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

Includes supplementary material: sn.pub/extras

Part I. Design of Energy Transfer ProbesSelection of Fluorophore and Quencher Pairs for Fluorescent Nucleic Acid Hybridization ProbesSalvatore A. E. MarrasChoosing Reporter-Quencher Pairs for Efficient Quenching Through Formation of Intramolecular DimersMary Katherine JohanssonPart II. Energy Transfer Probes for DNA and RNA Hybridization Detection and MonitoringDetection of DNA Hybridization Using Induced Fluorescence Resonance Energy TransferW. Mathias HowellDetecting RNA/DNA Hybridization Using Double-Labeled Donor Probes With Enhanced Fluorescence Resonance Energy Transfer SignalsYukio Okamura and Yuichiro WatanabePart III. Energy Transfer Probes for DNA Breaks Detection and DNA Cleavage MonitoringOscillating Probe for Dual Detection of 5'PO4 and 5'OH DNA Breaks in Tissue SectionsVladimir V. DidenkoUsing Molecular Beacons for Sensitive Fluorescence Assays of the Enzymatic Cleavage of Nucleic AcidsChaoyong James Yang, Jeff Jianwei Li, and Weihong TanA Continuous Assay for DNA Cleavage Using Molecular Break LightsJohn B. Biggins, James R. Prudent, David J. Marshall, and Jon S. ThorsonPart IV. Monitoring of DNA Synthesis and Amplification Using Energy Transfer ProbesHomogenous Detection of Nucleic Acids Using Self-Quenched Polymerase Chain Reaction Primers Labeled With a Single Fluorophore (LUXtm Primers)Irina NazarenkoUse of Self-Quenched, Fluorogenic LUXtm Primers for Gene Expression ProfilingWolfgang KusserTaqMan® Reverse Transcriptase-Polymerase Chain Reaction Coupled With Capillary Electrophoresis for Quantification and Identification of bcr-abl Transcript TypeRajyalakshmi Luthra and L. Jeffrey MedeirosQuantitative TaqMan® Assay for the Detection and Monitoring of Cytomegalovirus Infection in Organ Transplant PatientsHeli Piiparinen and IrmeliLautenschlagerReal-Time Detection and Quantification of Telomerase Activity Utilizing Energy Transfer PrimersHiroshi UeharaPart V. DNA Sequence Analysis and Mutation Detection Using Fluorescence Energy TransferInvader® Assay for Single-Nucleotide Polymorphism Genotyping and Gene Copy Number EvaluationAndrea Mast and Monika de ArrudaReal-Time Quantitative Polymerase Chain Reaction Analysis of Mitochondrial DNA Point MutationLee-Jun C. Wong and Ren-Kui BaiMultiplex Single-Nucleotide Polymorphism Detection by Combinatorial Fluorescence Energy Transfer Tags and Molecular AffinityAnthony K. Tong and Jingyue JuHigh-Throughput Genotyping With Energy Transfer-Labeled PrimersYuri KhripinPart VI. Determination of Distance and DNA FoldingDistance Determination in Protein-DNA Complexes Using Fluorescence Resonance Energy TransferMike Lorenz and Stephan DiekmannMulti-Fluorophore Fluorescence Resonance Energy Transfer for Probing Nucleic Acids Structure and FoldingJuewen Liu and Yi LuPart VII. DNA-Based Biosensors Utilizing Energy TransferFluorescent DNAzyme Biosensors for Metal Ions Based on Catalytic Molecular BeaconsJuewen Liu and Yi LuFluorescent Energy Transfer Readout of an Aptazyme-Based BiosensorDavid Rueda and Nils G. WalterFluorescence Resonance Energy Transfer in the Studies of Guanine QuadruplexesBernard Juskowiak and Shigeori TakenakaSolution-Phase Molecular-Scale Computation With Deoxyribozyme-Based Logic Gates and Fluorescent ReadoutsJoanne Macdonald, Darko Stefanovic, and Milan N. StojanovicIndex