Oligonucleotide Sensor Based on Selective Capture of Upconversion Nanoparticles Triggered by Target Induced DNA Inter-Strand Ligand Reaction

Abstract

We present a sensor that exploits the phenomenon of upconversion luminescence to detect the presence of specific sequences of small oligonucleotides like miRNAs among others. The sensor is based on NaYF4:Yb,Er@SiO2 nanoparticles functionalized with ssDNA that contain azide groups on the 3' ends. In the presence of a target sequence, inter-strand ligation is possible via click-reaction between one azide of the upconversion probe and a DBCO-ssDNA-biotin probe present in the solution. As result of this specific and selective process, biotin is covalently attached to the surface of the upconversion nanoparticles. The presence of biotin on the surface of the nanoparticles allows their selective capture on a streptavidin-coated support, giving a luminescent signal proportional to the amount of target present in the test samples. With the aim of studying the analytical properties of the sensor, total RNA samples were extracted from healthy mosquitoes and spiked-in with a specific target sequence at different concentrations. The result of these experiments revealed that the sensor was able to detect 10-17 moles (100 fM) of the target sequence in mixtures containing 100 ng of total RNA per well. Similar limit of detection was found for spiked human serum samples, demonstrating its suitability for detecting specific sequences of small oligonucleotides under real conditions. By contrast, under the presence of non-complementary sequences or sequences having mismatches, the luminescent signal was negligible or conspicuously reduced.