SOMAmer Sandwich Assays: A New Diagnostic Flavor

The famous chef, Emeril Lagasse, delights his audience with his approach to cooking. As he cooks, he theatrically takes the dish to the “next level” by adding another ingredient to the flavor. Bam! The food is even better.

In many ways, laboratory work mirrors cooking. Researchers routinely look to bring out the best “flavors” in any particular experiment. Recently, a group of SomaLogic scientists figured out how to take the already impressive utility of SOMAmer® reagents (small pieces of synthetic DNA with modified nucleotides) up a notch. They recognized that the very properties that make SOMAmer reagents special could be harnessed for traditional antibody-based applications, such as diagnostic sandwich assays (where one binding reagent captures a protein and other one is used to detect the protein).1, 2  Because of ongoing problems with antibody consistency and availability, the use of SOMAmer reagents (easily made by synthetic means) in these assays could be significantly beneficial for both research and clinical applications.

The group devised a way to make a pair of SOMAmer reagents that bind to different places on the same protein. Using Clostridium difficile binary toxin (CdtA) as the target protein, Urs Ochsner and his colleagues modified the “recipe” for whipping up SOMAmer reagents to create tens of thousands of candidates.2, 3 The significant change to the process was including a new ingredient, a previously identified CdtA SOMAmer reagent 4758-6. For comparison, they performed the same procedure, but left out 4758-6.

Upon completion, Ochsner and colleagues looked at the results. In comparing the sequences generated by the method lacking 4758-6 to those from the method that included the older SOMAmer reagent, they saw clear differences in sequence patterns and sequence abundance, as well as some similar sequences. The differences observed suggest that addition of 4758-6 may have worked. Several sequences were chosen for testing in sandwich assays, which revealed that new sequence 5579–12 paired the best with 4758-6. The researchers also conducted additional experiments to confirm that these two SOMAmers did indeed bind to different sites on the protein: a SOMAmer reagent sandwich pair had been created.

Based on the success of their trial run, the investigators decided to make SOMAmer reagent pairs for eight more proteins. In the first phase, the researchers sifted through existing SOMAmer reagents for suitable pairings, finding existing candidates for three of the proteins. In the second phase, they performed the modified procedure to identify the best pairings for the five remaining proteins, successfully identifying SOMAmer reagent pairs for four of them (in line with the usual success rate in generating new SOMAmer reagents).

Compared to antibodies (the traditional protein-binding reagents used in most sandwich assays), SOMAmer reagents are chemically synthesized resulting in better consistency between batches. They also have tremendous multiplexing capabilities, with the possibility of combining thousands of SOMAmer reagents into same experiment. The use of diagnostic sandwich assays incorporating SOMAmer reagent sandwich pairs rather than antibodies may indeed take disease research and diagnostic proteomics up a notch. Bam!

References

Davies DR et al. (2012) Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets. Proc. Natl. Acad. Sci. 109: 19971–19976.

Ochsner UA et al. (2014) Systematic selection of modified aptamer pairs for diagnostic sandwich assays. BioTechniques 56(3): 125–133.

Gold LD et al. (2010) Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS ONE 5: e15004.