Structure‐Switching Signaling Aptamers: Transducing Molecular Recognition into Fluorescence Signaling
- 7 April 2004
- journal article
- concept
- Published by Wiley in Chemistry – A European Journal
- Vol. 10 (8) , 1868-1876
- https://doi.org/10.1002/chem.200305470
Abstract
The development of aptamer technology considerably broadens the utility of nucleic acids as molecular recognition elements, because it allows the creation of DNA or RNA molecules for binding a wide variety of analytes (targets) with high affinity and specificity. Several recent studies have focused on developing rational design strategies for transducing aptamer–target recognition events into easily detectable signals, so that aptamers can be widely exploited for detection directed applications. We have devised a generalizable strategy for designing nonfluorescent aptamers that can be turned into fluorescence‐signaling reporters. The resultant signaling probes are denoted “structure‐switching signaling aptamers” as they report target binding by switching structures from DNA/DNA duplex to DNA/target complex. The duplex is formed between a fluorophore‐labeled DNA aptamer and an antisense DNA oligonucleotide modified with a quencher (denoted QDNA). In the absence of the target, the aptamer hybridizes with QDNA, bringing the fluorophore into close proximity of the quencher for efficient fluorescence quenching. When this system is exposed to the target, the aptamer switches its binding partner from QDNA to the target. This structure‐switching event is coupled to the generation of a fluorescent signal through the departure of QDNA, permitting the real‐time monitoring of the aptamer–target recognition. In this article, we discuss the conceptual framework of the structure‐switching approach, the essential features of structure‐switching signaling aptamers as well as remaining challenges and possible solutions associated with this new methodology.Keywords
This publication has 38 references indexed in Scilit:
- A novel RNA motif that binds efficiently and specifically to the Tat protein of HIV and inhibits the trans‐activation by Tat of transcription in vitro and in vivoGenes to Cells, 2000
- Designed Signaling Aptamers that Transduce Molecular Recognition to Changes in Fluorescence IntensityJournal of the American Chemical Society, 2000
- DNA chips: State-of-the artNature Biotechnology, 1998
- Molecular Beacons: Probes that Fluoresce upon HybridizationNature Biotechnology, 1996
- Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA MicroarrayScience, 1995
- A DNA Aptamer That Binds Adenosine and ATPBiochemistry, 1995
- An RNA motif that binds ATPNature, 1993
- Selection of single-stranded DNA molecules that bind and inhibit human thrombinNature, 1992
- In vitro selection of RNA molecules that bind specific ligandsNature, 1990
- Systematic Evolution of Ligands by Exponential Enrichment: RNA Ligands to Bacteriophage T4 DNA PolymeraseScience, 1990