Fluorescent Energy Transfer Nucleic Acid Probes Designs and Protocols

About this book

The first comprehensive treatment of energy transfer (ET) nucleic acid probes. Hands-on experts thoroughly describe all the major probes, both fluorescence resonance energy transfer (FRET)-based and non-FRET-based, and provide a complete set of techniques to monitor DNA and RNA reactions, including hybridization, amplification, cleavage, folding, and associations with proteins, other molecules, and metal ions. Optimal design strategies for customized ET probes are presented, as well as techniques for distance determination in protein-DNA complexes and the detection of topological DNA alterations, mutations, DNA breaks and single nucleotide polymorphisms. Merging work on nanotechnology, and fluorescent probes, authors describe in detail the design and application of ET-using molecular devices, such as biosensors, molecular machines, and logic gates for molecular scale computation.

Contents

Part I. Design of Energy Transfer Probes Selection of Fluorophore and Quencher Pairs for Fluorescent Nucleic Acid Hybridization Probes Salvatore A. E. Marras Choosing Reporter-Quencher Pairs for Efficient Quenching Through Formation of Intramolecular Dimers Mary Katherine Johansson Part II. Energy Transfer Probes for DNA and RNA Hybridization Detection and Monitoring Detection of DNA Hybridization Using Induced Fluorescence Resonance Energy Transfer W. Mathias Howell Detecting RNA/DNA Hybridization Using Double-Labeled Donor Probes With Enhanced Fluorescence Resonance Energy Transfer Signals Yukio Okamura and Yuichiro Watanabe Part III. Energy Transfer Probes for DNA Breaks Detection and DNA Cleavage Monitoring Oscillating Probe for Dual Detection of 5'PO4 and 5'OH DNA Breaks in Tissue Sections Vladimir V. Didenko Using Molecular Beacons for Sensitive Fluorescence Assays of the Enzymatic Cleavage of Nucleic Acids Chaoyong James Yang, Jeff Jianwei Li, and Weihong Tan A Continuous Assay for DNA Cleavage Using Molecular Break Lights John B. Biggins, James R. Prudent, David J. Marshall, and Jon S. Thorson Part IV. Monitoring of DNA Synthesis and Amplification Using Energy Transfer Probes Homogenous Detection of Nucleic Acids Using Self-Quenched Polymerase Chain Reaction Primers Labeled With a Single Fluorophore (LUXtm Primers) Irina Nazarenko Use of Self-Quenched, Fluorogenic LUXtm Primers for Gene Expression Profiling Wolfgang Kusser TaqMan(R) Reverse Transcriptase-Polymerase Chain Reaction Coupled With Capillary Electrophoresis for Quantification and Identification of bcr-abl Transcript Type Rajyalakshmi Luthra and L. Jeffrey Medeiros Quantitative TaqMan(R) Assay for the Detection and Monitoring of Cytomegalovirus Infection in Organ Transplant Patients Heli Piiparinen and Irmeli Lautenschlager Real-Time Detection and Quantification of Telomerase Activity Utilizing Energy Transfer Primers Hiroshi Uehara Part V. DNA Sequence Analysis and Mutation Detection Using Fluorescence Energy Transfer Invader(R) Assay for Single-Nucleotide Polymorphism Genotyping and Gene Copy Number Evaluation Andrea Mast and Monika de Arruda Real-Time Quantitative Polymerase Chain Reaction Analysis of Mitochondrial DNA Point Mutation Lee-Jun C. Wong and Ren-Kui Bai Multiplex Single-Nucleotide Polymorphism Detection by Combinatorial Fluorescence Energy Transfer Tags and Molecular Affinity Anthony K. Tong and Jingyue Ju High-Throughput Genotyping With Energy Transfer-Labeled Primers Yuri Khripin Part VI. Determination of Distance and DNA Folding Distance Determination in Protein-DNA Complexes Using Fluorescence Resonance Energy Transfer Mike Lorenz and Stephan Diekmann Multi-Fluorophore Fluorescence Resonance Energy Transfer for Probing Nucleic Acids Structure and Folding Juewen Liu and Yi Lu Part VII. DNA-Based Biosensors Utilizing Energy Transfer Fluorescent DNAzyme Biosensors for Metal Ions Based on Catalytic Molecular Beacons Juewen Liu and Yi Lu Fluorescent Energy Transfer Readout of an Aptazyme-Based Biosensor David Rueda and Nils G. Walter Fluorescence Resonance Energy Transfer in the Studies of Guanine Quadruplexes Bernard Juskowiak and Shigeori Takenaka Solution-Phase Molecular-Scale Computation With Deoxyribozyme-Based Logic Gates and Fluorescent Readouts Joanne Macdonald, Darko Stefanovic, and Milan N. Stojanovic Index

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