribozyme, J. Mol. Recognit., 20, 1, 10.1002/jmr.806 Mayaan, 2007, CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes, J. Comput. Chem., 28, 495, 10.1002/jcc.20474 Foloppe, 2000, All-atom empirical force field for nucleic acids: I Parameter optimization based on small molecule and condensed phase macromolecular target data, J. Comput. Chem., 21, 86, 10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G MacKerell, 2000, All-Atom empirical force field for nucleic Acids: II. application to molecular dynamics simulations of DNA and RNA in solution, J. Comput. Chem., 21, 105, 10.1002/(SICI)1096-987X(20000130)21:2<105::AID-JCC3>3.0.CO;2-P Nam, 2007, Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms, J. Chem. Theory Comput., 3, 486, 10.1021/ct6002466 Brooks, 1983, Charmm: a program for macromolecular energy minimization and dynamics calculations, J. Comput. Chem., 4, 187, 10.1002/jcc.540040211 Jorgensen, 1983, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys., 79, 926, 10.1063/1.445869 Andersen, 1980, Molecular dynamics simulations at constant pressure and/or temperature, J. Chem. Phys., 72, 2384, 10.1063/1.439486 Hoover, 1985, Canonical dynamics: equilibration phase-space distributions, Phys. Rev. A, 31, 1695, 10.1103/PhysRevA.31.1695 Nose, 1983, Constant pressure molecular dynamics for molecular systems, Mol. Phys., 50, 1055, 10.1080/00268978300102851 Essmann, 1995, A smooth particle mesh Ewald method, J. Chem. Phys., 103, 8577, 10.1063/1.470117 Sagui, 1999, Molecular dynamics simulations of biomolecules: long-range electrostatic effects, Annu. Rev. Biophys. Biomol. Struct., 28, 155, 10.1146/annurev.biophys.28.1.155 Allen, 1987 Ryckaert, 1977, Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-Alkanes, J. Comput. Phys., 23, 327, 10.1016/0021-9991(77)90098-5 Ponomarev, 2004, Ion motions in molecular dynamics simulations on DNA, Proc. Natl. Acad. Sci. USA., 101, 14771, 10.1073/pnas.0406435101 Hutter, 1998, Modeling the bacterial photosynthetic reaction center. 1. magnesium parameters for the semiempirical AM1 method developed using a genetic algorithm, J. Phys. Chem. B, 102, 8080, 10.1021/jp9805205 Gao, 1998, A generalized hybrid orbital (GHO) method for the treatment of boundary atoms in combined QM/MM calculations, J. Phys. Chem. A, 102, 4714, 10.1021/jp9809890 Nam, 2005, An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations, J. Chem. Theory Comput., 1, 2, 10.1021/ct049941i Lambert, 2006, Three conserved guanosines approach the reaction site in native and minimal hammerhead ribozymes, Biochemistry, 45, 7140, 10.1021/bi052457x Boots, 2008, Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme, RNA, 14, 2212, 10.1261/rna.1010808 Roychowdhury-Saha, 2007, Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme, RNA, 13, 841, 10.1261/rna.339207 Ward, 2012, Ground-state coordination of a catalytic metal to the scissile phosphate of a tertiary-stabilized hammerhead ribozyme, RNA, 18, 16, 10.1261/rna.030239.111 Imhof, 2006, AM1/d Parameters for magnesium in metalloenzymes, J. Chem. Theory Comput., 2, 1050, 10.1021/ct600092c Perez, 2007, Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers, Biophys. J., 92, 3817, 10.1529/biophysj.106.097782 Horn, 2004, Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew, J. Chem. Phys., 120, 9665, 10.1063/1.1683075 Joung, 2008, Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations, J. Phys. Chem. B, 112, 9020, 10.1021/jp8001614 Torrie, 1977, Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling, J. Comput. Phys., 