Eight separate tests were carried out to evaluate the selectivity of the system and our ability to determine the number and types of strands in solutions containing mixtures of the different targets (Figs. 2 and 3). The concentrations of the target strands were kept constant for all of these experiments (100 pM each), and the hybridization conditions were as described above. In the first test (Fig. 3, row 1), all spots show the same intense gray color associated with Ag deposition. However, they can be differentiated simply by using the Raman scanning method. Once the spectroscopic fingerprint of the Ag-containing spot has been determined, the correct Raman label and, therefore, target sequence can be identified. To simplify the analysis, we assigned a color (rectangular box) to each Raman-labeled probe (Fig. 2A and Fig. 3B). In the first test (Fig. 3A), all six targets were present, and all showed strong gray-scale values when measured by means of the flatbed scanner as well as the expected Raman fingerprints. In the next seven tests, we systematically removed one or more of the targets to evaluate the suitability of this method for multiplexing. With the single-color gray-scale method one cannot determine if any cross-hybridization has occurred. However, with this “multiple color” scanning Raman method, one can carefully study the SERS spectra of each spot to determine which labels make up each spot. For the experiments described in Fig. 3, where the sequences are very dissimilar, we found that other than the expected spectroscopic probe signature for each target, there were virtually no other detectable Raman lines, indicating no cross-hybridization between different targets and probes. The SERS signal was obtained only from areas of the substrate where the Raman dye-labeled Au particles have initiated Ag formation. Therefore, this “multiple color” scanning Raman detection method does not record background signal due to Ag deposition where Au particles do not exist. This is not the case for the previous gray-scale scanometric approach, especially at ultralow target concentrations (≤50 fM) (1–3). The current unoptimized detection limit of this Raman scanning method is 20 fM (11).