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Contents Preface v Contributors xi PART 1 DESIGN OF ENERGY TRANSFER PROBES 1 Selection of Fluorophore and Quencher Pairs for Fluorescent Nucleic Acid Hybridization Probes Salvatore A. E. Marras 3 2 Choosing Reporter-Quencher Pairs for Efficient Quenching Through Formation of Intramolecular Dimers Mary Katherine Johansson x PART 2 ENERGY TRANSFER PROBES FOR DNA AND RNA HYBRIDIZATION DETECTION AND MONITORING 3 Detection of DNA Hybridization Using Induced Fluorescence Resonance Energy Transfer (iFRET) W. Mathias Howell xx 4 Detecting RNA/DNA Hybridization Using Double-Labeled Donor Probes With Enhanced FRET Signals Yukio Okamura and Yuichiro Watanabe xx PART 3 ENERGY TRANSFER PROBES FOR DNA BREAKS DETECTION AND DNA CLEAVAGE MONITORING 5 Oscillating Probe for Dual Detection of 5'PO4 and 5'OH DNA Breaks in Tissue Sections Vladimir V. Didenko xx 6 Using Molecular Beacons for Sensitive Fluorescence Assays of the Enzymatic Cleavage of Nucleic Acids Weihong Tan xx 7 A Continuous Assay for DNA Cleavage Using Molecular Break Lights John B. Biggins, James R. Prudent, David J. Marshall, and Jon S. Thorson xxx PART 4 MONITORING OF DNA SYNTHESIS AND AMPLIFICATION USING ET PROBES 8 Homogenous Detection of Nucleic Acids Using Self-Quenching PCR Primers Labeled With a Single Fluorophore (LUXTM Primers) Irina Nazarenko xxx 9 Use of Self-Quenched, Fluorogenic LUXTM Primers for Gene Expression Profiling Wolfgang Kusser xxx 10 TaqMan RT-PCR Coupled With Capillary Electrophoresis for Quantification and Identification of bcr-abl Transcript Type Rajyalakshmi Luthra and L. Jeffrey Medeiros xxx 11 Quantitative TaqMan Assay for the Detection and Monitoring of CMV Infection in Transplant Patients Heli Piiparinen and Irmeli Lautenschlager xxx 12 Real-Time Detection and Quantification of Telomerase Activity Utilizing Energy Transfer Primers (Real-Time TRAP Assay) Hiroshi Uehara xxx PART 5 DNA SEQUENCE ANALYSIS AND MUTATION DETECTION USING FLUORESCENT ENERGY TRANSFER 13 Invader® Assay for SNP Genotyping and Gene Copy Number Evaluation Andrea Mast and Monika de Arruda xxx 14 Real-Time Quantitative PCR Analysis of Mitochondrial DNA Point Mutation Lee-Jun C. Wong and Ren-Kui Bai xxx 15 Multiplex Single Nucleotide Polymorphism Detection by Combinatorial Fluorescence Energy Transfer Tags and Molecular Affinity Anthony K. Tong and Jingyue Ju xxx 16 High-Throughput Genotyping With Energy Transfer-Labeled Primers Yuri Khripin xxx PART 6 DETERMINATION OF DISTANCES AND DNA FOLDING 17 Distance Determination in Protein/DNA Complexes Using FRET Mike Lorenz and Stephan Diekmann xxx 18 Multi-Fluorophore Fluorescence Resonance Energy Transfer (FRET) for Probing Nucleic Acids Structure and Folding Juewen Liu and Yi Lu xxx PART 7 DNA-BASED BIOSENSORS UTILIZING ENERGY TRANSFER 19 Detecting Metal Ions With Fluorescent DNAzyme Biosensors Juewen Liu and Yi Lu xxx 20 Fluorescent Energy Transfer Readout of an Aptazyme-Based Biosensor David Rueda and Nils G. Walter xxx 21 FRET in the Studies of Guanine Quadruplexes Bernard Juskowiak and Shigeori Takenaka xxx 22 Solution-Phase Molecular-Scale Computation With Deoxyribozyme-Based Logic Gates and Fluorescent Readouts Joanne Macdonald, Darko Stefanovic, and Milan N. Stojanovic xxx Index........................................................................................xxx
Library of Congress Subject Headings for this publication:
Nucleic acid probes.
Nucleic Acid Probes.
Fluorescence Resonance Energy Transfer -- methods.
Genetic Techniques.