Fluorescent energy transfer nucleic acid probes : designs and protocols

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Fluorescent energy transfer nucleic acid probes : designs and protocols

edited by Vladimir V. Didenko

（Methods in molecular biology / John M. Walker, series editor, v. 335）

Humana Press, c2006

  • : alk. paper

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注記

Includes bibliographical references and index

内容説明・目次

内容説明

Fluorescent nucleic acid probes, which use energy transfer, include such constructs as molecular beacons, molecular break lights, Scorpion primers, TaqMan probes, and others. These probes signal detection of their targets by changing either the intensity or the color of their fluorescence. Not surpr- ingly, these luminous, multicolored probes carry more flashy names than their counterparts in the other fields of molecular biology. In recent years, fluor- cent probes and assays, which make use of energy transfer, have multiplied at a high rate and have found numerous applications. However, in spite of this explosive growth in the field, there are no manuals summarizing different p- tocols and fluorescent probe designs. In view of this, the main objective of Fluorescent Energy Transfer Nucleic Acid Probes: Designs and Protocols is to provide such a collection. Oligonucleotides with one or several chromophore tags can form fluor- cent probes capable of energy transfer. Energy transport within the probe can occur via the resonance energy transfer mechanism, also called Foerster tra- fer, or by non-Foerster transfer mechanisms. Although the probes using Foerster transfer were developed and used first, the later non-Foerster-based probes, such as molecular beacons, now represent an attractive and widely used option. The term "fluorescent energy transfer probes" in the title of this book covers both Foerster-based fluorescence resonance energy transfer (FRET) probes and probes using non-FRET mechanisms. Energy transfer probes serve as molecule-size sensors, changing their fluorescence upon detection of various DNA reactions.

目次

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 IrmeliLautenschlager 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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