Detecting Nucleic Acids by Direct SERS in the Presence of Spermine: Surface Adsorption Hierarchies are Unveiled Thanks to a Unified Nanoparticle Platform

Spermine is a polyamine that is ubiquitous to most analytical protocols for the direct detection of nucleic acids by surface enhanced Raman spectroscopy (SERS), where it is either used as a nanoparticle capping species or a sample aggregating agent. An attentive examination of the literature reveals the existence, in the experimental design of past recent works involving spermine and plasmonic nanoparticles, of important confounding factors relative to the surface chemistry of colloids, limiting the reach of the associated mechanistic hypotheses.
We present a thermodynamics-based framework for comparative SERS studies with no confounding bias related to surface chemistry. This framework is enabled by a unified colloidal nanoparticle platform, constituting the surface chemistry baseline for all the investigated sample preparation scenarios, i.e., with and without spermine. The nanoparticle platform is a natively negatively charged, surfactant-free, gold-silver nanostar that is sparingly and weakly capped, such that it can be functionalized by common adsorbing ligands, including spermine, by simple post-synthesis addition, thus providing us with a spermine-free and spermine-bearing system using the same nanoparticle synthesis. By maintaining the synthesis constant, the confounding bias related to the baseline nanoparticle surface chemistry is eliminated, posing fair grounds to “isolate” and compare the different pairwise interactions that are established, as a function of sample preparation order, in the SERS sample, where the thermodynamic equilibria dictate the adsorbate landscape, and thus, the SERS spectrum. The validation of a “minimal working example” analyte for fundamental studies on ssDNA systems is also presented, introducing the advantage of experimentally and computationally minimizing the system, for accessible DFT-aided vibrational elucidation.
The thermodynamic and spectroscopic data gathered in this study allow for a reframing of the mechanistic hypotheses relative to spermine-containing SERS samples: It is demonstrated that the spermine-nucleic acid interaction is thermodynamically dominant, and that the equilibria that are established at the nanoscale surface in the presence of spermine are independent of the sample preparation order.
Our results and methodological approach are key to the development of selectivity-optimized SERS methods for nucleic acid detection, and have a wide interest reach for all those nano- and biotechnological fields that exploit surface chemistry interactions.
NOVELTY STATEMENT: A fair comparison of SERS sample preparations is achieved via the elimination of the confounding bias related to the nanoparticle surface chemistry.