A universal label for the detection of PCR amplicons based on gold nanorods

Owing to their optical versatility, gold nanorods represent an outstanding platform of plasmonic labels for a wide variety of photonic biosensors. Here, we address the feasibility of a universal system to label PCR amplicons with gold nanorods, based on their coupling to a nucleotidic tag of arbitrary choice and the use of primers modified with the complementary anti-tag sequence. This general concept is suitable for different formats of genosensors. For instance, when both the forward and the reverse primers are modified with the same anti-tag sequence, their daughter amplicons behave as homobifunctional cross-linkers for the polymerization of the gold nanorods and so trigger a specific discoloration of their suspension. This homogeneous approach seems to be robust against a change of DNA target, but to require a careful choice of the hybridization buffer, and to exhibit a limited dynamic range in the order of 10 dB. Instead, when the amplicons are purified and immobilized on a solid substrate such as a paper strip, a single primer bearing the anti-tag sequence is enough to capture the gold nanorods and generate a visible stain that correlates with their concentration. This heterogeneous platform ensures a dynamic range exceeding 30 dB where it is suitable for quantitative readout, but it suffers from spurious interactions that may originate from the onset of denaturation of the spotted amplicons. Altogether, we found that the tested principles work as intended by design, but there may be practical limitations to their generic use in terms of the choice of both the analytical protocol and the nucleotidic tags, particularly in view of leveraging the optical versatility of gold nanorods in a multiplexable format.