Fluorescent energy transfer nucleic acid probes : designs and protocols / edited by Vladimir V. Didenko.

Contributor(s): Didenko, Vladimir V
Material type: TextTextSeries: Methods in molecular biology (Clifton, N.J.): v. 335.Publisher: Totowa, N.J. : Humana Press, ©2006Description: 1 online resource (xv, 372 pages) : illustrationsContent type: text Media type: computer Carrier type: online resourceISBN: 1588293807; 9781588293800; 9781597450690; 1597450693; 1280832096; 9781280832093Subject(s): Nucleic acid probes | Fluorescence Resonance Energy Transfer -- methods | Nucleic Acid Probes | Genetic Techniques | Molecular Probes | Investigative Techniques | Energy Transfer | Nucleic Acids | Spectrometry, Fluorescence | Analytical, Diagnostic and Therapeutic Techniques and Equipment | Biochemical Phenomena | Fluorometry | Biophysical Phenomena | Nucleic Acids, Nucleotides, and Nucleosides | Laboratory Chemicals | Specialty Uses of Chemicals | Chemical Phenomena | Luminescent Measurements | Physical Phenomena | Chemicals and Drugs | Chemical Actions and Uses | Photometry | Phenomena and Processes | Chemistry Techniques, Analytical | Fluorescence Resonance Energy Transfer | Methods | SCIENCE -- Life Sciences -- Molecular Biology | Nucleic acid probes | Human Anatomy & Physiology | Health & Biological Sciences | Animal BiochemistryGenre/Form: CD-ROMs. | Electronic books. | CD-ROMs. Additional physical formats: Print version:: Fluorescent energy transfer nucleic acid probes.DDC classification: 572.8/4 LOC classification: QP624.5.D73 | F558 2006Online resources: Click here to access online
Contents:
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 transfer 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 [and others].
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.
Summary: 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.
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Includes bibliographical references and index.

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 transfer 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 [and others].

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.

Print version record.

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.

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