Challenges and opportunities for small molecule aptamer development

Abstract

Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.

Figure 1

The systematic evolution of ligands by exponential enrichment process (SELEX). Beginning with a large library of DNA, iterative cycles of target incubation, library partitioning, and amplification are performed to select aptamers.

Figure 2

Breakdown, by target type, of aptamers selected between 1990 and 2011. This list was generated using the Aptamer Base [41] http://aptamerbase.semanticscience.org/ (accessed July 9, 2012) (accessed July 9, 2012).

Figure 3

Illustration of sample electrochemical, fluorescence, and colorimetric assays using the structure switching strategy and small molecule-binding aptamers.

Figure 4

(a) Confirmation of aptamer-mediated inhibition of hemozoin formation within parasite lysates. Heme-binding DNA aptamers (OKA 26-5 and 26-3; PS26, PS21, and PS2M) inhibit hemozoin formation but control oligonucleotides (PS2M_Mod and PS2R) have no effect. (b) The growth of parasites incubated in red blood cells that had been preloaded with nuclease resistant DNA aptamers (PS2M_idT and PS26-idT) is significantly inhibited in comparison to those exposed to red blood cells loaded with control oligonucleotides (PS2M_Mod-idT). Used with permission from PNAS.

Figure 5

(a) Pretreatment of animals with the dopamine aptamer reversed the effects of MK-801 administration. Animals given MK-801 (empty diamonds; 0 nM/MK) show higher cumulative presses in this behavioural test in comparison to animals not given this drug (empty squares, dashed line; 0 nM/Saline). The group receiving aptamer pretreatment (filled triangles; 200 nM/MK), however, showed similar levels of cumulative presses as those that were not given any MK-801. A random oligonucleotide pretreatment, however, had no dampening effect on the number of presses (X with dashed line; Random/MK). (b) Aptamer pretreatment (200 nM/MK) did not significantly affect locomotor activity as measured by distance traveled in an elevated cross maze. Used with permission from PLoS One.