Fluorescent DNA-based enzyme sensors

Abstract

Fluorescent sensors that make use of DNA structures have become widely useful in monitoring enzymatic activities. Early studies focused primarily on enzymes that naturally use DNA or RNA as the substrate. However, recent advances in molecular design have enabled the development of nucleic acid sensors for a wider range of functions, including enzymes that do not normally bind DNA or RNA. Nucleic acid sensors present some potential advantages over classical small-molecule sensors, including water solubility and ease of synthesis. An overview of the multiple strategies under recent development is presented in this critical review, and expected future developments in microarrays, single molecule analysis, and in vivo sensing are discussed (160 references).

Efficient synthesis of fluorescent alkynyl C-nucleosides via Sonogashira coupling for the preparation of DNA-based polyfluorophores

“…14, 15 ODFs have also been extensively applied for sensing of small molecules and as well as metal cations and inorganic anions. 16–20 …”

Nucleic Acid Fluorescent Probes for Biological Sensing

“…1F) has been successfully applied for the detection of esterases and lipases in vitro and in cells. 7,131 …”

“…128 DNA-scaffolded oligodeoxyriboside fluorophores (ODFs) have been developed by Kool and co-workers for cellular enzyme imaging. 7 In the ODF system, the DNA bases are replaced by several fluorophores that are directly attached to the backbone in close proximity. 129,130 By conjugation with a specific substrate structure, these ODFbased fluorescence sensors can be used as the reporters in turn-on sensing of cleaving activities of the corresponding enzymes.…”

“…Another chemical property of nucleic acids is to act as substrates for various nucleic acid enzymes. This property can be utilized not only to detect those enzymes and screen their inhibitors, 2,6,7 but also employed to develop powerful signal amplification systems, finding extensive applications. [8][9][10][11][12][13] In addition to these versatile functions of DNA structure, nucleic acid fluorescent probes also benefit from excellent water solubility and ease of synthesis and modification.…”

Real-time detection of TDP1 activity using a fluorophore–quencher coupled DNA-biosensor

“…Although many different types of biosensors exist there are several advantages to use DNA-biosensors (Dai and Kool, 2011;Stougaard et al, 2011). One is that DNA is an easily manipulated nano-scale material and the sequence of the sensor may be designed to self-assemble into desired structures, which is especially useful in quencher-fluorophore setups.…”