Rational design enabling aptamer-based sensors for surface-enhanced Raman detection of small molecules

Homogeneous surface-enhanced Raman scattering (SERS) sensors could have a significant impact in environmental analysis. The reagentless mechanism of these sensors makes them capable for in situ analysis and continuous monitoring of environmental pollutants, without having to collect environmental samples for laboratory analysis. Homogeneous SERS sensors take advantage of functional DNA strands on the surface of a SERS-active particle. These sensors are commonly used for the detection of genomic targets. A clear path to adapt these homogeneous sensors to detect small molecules is to employ aptamer sequences. In particular, the use of duplex aptamer can make these sensors highly adaptable to different target molecules. Although there have been examples of SERS duplex aptamer sensors to detect small molecules, the design rules for this type of sensors have not been elucidated. Without design rules or a design protocol, we would not be able to fully take advantage of the adaptability of this approach to focus on new targets and applications (e.g., environmental analysis). Herein, we aim to define a protocol for the design of aptamer-based homogeneous SERS sensors. First, we demonstrate their nonequilibrium character and the necessary length for the complementary element for the sensors to work. We demonstrate the design protocol on a well-characterized aptamer sequence for ATP binding and then transfer the knowledge gained on an aptamer for estradiol, a common water contaminant. In this work, we establish the design protocol for a short aptamer (i.e., ATP) and analyze the issues and remedies associated with extending this protocol to longer aptamer sequences (e.g., E2).