A Comparison of 2-part and 3-part Nanoparticle-Based Sensor

There has long been a drive to produce sensors with ever-increasing sensitivity and selectivity, while also achieving robustness and ease of use. Nanoparticle-based sensing approaches have generated a great deal of attention and excitement, because they possess such qualities. For these assays to function properly, it requires the integration of molecular recognition motifs and materials with outstanding optical properties. Aptamers are DNA or RNA sequences that bind analytes with high specificity, which makes them a suitable choice as recognition elements. Changes in the surface plasmon resonance (SPR) of gold nanoparticles (AuNPS) as a function of interparticle distance, has been used as an optical signal to detect the presence of different species in solution by the naked eye. In this work, we coated gold nanoparticles with short oligonucleotides and aptamers for the design of sensors that can be used under different conditions, including salt concentration, pH and temperatures. Three aptamer sensors were developed using this approach 1) riboflavin, as a general indicator of biological activity, 2) ricin, a toxin that is of broad interest, and 3) theophylline, an adenosine antagonist. Our designs are based on two approaches, the first method consisted of the use of two sets of AuNPs, each coated with a short oligonucleotide complementary to a different part of the sequence of the aptamer of interest. Hybridization of the DNA-coated particles (DNA-AuNPs) with the free aptamer produced aggregates, i.e. 3-part design. The second approach consisted of the use of only two sets of DNA-AuNPs, one coated with an aptamer that contains a thiol group in its 5 ́ end, and the second set of AuNPs coated with a sequence complementary to part of the aptamer. Hybridization of these two sets of particles produced aggregates, i.e. 2-part design. In both cases, the presence of the analyte promoted a change in the conformation of the aptamer, which caused the dehybridization of the complementary sequences. This conformational change of the aptamer upon binding of the analyte produced the dissociation of the nanoparticle aggregates, which is translated into a change in the color of the suspensions from blue to red. In this presentation, we will compare the advantages and disadvantages associated with a 3-part versus a 2-part nanoparticle-oligonucleotide reporting assay.