Aptamers and the RNA world, past and present

Abstract

Aptamers and the SELEX process were discovered over two decades ago. These discoveries have spawned a productive academic and commercial industry. The collective results provide insights into biology, past and present, through an in vitro evolutionary exploration of the nature of nucleic acids and their potential roles in ancient life. Aptamers have helped usher in an RNA renaissance. Here we explore some of the evolution of the aptamer field and the insights it has provided for conceptualizing an RNA world, from its nascence to our current endeavor employing aptamers in human proteomics to discover biomarkers of health and disease.

Figure 1.

Thymadine-monophosphate (TMP) and the modified nucleotide 5-benzylaminocarbonyl-deoxyuridine-monophosphate (BndUMP).

Figure 2.

Overview of the SomaLogic proteomics assay. In step 1, the specific protein to be measured (Pi) binds tightly to its cognate SOMAmer binding molecule (S), which includes a photo-cleavable biotin (PCB) and fluorescent label (L) at the 5′ end. In step 2, bound protein-SOMAmer complexes are captured onto streptavidin coated beads (SB) by the photo-cleavable biotin on the SOMAmer. Unbound proteins are washed away. Bound proteins are tagged with NHS-biotin (B). In step 3, the photo-cleavable biotin is cleaved by UV light (hv) and the protein-SOMAmer complexes are released into solution. In step 4, the protein-SOMAmer complexes are captured onto streptavidin coated magnetic beads and the SOMAmer are eluted into solution and recovered for quantification in step 6, hybridization to a custom DNA microarray. Each probe spot contains DNA with sequence complementary to a specific SOMAmer, and the fluorescent intensity of each probe spot is proportional to the amount of SOMAmer recovered, and thus directly proportional to the amount of protein present in the original sample.