Cations in charge: magnesium ions in RNA folding and catalysis.

[1]  M. Eigen,et al.  Kinetics and mechanism of reactions of main group metal ions with biological carriers , 1969 .

[2]  J. Šponer,et al.  Outer-Shell and Inner-Shell Coordination of Phosphate Group to Hydrated Metal Ions (Mg2+, Cu2+, Zn2+, Cd2+) in the Presence and Absence of Nucleobase. The Role of Nonelectrostatic Effects , 2003 .

[3]  M. Maguire,et al.  Magnesium chemistry and biochemistry , 2002, Biometals.

[4]  H. Al‐Hashimi,et al.  NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P , 2010, Proceedings of the National Academy of Sciences.

[5]  K. Weeks,et al.  Exploring RNA structural codes with SHAPE chemistry. , 2011, Accounts of chemical research.

[6]  T. Cech,et al.  Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA--solvent interactions. , 2001, Structure.

[7]  T. Steitz,et al.  The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. , 2000, Science.

[8]  C. Baes,et al.  The hydrolysis of cations , 1986 .

[9]  J. Šponer,et al.  Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In , 2009, Accounts of chemical research.

[10]  J. Cowan,et al.  A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage. , 1997, Chemistry & biology.

[11]  Chiaolong Hsiao,et al.  Peeling the onion: ribosomes are ancient molecular fossils. , 2009, Molecular biology and evolution.

[12]  J. Šponer,et al.  QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms. , 2011, The journal of physical chemistry. B.

[13]  Michael P Robertson,et al.  The Structural Basis of Ribozyme-Catalyzed RNA Assembly , 2007, Science.

[14]  I. D. Brown,et al.  Chemical and Steric Constraints in Inorganic Solids , 1992 .

[15]  J. Glusker,et al.  The Arrangement of First- and Second-shell Water Molecules Around Metal Ions: Effects of Charge and Size , 2006 .

[16]  S. Woodson,et al.  Compact intermediates in RNA folding. , 2010, Annual review of biophysics.

[17]  Wei Yang,et al.  Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations. , 2011, Journal of the American Chemical Society.

[18]  Adelene Y. L. Sim,et al.  Electrostatics of nucleic acid folding under conformational constraint. , 2012, Journal of the American Chemical Society.

[19]  Sebastian Doniach,et al.  Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations. , 2004, Journal of molecular biology.

[20]  Julie L. Fiore,et al.  Entropic origin of Mg2+-facilitated RNA folding , 2012, Proceedings of the National Academy of Sciences.

[21]  A. Tannenbaum,et al.  Chapter 1:Complexes of Nucleic Acids with Group I and II Cations , 2008 .

[22]  W. Scott,et al.  The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. , 1998, Chemistry & biology.

[23]  A. Ferré-D’Amaré,et al.  Structural Basis of glmS Ribozyme Activation by Glucosamine-6-Phosphate , 2006, Science.

[24]  D. Herschlag,et al.  Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs. , 2008, Current opinion in structural biology.

[25]  Eric Westhof,et al.  Metal ion binding to RNA. , 2011, Metal ions in life sciences.

[26]  L. Pollack SAXS studies of ion-nucleic acid interactions. , 2011, Annual review of biophysics.

[27]  J. R. Fresco,et al.  Renaturation of transfer ribonucleic acids through site binding of magnesium. , 1966, Proceedings of the National Academy of Sciences of the United States of America.

[28]  N. Walter,et al.  Metal ions: supporting actors in the playbook of small ribozymes. , 2011, Metal ions in life sciences.

[29]  J. Doudna,et al.  A magnesium ion core at the heart of a ribozyme domain , 1997, Nature Structural Biology.

[30]  B. Kankia Inner‐sphere complexes of divalent cations with single‐stranded poly(rA) and poly(rU) , 2004, Biopolymers.

[31]  P. Carey,et al.  A quantitative Raman spectroscopic signal for metal-phosphodiester interactions in solution. , 2010, Biochemistry.

[32]  Gregory K. Schenter,et al.  Natural Energy Decomposition Analysis: The Linear Response Electrical Self Energy , 1996 .

[33]  M. Erat,et al.  Methods to detect and characterize metal ion binding sites in RNA. , 2011, Metal ions in life sciences.

[34]  Stefanie A. Mortimer,et al.  Time-resolved RNA SHAPE chemistry: quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution , 2009, Nature Protocols.

[35]  S. Harvey,et al.  Bidentate RNA-magnesium clamps: on the origin of the special role of magnesium in RNA folding. , 2011, RNA.

[36]  N. Holm The significance of Mg in prebiotic geochemistry , 2012, Geobiology.

[37]  Charles W. Bock,et al.  Manganese as a Replacement for Magnesium and Zinc: Functional Comparison of the Divalent Ions , 1999 .

[38]  A. Petrov,et al.  Calculation of the binding free energy for magnesium–RNA interactions , 2005, Biopolymers.

[39]  David E Draper,et al.  Effects of Mg2+ on the free energy landscape for folding a purine riboswitch RNA. , 2011, Biochemistry.

[40]  Shi-jie Chen,et al.  Importance of diffuse metal ion binding to RNA. , 2011, Metal ions in life sciences.

[41]  J. Wedekind Metal ion binding and function in natural and artificial small RNA enzymes from a structural perspective. , 2011, Metal ions in life sciences.

[42]  J. Šponer,et al.  Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. , 2009, Methods.

[43]  Barry Honig,et al.  Reevaluation of the Born model of ion hydration , 1985 .

[44]  Igor N. Serdyuk,et al.  Methods in Molecular Biophysics: Structure, Dynamics, Function , 2007 .

