Fluorescence-Signaling Nucleic Acid-Based Sensors

It is widely known that two single-stranded nucleic acids with complementary sequences have the inherent ability to form Watson-Crick duplex structures. The simplicity and sequence-specificity of duplex structure formation, the high chemical stability of a duplex, and the convenience of automated synthesis have made DNA oligonucleotides an ideal choice as probes for the detection of nucleic acids. Recently developed in vitro selection techniques permit creation of DNA and RNA “aptamers” that are capable of binding a wide variety of nonnucleic acid targets with high affinity and specificity. Aptamers have considerably broadened the utility of nucleic acids as probes for detection of biological and nonbiological targets. In vitro selection also allows generation of artificial ribozymes (catalytic RNAs) and deoxyribozymes (catalytic DNAs) with desirable functions. Aptamers, ribozymes, and deoxyribozymes have become increasingly valuable molecular tools in the form of switches and sensors. Unfortunately, binding or catalytic actions by these switches and sensors do not usually lead to an easily detectable signal, and the lack of a facile reporting method could substantially reduce their value. To facilitate the exploitation of nucleic acid switches and sensors for detection-related applications, many recent studies have explored fluorescence signaling as a convenient approach for the reporting of binding and catalytic events. This chapter is devoted to the discussion of these efforts. The reporter molecules to be described include molecular beacons, signaling aptamers, and signaling ribozymes and deoxyribozymes.