Ribozymes : methods and protocols / edited by Jorg S. Hartig. — New York : Humana Press : Springer, c2012. – (58.17/M592/v.848)

Contents

    CONTENTS
    
    Preface
    Contributors
    
    1 Introduction 1
    2 Characterization of Hammerhead Ribozyme Reactions 5
    3 Mechanistic Analysis of the Hepatitis Delta Virus (HDV) Ribozyme: Methods for RNA Preparation， Structure Mapping， Solvent Isotope Effects， and Co-transcriptional Cleavage 21
    4 Kinetic Characterization of Hairpin Ribozyme Variants 41
    5 Characterization of RNase P RNA Activity 61
    6 Group I Intron Ribozymes
    7 Kinetic Characterization of Group II Intron Folding and Splicing
    8 Mechanism and Distribution ofglmS Ribozymes
    9 Structure-Based Search and In Vitro Analysis of Self-Cleaving Ribozymes 131
    10 Discovery of RNA Motifs Using a Computational Pipeline that Allows Insertions in Paired Regions and Filtering of Candidate Sequences 145
    11 Crystallographic Analysis of Small Ribozymes and Riboswitches
    12 Functional Dynamics of RNA Ribozymes Studied by NMR Spectroscopy 185
    13 Deoxyribozyme-Based， Semisynthetic Access to Stable Peptidyl-tRNAs Exemplified by tRNATM Carrying a Macrolide Antibiotic Resistance Peptide 201
    14 Probing Functions of the Ribosomal Peptidyl Transferase Center by Nucleotide Analog Interference
    15 Single Molecule FRET Characterization of Large Ribozyme Folding
    16 Metal Ion-RNA Interactions Studied via Multinuclear NMR 253
    17 Analysis of Catalytic RNA Structure and Function by Nucleotide Analog Interference Mapping 275
    18 In Vitro Selection of Metal Ion-Selective DNAzymes 297
    19 Selecting Allosteric Ribozymes
    20 Screening Effective Target Sites on mRNA: A Ribozyme Library Approach
    21 A Computational Approach to Predict Suitable Target Sites for trans-Acting Minimal Hammerhead Ribozymes
    22 Targeting mRNAs by Engineered Sequence-Specific RNase P Ribozymes
    23 Target-Induced SOFA-HDV Ribozyme
    24 Ribozyme-Mediated Trans Insertion-Splicing into Target RNAs
    25 Developing Fluorogenic RNA-Cleaving DNAzymes for Biosensing Applications 395
    26 Development of Trainable Deoxyribozyme-Based Game Playing Automaton 419
    27 Rational Design and Tuning of Ribozyme-Based Devices 439
    28 In Vivo Screening of Ligand-Dependent Hammerhead Ribozymes 455
    29 Flexizymes as a tRNA Acylation Tool Facilitating Genetic Code Reprogramming
    Index 479