23, 187, 10.1016/0021-9991(77)90121-8 Kumar, 1992, The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method, J. Comput. Chem., 13, 1011, 10.1002/jcc.540130812 Roux, 1995, The calculation of the potential of mean force using computer simulations, Comput. Phys. Commun., 91, 275, 10.1016/0010-4655(95)00053-I Murray, 1998, The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone, Chem. Biol., 5, 587, 10.1016/S1074-5521(98)90116-8 O'Rear, 2001, Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations, RNA, 7, 537, 10.1017/S1355838201002461 Curtis, 2001, The hammerhead cleavage reaction in monovalent cations, RNA, 7, 546, 10.1017/S1355838201002357 Lee, 2009, Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation, J. Mol. Biol., 388, 195, 10.1016/j.jmb.2009.02.054 Schnabl, 2010, Controlling ribozyme activity by metal ions, Curr. Opin. Chem. Biol., 14, 269, 10.1016/j.cbpa.2009.11.024 Torres, 1998, Molecular dynamics study displays near in-line attack conformations in the hammerhead ribozyme self-cleavage reaction, Proc. Natl. Acad. Sci. USA., 95, 11077, 10.1073/pnas.95.19.11077 MacQueen, 1967, Some methods for classification and analysis of multivariate observations, Vol. 1, 281 Davis, 2007, Role of metal ions in the tetraloop-receptor complex as analyzed by NMR, RNA, 13, 76, 10.1261/rna.268307 Vogt, 2006, Coordination environment of a site-bound metal ion in the hammerhead ribozyme determined by 15N and 2H ESEEM spectroscopy, J. Am. Chem. Soc., 128, 16764, 10.1021/ja057035p Burke, 2005, Low-magnesium, trans-cleavage activity by type III, tertiary stabilized hammerhead ribozymes with stem 1 discontinuities, BMC Biochem., 6, 14, 10.1186/1471-2091-6-14 Persson, 2002, Selection of hammerhead ribozyme variants with low Mg2+ requirement: importance of stem-loop II, Chembiochem, 3, 1066, 10.1002/1439-7633(20021104)3:11<1066::AID-CBIC1066>3.0.CO;2-G Roychowdhury-Saha, 2006, Extraordinary rates of transition metal ion-mediated ribozyme catalysis, RNA, 12, 1846, 10.1261/rna.128906 Fedoruk-Wyszomirska, 2009, Highly active low magnesium hammerhead ribozyme, J. Biochem., 145, 451, 10.1093/jb/mvn182 Cornell, 1995, A second generation force field for the simulation of proteins, nucleic acids and organic molecules, J. Am. Chem. Soc., 117, 5179, 10.1021/ja00124a002 Case, 2008 Case, 2002 Pearlman, 1995, AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structure and energetic properties of molecules, Comput. Phys. Commun., 91, 1, 10.1016/0010-4655(95)00041-D Burgin, 1996, Chemically modified hammerhead ribozymes with improved catalytic rates, Biochemistry, 35, 14090, 10.1021/bi961264u Baidya, 1997, A kinetic and thermodynamic analysis of cleavage site mutations in the hammerhead ribozyme, Biochemistry, 36, 1108, 10.1021/bi962165j Nelson, 2008, Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis, RNA, 14, 43, 10.1261/rna.717908 Soukup, 1999, Relationship between internucleotide linkage geometry and the stability of RNA, RNA, 5, 1308, 10.1017/S1355838299990891 Emsley, 2004, Coot: model-building tools for molecular graphics, Acta Crystallogr. D, 60, 2126, 10.1107/S0907444904019158 Fürtig, 2008, NMR-spectroscopic characterization of phosphodiester bond cleavage catalyzed by the minimal hammerhead ribozyme, RNA Biol., 5, 41, 10.4161/rna.5.1.5704 Uhlenbeck, 1987, A small catalytic oligoribonucleotide, Nature, 328, 596, 10.1038/328596a0 Humphrey, 1996, VMD: visual molecular dynamics, J. Mol. Grapics, 14, 33, 10.1016/0263-7855(96)00018-5