FöRster Resonance Energy Transfer (FRET) between Nucleobase Analogs - A Tool for Detailed Structure and Dynamics Investigations

Book chapter, 2016

The three-dimensional structure and the conformational dynamics of nucleic acids and their conformational changes upon interaction with other biomolecules are fundamental to the understanding of these key players of life and their role in the central dogma of molecular biology as well as RNAi-mediated gene activity moderation. To enable accurate Forster resonance energy transfer (FRET) in nucleic acid-containing systems, the author group has developed a family of base analogs, the tricyclic cytosines, which meet most of the criteria that are important to become a member of an excellent FRET pair. This chapter discusses the development and characterization of these cytosine analogs, their use as the first nucleic acid base analog FRET pair, and some recent applications. The first nucleic acid base analog FRET pair, tCo-tCnitro, has all the features necessary for such probe molecules as well as being excellent analogs of cytosine.