Exploration of Structure-Switching in the Design of Aptamer Biosensors

Abstract

The process of "structure-switching" enables biomolecular switches to function as effective biosensing tools. Biomolecular switches can be activated or inactivated by binding to a specific target that triggers a precise conformational change in the biomolecules involved. Although many examples of aptamer-based biomolecular switches can be found in nature, substantial effort has been made in the last decade to engineer structure-switching aptamer sensors by coupling aptamers to a signal transduction method to generate a readout signal upon target binding to the aptamer domain. This chapter focuses on the progress of research on engineered structure-switching aptamer sensors. We begin by discussing the origin of the structure-switching aptamer design, highlight the key developments of structure-switching DNA aptamers for fluorescence-, electrochemistry-, and colorimetry-based detection, and introduce our recent efforts in exploring RNA aptamers to create structure-switching molecular sensors.

Functional nucleic acid biosensors utilizing rolling circle amplification

“…Structure-switching aptamers are designed to switch between a duplex form, which has a short NA strand hybridized across the aptamer domain and a primer extension, and a complex formed between the target and aptamer, which displaces the hybridized NA strand. 114–117 While often used to directly generate fluorescence signals based on displacement of adjacent quencher- and fluorophore-labelled strands, 114–117 this method can also be used as a means to initiate RCA by using the displaced NA strand as the RCA primer. In an early example, Hu et al utilized the thrombin-binding structure-switching aptamer to regulate RCA via target-induced primer displacement.…”

Aptamer-based biosensors for biomedical diagnostics

“…78 Compared to the small end-to-end distance change within the aptamer, this method generates a much larger distance change and uorescence enhancement. [79][80][81][82][83][84][85] The uorophore/quencher can be replaced by other signaling moieties such as electrode surfaces, 86,87 quantum dots, 88 or metal nanoparticles 89 for other types of signal transduction. In addition to using cDNA to lock the initial aptamer conformation, a variation is to use an inorganic surface to adsorb the DNA probe.…”

Electrochemical Aptatoxisensor Responses on Nanocomposites Containing Electro-Deposited Silver Nanoparticles on Poly(Propyleneimine) Dendrimer for the Detection of Microcystin-LR in Freshwater

“…Generally, in water algal bloom, MC-LR may coexist with some algal toxins such as Nodularin-R (NODLR), MC-RR, MC-YR, 17β-estradiol (EE2), as well as some food toxins such as zearalenone (ZEO) [38,39,40,41]. Therefore, there is a need to evaluate the cross-reactivity of the aptatoxisensor.…”