Alternative Roles for Metal Ions in Enzyme Catalysis and the Implications for Ribozyme Chemistry

Abstract

Contents 1. Introduction 97 2. Increased Complexity of Group-Transfer Catalysis by Metalloenzymes 98 3. Metal-Ion Binding Sites in Proteins and Ribozymes 99 3.1. Metal-Ion Binding Sites in Proteins 99 3.2. Metal-Ion Binding Sites in RNA 100 4. Promoting Catalysis with Charge: Electrostatic Effects 101 4.1. Localized Charges Can Modulate the Reactivity of Enzyme Functional Groups 101 4.2. Electrostatic Induction by Divalent Metal Ions 103 4.3. Switching Charge Types in Proteins: Metals for Lysine and Vice Versa 103 4.4. Electrostatic Induction of pK a Shifts in Nucleic Acids: Lessons from Nucleobase Model Systems 104 4.4.1. Modification of Purine Acidity 104 4.4.2. Modification of Pyrimidine Acidity 105 4.4.3. Effects on Backbone Functionalities 105 4.4.4. Additional Reasons for pK a Shifts in Nucleobases 105 4.4.5. Water−Hydroxide Equilibria and the "Metal-Ion Switch Experiment" 105 4.5. Distance Dependence and Additivity of Charge Effects 105 5. Metal-Ion Catalysis through Outer-Sphere Interactions 107 6. Catalysis by Monovalent Metal Ions 108 7. Reduced Solvent Polarity Promotes Reactivity 110 8. Conclusions 110 9. Acknowledgments 111 10. References 111

Metal‐Induced Specific and Nonspecific Oligonucleotide Folding Studied by FRET and Related Biophysical and Bioanalytical Implications

“…As mentioned previously, this is less of a problem for naturally occurring functional nucleic acids. For example, large ribozymes, [47][48][49] riboswitches, [50] as well as small functional nucleic acids including transfer RNA, [51] small ribozymes, [52,53] and DNAzymes [54,55] contained a relatively rigid structure with extensive double-stranded regions. Analytical chemists have also designed similar sensors.…”

Metal ion-N7 coordination in a ribozyme branch domain by NMR

“…Hence, all ribozymes can be considered to be obligate metallo-ribozymes depending strongly on the presence of monovalent as well as divalent metal ions. 1 In order to understand the role of M n+ ions in folding and catalysis of large RNAs like group II intron ribozymes, 2,3 the exact coordination sphere of crucial ions for these processes needs to be known. However, it is highly challenging to determine the exact coordination sphere of kinetically labile metal ions in larger RNA structures in solution state.…”

An Ultrasensitive Light-up Cu2+ Biosensor Using a New DNAzyme Cleaving a Phosphorothioate-Modified Substrate

“…The initial library contained ~10 13 random DNA sequences, and we hoped to isolate a sub-population that can selectively use Cu 2+ for cleavage.…”

“…[8][9][10][11] DNAzymes are DNA-based catalysts that often require divalent metal ions for activity. [12][13][14] In vitro selection has been intentionally carried out in the presence of specific metal ions to isolate sensor DNAzymes. 15,16 A Cu 2+ biosensor was reported using a DNAzyme that performs oxidative DNA cleavage.…”