Pt. 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 -- Pt. 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 tranfer signals / Yukio Okamura and Yuichiro Watanabe -- Pt. 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 -- Acontinuous assay for DNA cleavage using molecular break lights / John B. Biggins ... [et al.] --
Pt. 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 (LUX primers) / Irina Nazarenko -- Use of self-quenched, fluorogenic LUX 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 Irmeli Lautenschlager -- Real-time detection and quantification of telomerase activity utilizing energy transfer primers / Hiroshi Uehara -- Pt. 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 in combinatorial fluorescence energy transfer tags and molecular affinity / Anthony K. Tong and Jingyue Ju -- High-throughput genotyping with energy transfer-labeled primers / Yuri Khripin -- Pt. 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 -- Pt. 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.
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Fluorescent energy transfer nucleic acid probes : designs and protocols