Aptamers are short single-stranded oligonucleotides that fold into diverse and intricate molecular structures that can bind with high affinity and specificity to a variety of proteins, peptides and small molecules. Since they were first described in 1990, more than 10,000 publications applying aptamers to many diverse areas of biomedical science have been published.
Traditional aptamers, which consist of unmodified DNA or RNA, can be selected against ~30% of human proteins. However, there are many other biologically and medically important proteins for which the standard RNA and DNA SELEX (Systematic Evolution of Ligands by EXponential enrichment) process does not yield adequate aptamer reagents. To overcome the limitations of traditional aptamers, SomaLogic scientists had developed a next generation aptamer platform (Slow Off-rate Modified Aptamers, or SOMAmers), and published the first example of the use of these reagents in a highly multiplexed proteomic assay in 2010.1
Affinity and Specificity
Like aptamers, SOMAmers are short, single-stranded deoxyoligonucleotides selected in vitro from large random libraries for their ability to bind to discrete molecular targets. To give them greater target diversity as well as high affinity, SomaLogic scientists endowed them with protein-like properties by adding functional groups that mimic amino acid side chains, thereby expanding their chemical diversity.1 Based on this work, SOMAmer reagents today are engineered with dU residues functionalized at the 5-position with different protein-like moieties (e.g., benzyl, 2-napthyl or 3-indolyl-carboxamide). These modifications can interact with more epitopes on a greater range of target molecules, largely as a result of the novel secondary and tertiary structures formed within the SOMAmer reagent itself. 2
SOMAmer reagents are selected not just for their affinity for their respective target proteins, but also for low dissociation rates (slow off-rates) with their targets. By introducing this second, kinetics-based element of specificity into the selection process (and thus into the reagent itself), SOMAmer reagents can be used in protein assays without requiring a second detection ligand. In addition, researchers using SOMAmer reagents can use a large amount of a non-specific polyanionic competitor1 to disrupt any non-specific binding interactions.
Nucleic acid–based reagents are susceptible to nuclease degradation, and unfortunately, most aptamers degrade quickly. The hydrophobic modifications made to the 5-position of deoxyuridine nucleotides in SOMAmer reagents results in a substantial increase in resistance to DNase-mediated degradation in comparison to aptamers, though the degree of improvement depends idiosyncratically on both the sequence and the nature of 5-position modification.
Writing in a 2016 review of a 2010 article, Brody3 states that the best SOMAmer reagents allow limits of detection (LODs) at approximately 50 fM, and that approximately half the available analytes show measured LODs below 1 pM.
Compared with aptamers, SOMAmers can be selected that have higher affinity to and specificity for more diverse proteins, and are less vulnerable to nuclease degradation. These qualities, along with the other stability and production advantages aptamers have over antibodies, make SOMAmer reagents attractive for use in virtually every protein measurement application from the laboratory to the clinic.
- Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249(4968):505–510
- Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346(6287):818–822
- Gold L et al. (2010) Aptamer-Based Multiplexed Proteomic Technology for Biomarker Discovery. PLoS ONE 5(12): e15004. doi:10.1371/journal.pone.0015004
- Rohlof JC et al. (2014) Nucleic Acid Ligands with Protein-like Side Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents. Mol Ther Nucleic Acids 3(10): e201. doi: 10.1038/mtna.2014.49
- Brody EN et al. (2010) High-content Affinity-based Proteomics: Unlocking Protein Biomarker Discovery. Expert Review of Molecular Diagnostics 10(8): 1013–1022. doi: 10.1586/erm.10.89