Direct SERS Detection of Nucleic Acids in the Presence of Spermine: A Unified Nanoparticle Platform Allows for the Elucidation of Surface Adsorption Hierarchies

Abstract

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. Our work introduces a thermodynamics-based framework for comparative SERS studies with no confounding bias related to surface chemistry. Such experimental design is enabled by a unified colloidal nanoparticle platform, constituting the surface chemistry baseline for all of the investigated sample preparation scenarios, with and without spermine. The validation of a “minimal working example” analyte for fundamental studies on ssDNA systems is also presented, which introduces the advantage of experimentally and computationally minimizing the system, for accessible DFT-aided vibrational elucidation. The ensemble of thermodynamic and spectroscopic data gathered in this study allows for a reframing of the mechanistic hypotheses relative to spermine-containing SERS samples by decoupling the system into its pairwise interaction equilibria. 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 of those nano- and biotechnological fields that exploit surface chemistry interactions.