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.