Pub. Date:
Springer-Verlag New York, LLC
Fluorescent Energy Transfer Nucleic Acid Probes: Designs and Protocols / Edition 1

Fluorescent Energy Transfer Nucleic Acid Probes: Designs and Protocols / Edition 1

by Vladimir V. Didenko


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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- ols and fluorescent probe designs. In view of this, the main objective of Fluorescent Energy Transfer Nucleic Acid Probes: Designs and Prools 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.

Product Details

ISBN-13: 9781588293800
Publisher: Springer-Verlag New York, LLC
Publication date: 04/01/2006
Series: Methods in Molecular Biology , #335
Edition description: 2006
Pages: 372
Product dimensions: 6.10(w) x 9.25(h) x 0.04(d)

Table of Contents

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 Mihondrial 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. Stojanović


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