Fluorescent Energy Transfer Nucleic Acid Probes: Designs and Protocols

ISBN-13: 9781617375316 / Angielski / Miękka / 2010 / 372 str.

Vladimir V. Didenko

Opis

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 Forster tra- fer, or by non-Forster transfer mechanisms. Although the probes using Forster transfer were developed and used first, the later non-Forster-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 Forster-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."

Recenzje

From the reviews:

"The content of the book provides a complete source of information in the DNA/RNA area and related fields. ... In brief, the book is a useful, practical source of information. ... The group of scientists and researchers ... that forms the potential market for this book can be extended with an important category: undergraduate and graduate students and postdoctoral researchers. Some materials can be adapted for interdisciplinary courses in molecular life sciences." (Dr. Ton Visser, Molecular Biotechnology, Vol. 34, September, 2006)

"Fluorescence Energy Transfer Nucleic Acid Probes, Design and Protocols is a timely book. It is the first concise collection of fluorescence methods and assays used in exploring biomolecular structure, dynamic and interaction. ... a rich compendium of information for the beginner in the field, as well as a source of ideas and inspiration for the advanced researcher. It is a book that should be on the shelf in all laboratories using fluorescent-probe techniques in biochemistry and molecular biology." (Sabine Müller, ChemBioChem, Vol. 8, 2007)

Spis treści

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® 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® 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® 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

Blurb

Although fluorescent probes and assays, which use energy transfer (ET) for monitoring DNA reactions, have multiplied in recent years, until now there have been no manuals summarizing the many different protocols and probe designs. Fluorescent Energy Transfer Nucleic Acid Probes: Designs and Protocols is the first publication to provide such a collection. In the volume, hands-on experts-often the original developers of the technique-comprehensively describe a variety of fluorescent probes and devices that use ET, including molecular beacons, molecular break lights, TaqMan® probes, LUX™ primers, Invader® assay, aptazymes, DNAzymes, molecular machines, biosensors, and logic gates for molecular-scale computation. Merging work on nanotechnology and fluorescent probes, the authors assemble the first comprehensive treatment of all the key DNA- and RNA-based ET probes and present strategies for their optimized custom design. They discuss both fluorescence resonance energy transfer (FRET)-based and non-FRET-based constructs, and provide a complete set of techniques to monitor DNA and RNA reactions, such as hybridization, amplification, cleavage, folding, and associations with proteins, other molecules, and metal ions. Detailed protocols are provided for distance determination in protein-DNA complexes and the detection of topological DNA alterations, mutations, and single-nucleotide polymorphisms. The protocols follow the successful Methods in Molecular Biology™ series format, each offering an outline of the principles behind the technique, step-by-step detailed instructions, and comprehensive troubleshooting.
Exhaustive and state-of-the-art, Fluorescent Energy Transfer Nucleic Acid Probes: Designs and Protocols is an invaluable resource for both novice and experienced researchers who wish to use the latest developments in fluorescent probes in any field of molecular biology.