The first comprehensive treatment of energy transfer (ET) nucleic acid probes. Hands-on experts thoroughly describe all the major probes, both fluorescence resonance energy transfer (FRET)-based and non-FRET-based, and provide a complete set of techniques to monitor DNA and RNA reactions, including hybridization, amplification, cleavage, folding, and associations with proteins, other molecules, and metal ions. Optimal design strategies for customized ET probes are presented, as well as techniques for distance determination in protein-DNA complexes and the detection of topological DNA alterations, mutations, DNA breaks and single nucleotide polymorphisms. Merging work on nanotechnology, and fluorescent probes, authors describe in detail the design and application of ET-using molecular devices, such as biosensors, molecular machines, and logic gates for molecular scale computation.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.
