While the high-selectivity and tight-binding of RNA aptamers have generated interest in their use as pharmaceuticals, there are many problems which have prevented them from being successful in vivo. For one, without modifications RNA aptamers are degraded after being introduced into the body by nucleases in the span of a few minutes. Also, due to their small size, RNA aptamers can be removed from the bloodstream by the renal system. Because of their negative charge, RNA aptamers are additionally known to bind proteins in the bloodstream, leading to non-target tissue delivery and toxicity. Care must also be taken when isolating the RNA aptamers, as aptamers which contain repeated Cytosine-Phosphate-Guanine (CpG) sequences will cause immune system activation through the Toll-like receptor pathway.
In order to combat some of the in vivo limitations of RNA aptamers, various modifications can be added to the nucleotides to aid in efficacy of the aptamer. For instance, a polyethylene glycol (PEG) moiety can be attached to increase the size of the aptamer, thereby preventing its removal from the bloodstream by the renal glomerulus. However, PEG has been implicated in allergic reactions during in vivo testing. Furthermore, modifications can be added to prevent nuclease degradation, such as a 2’ fluoro or amino group as well as a 3’ inverted thymidine. Additionally, the aptamer can be synthesized so that the ribose sugar is in the L-form instead of the D-form, further preventing nuclease recognition. Such aptamers are known as Spiegelmers. In order to prevent Toll-like receptor pathway activation, the cytosine nucleobases within the aptamer can be methylated. Nevertheless, despite these potential solutions to reduced in vivo efficacy, it is possible that chemically modifying the aptamer may weaken its binding affinity towards its target.