Conformation Change Of Aptamer Research Articles

Aptamer-based colorimetric biosensing of Ochratoxin A using unmodified gold nanoparticles indicator

This work presents an aptasensor for Ochratoxin A (OTA) using unmodified gold nanoparticles (AuNPs) indicator. The assay method is based on the conformation change of OTA's aptamer in phosphate buffered saline (PBS) containing Mg 2+ and OTA, and the phenomenon of salt-induced AuNPs aggregation. A single measurement took only five minutes. Circular dichroism spectroscopic experiments revealed for the first time that upon the addition of OTA, the conformation of OTA's aptamer in PBS buffer changed from random coil structure to compact rigid antiparallel G-quadruplex structure. This compact rigid G-quadruplex structure could not protect AuNPs against salt-induced aggregation, and thus the color change from red to blue could be observed by the naked eye. The linear range of the colorimetric aptasensor covered a large variation of OTA concentration from 20 to 625 nM and the detection limit of 20 nM (3 σ) was obtained.

Direct Optical Detection of Aptamer Conformational Changes Induced by Target Molecules

Aptamers are single-stranded DNA/RNA oligomers that fold into three-dimensional conformations in the presence of specific molecular targets. Surface-enhanced Raman spectroscopy (SERS) of thiol-bound DNA aptamer self-assembled monolayers on Au nanoshell surfaces provides a direct, label-free detection method for the interaction of DNA aptamers with target molecules. A spectral cross-correlation function, Gamma, is shown to be a useful metric to quantify complex changes in the SERS spectra resulting from conformational changes in the aptamer induced by target analytes. While the pristine, unexposed anti-PDGF (PDGF = platelet-derived growth factor) aptamer yields highly reproducible spectra with Gamma = 0.91 +/- 0.01, following incubation with PDGF, the reproducibility of the SERS spectra is dramatically reduced, yielding Gamma = 0.67 +/- 0.02. This approach also allows us to discriminate the response of a cocaine aptamer to its target from its weaker response to nonspecific analyte molecules.

Aptamer biosensor for protein detection based on guanine-quenching

Based on fluorescence quenching between guanine bases and fluorophore, a cost-effective biosensor for protein detection is developed. In this biosensor, the label-free protein is detected through variation in fluorescence induced by aptamer conformational change during the recognition between aptamer and protein. Using thrombin-binding aptamer and thrombin as a model system, two design strategies, which are named as hairpin design and duplex design, are developed. Moreover, we investigated how the detection limit is influenced by the modifications, the stem length, and the number of quenching guanine bases in the hairpin design, or the length of the complementary sequence in the duplex design. Our results showed that, to optimize the detection limit, the balance between binding ability of aptamer to protein and quenching efficiency of guanine quenching aptamer have to be achieved.