[45]  The dynamics of unfolded versus folded tRNA: the role of electrostatic interactions. , 2011, Journal of the American Chemical Society.

[46]  D. Thirumalai,et al.  Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations. , 2001, Journal of molecular biology.

[47]  Nathan A. Baker,et al.  PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations , 2004, Nucleic Acids Res..

[48]  Anna Marie Pyle,et al.  Crystal Structure of a Self-Spliced Group II Intron , 2008, Science.

[49]  S. Harvey,et al.  Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state. , 2012, RNA.

[50]  D. Thirumalai,et al.  Metal ion dependence of cooperative collapse transitions in RNA. , 2009, Journal of molecular biology.

[51]  P. Schimmel,et al.  Cooperative binding of magnesium to transfer ribonucleic acid studied by a fluorescent probe. , 1974, Biochemistry.

[52]  N. Hud,et al.  Chapter 4:Metal Ion Interactions with G-Quadruplex Structures , 2008 .

[53]  E. Westhof,et al.  Hierarchy and dynamics of RNA folding. , 1997, Annual review of biophysics and biomolecular structure.

[54]  M. Brenowitz,et al.  Complementing global measures of RNA folding with local reports of backbone solvent accessibility by time resolved hydroxyl radical footprinting. , 2009, Methods.

[55]  A. Magistrato,et al.  The structural role of Mg2+ ions in a class I RNA polymerase ribozyme: a molecular simulation study. , 2012, The journal of physical chemistry. B.

[56]  A. Ferré-D’Amaré,et al.  The roles of metal ions in regulation by riboswitches. , 2011, Metal ions in life sciences.

[57]  The mode of Mg++ binding to oligonucleotides. Inner sphere complexes as markers for recognition? , 1979 .

[58]  Alexander D. MacKerell,et al.  Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. , 2010, Journal of chemical theory and computation.

[59]  W. Winkler,et al.  Magnesium-sensing riboswitches in bacteria , 2010, RNA biology.

[60]  A. Serganov,et al.  Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. , 2004, Chemistry & biology.

[61]  W. Webb,et al.  Ionic strength-dependent persistence lengths of single-stranded RNA and DNA , 2011, Proceedings of the National Academy of Sciences.

[62]  T. Steitz,et al.  The contribution of metal ions to the structural stability of the large ribosomal subunit. , 2004, RNA.

[63]  A. Petrov,et al.  Calculations of Magnesium−Nucleic Acid Site Binding in Solution , 2004 .

[64]  Eric D. Glendening,et al.  Natural energy decomposition analysis: Explicit evaluation of electrostatic and polarization effects with application to aqueous clusters of alkali metal cations and neutrals , 1996 .

[65]  D. York,et al.  Characterization of the Structure and Dynamics of the HDV Ribozyme at Different Stages Along the Reaction Path. , 2011, The journal of physical chemistry letters.

[66]  Daniel Herschlag,et al.  Biological phosphoryl-transfer reactions: understanding mechanism and catalysis. , 2011, Annual review of biochemistry.

[67]  S. Woodson RNA folding pathways and the self-assembly of ribosomes. , 2011, Accounts of chemical research.

[68]  B. Kankia Binding of Mg2+ to single-stranded polynucleotides: hydration and optical studies. , 2003, Biophysical chemistry.

[69]  L. Pollack,et al.  Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA , 2009, Nucleic acids research.

[70]  Shi-jie Chen,et al.  Predicting electrostatic forces in RNA folding. , 2009, Methods in enzymology.

[71]  L. Williams,et al.  A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center , 2009, Nucleic acids research.

[72]  N. Špačková,et al.  Theoretical Study of Binding of Hydrated Zn(II) and Mg(II) Cations to 5‘-Guanosine Monophosphate. Toward Polarizable Molecular Mechanics for DNA and RNA , 2003 .

[73]  Shi-Jie Chen,et al.  Predicting ion binding properties for RNA tertiary structures. , 2010, Biophysical journal.

[74]  J. Feigon,et al.  Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex. , 1999, Journal of molecular biology.

[75]  K. Hampel,et al.  Rapid steps in the glmS ribozyme catalytic pathway: cation and ligand requirements. , 2011, Biochemistry.

[76]  D. Draper,et al.  RNA folding: thermodynamic and molecular descriptions of the roles of ions. , 2008, Biophysical journal.

[77]  D M Crothers,et al.  Equilibrium binding of magnesium(II) by Escherichia coli tRNAfMet. , 1976, Biochemistry.

[78]  V. DeRose,et al.  Ground-state coordination of a catalytic metal to the scissile phosphate of a tertiary-stabilized Hammerhead ribozyme. , 2012, RNA.

[79]  B. Golden,et al.  Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions. , 2011, Biochemistry.

[80]  J. Steitz,et al.  A general two-metal-ion mechanism for catalytic RNA. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[81]  J. Feigon,et al.  The effect of sodium, potassium and ammonium ions on the conformation of the dimeric quadruplex formed by the Oxytricha nova telomere repeat oligonucleotide d(G(4)T(4)G(4)). , 1999, Nucleic acids research.

[82]  J. Micklefield,et al.  Reengineering orthogonally selective riboswitches , 2010, Proceedings of the National Academy of Sciences.

[83]  Kevin M Weeks,et al.  RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts. , 2005, Journal of the American Chemical Society.

[84]  M. Fedor,et al.  An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis. , 1997, Chemistry & biology.

[85]  Gang Wu,et al.  Direct NMR detection of alkali metal ions bound to G-quadruplex DNA. , 2008, Journal of the American Chemical Society.

[86]  W. Scott Ribozymes , 1998, Current Biology.