18th July, 2017

Aptamer Affinity

Aptamers are affinity reagents, so the mechanism of binding to a target is a key characteristic. Today we discuss how aptamers bind and outline what we do to ensure that they are fit-for-purpose.

Aptamers bind to their target through weak noncovalent forces such as; hydrogen bonding, Van der Waals and electrostatics. These occur between different regions of the target and the aptamer nucleotides. The more interactions between an aptamer and the target, the stronger binding will be. Altering the composition of an aptamer changes how it interacts with a target. By taking advantage of this feature we can select the best aptamer for your target and intended application.

Successful aptamers have affinity in the nano- to pico-molar range. This makes them well suited for roles in purification, diagnostics and therapeutics.

Binding can be manipulated readily by changing the conditions the aptamers are subjected to. One example is our AptaBind platform, which uses an elution buffer to disrupt the forces between immobilised aptamer and target. This causes the target molecule to elute from the aptamer which enables simple purification.

How Aptamer Group monitor affinity during selection

At Aptamer Group we “Start with the End in Mind”. By doing this we ensure that the aptamers selected are in line with your specification for the intended use.

As the aptamer pool becomes more enriched during selection against your target, only the aptamers which best match your criteria will remain. After each round of selection, we measure affinity of the enriched pool to the target using a biophysical assay. The results, taken from a biosensor (see previous posts: Biosensors 1, Biosensors 2), are shown in the figure below.

Aptamer Affinity

Figure 1: Individual aptamer clones are assayed and the best are picked. In this case aptamers were ranked by off-rate.

By using this biosensor, we can see which aptamer pools have the greatest affinity to a target by comparing their binding rate. The aptamer pools here have been enriched against a target. Figure 1 shows individal aptamers with varying affinity. The data ensures that the best aptamer pool is progressed to the next round of selection, shown in Figure 2.

Figure 2: The aptamer which best fits the customer specification is selected.

If you are having issues with developing an optimised affinity reagent against a target, or want to discuss the use of aptamers in your research, discovery and development projects, then let us know here: