DNAzymes Methods and Protocols

This volume explores a collection of different protocols for the analysis and characterization of DNAzymes and their functions. The topics covered in this book range from bioinformatics and molecular dynamics simulations for the study or modification of nucleic acids to the descriptions of spectroscopic, fluorescence-based, or crystallographic methods to understand the structure and function of DNAzymes. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and comprehensive, DNAzymes: Methods and Protocols is a valuable resource for scientists and researchers interested in learning more about this evolving field. 

A Protocol for Gold Nanoparticle-Assisted Aptamer Selection for a Small Molecule Porphyrin to Develop DNAzyme.- Selection of Aptamer for N-methyl Mesoporphyrin IX to Develop Porphyrin Metalation DNAzyme.- PCR Methods for the Generation of Catalytic ssDNA.- Design of a DNAzyme: Prediction of mRNA Regions Accessible to a DNAzyme.- Fluorescence-Based Kinetic Measurements for RNA-Cleaving DNAzymes.- Stability and Activity of the 10-23 DNAzyme under Molecular Crowding Conditions.- Quantifying the Number and Affinity of Mn2+-Binding Sites with EPR Spectroscopy.- Obtaining Crystals of Nucleic Acids in Complex with the Protein U1A Using the Soaking Method.- Crystallization and Structural Determination of 8-17 DNAzyme.- Solution NMR Spectroscopy as a Tool to Study DNAzyme Structure and Function.- Molecular Modeling and Simulations of DNA and RNA: DNAzyme as a Model System.- Single-Molecule Kinetic Studies of Nucleic Acids by Förster Resonance Energy Transfer.- Chemical Dual End-Labeling of Large Ribozymes.- Spin Labeling of Long RNAs via Click Reaction and Enzymatic Ligation.- Preparation of Site-Specifically Spin-Labeled RNA by In Vitro Transcription using an Expanded Genetic Alphabet.- PELDOR Measurements on Nitroxide-Labelled Oligonucleotides.- Sensing Metal Ions with Phosphorothioate-Modified DNAzymes.- Enhancement of Activity for Peroxidase-Mimicking DNAzyme by Covalent Attachment of Hemin to G-quadruplex-Forming Oligonucleotide Using Click Chemistry.- Generation of RNA with 2’, 3’-cyclic Phosphates by Deoxyribozyme Cleavage in Frozen Solutions.