Small Molecules

Small molecule targets (such as antibiotics, many drugs, toxins, food additives etc) are often perceived as difficult target to obtain a suitable affinity ligand. Isolating antibodies against targets of this nature is often problematic as the targets are either poorly immunogenic or toxic. Where antibodies are available, they often have poor specificity and / or affinity, due to the relative inflexibility of antibodies (or other protein based affinity ligands).

Peptides & Proteins

Antibody generation does not give the opportunity to remove ‘binders’ which cross-react with related targets. As a result, antibody-based assays are often plagued by specificity issues. The in vitro nature of aptamer selection gives us the opportunity to include ‘counter-selection’ steps, to remove aptamers which cross-react with unwanted targets. This gives nucleic acid aptamers a significant ‘specificity advantage’. allowing them to discriminate between closely related targets e.g. proteins with and without post-translational modifications, single amino acid substitutions and even misfolded form of the same protein.

Cells and Tissues

A key advantage of the in vitro selection of aptamers is that we can isolate aptamers directly against very complex target types, such as whole cells (live or fixed; bacterial, mammalian, plant etc), viruses or even whole tissues (biopsies, tissue sections, fixed and / or wax embedded etc). This approach is not possible for antibodies; they are isolated against a purified form of the target protein and then screened for binding to cells, tissues etc.

Aptamers offer an alternative means of recognising small molecules. As nucleic acids are incredibly flexible; they are able to form complex folds and cage their targets. This interaction allows aptamers to form tighter, more specific interactions.

Aptamer Solutions has developed a proprietary automated selection approach, which allows us to isolate aptamers against small molecule targets without the need to modify or immobilise the target; enabling complete access for ligand binding. Aptamer Solutions uses unique methods to address the issues usually associated with selection of aptamers against small molecules. We also include counter-selection steps to ensure that the aptamers are specific to the target of interest. This gives aptamers greater specificity than can be achieved by other affinity ligands.

As with other Aptamer Group selection methodologies; we isolate our small molecule targeting aptamers using selection conditions tailored to the end application. This makes them especially useful as alternatives in ELISA-like assays, Lateral Flow Devices, Biosensors, etc.

In addition, their small size and flexible backbone mean that nucleic acid aptamers can bind to regions of proteins which are inaccessible to other, larger affinity ligands (such as antibodies).

We utilise our automated, high-throughput isolation processes to isolate aptamers against multiple targets in parallel. This gives us a significantly increased bandwidth, allowing us to handle many targets at a time. The automation also allows us to isolate our aptamers using Design of Experiment (DoE) principals; greatly increasing our success rate and reducing the time taken to reach the end goal.

As with all of our aptamer selection processes; projects involving protein targets are carried out with the end application in mind. For example, in protein purification applications, we isolate aptamers which are able to bind to the target in buffered cell lysate or culture harvest. We also include a customer defined ‘Elution Buffer’ to ensure that the aptamers release the target in a buffer that is compatible with the protein and downstream applications. This avoids issues associated with harsh elution conditions needed with antibody mediated chromatography.

The advantage of aptamer selection using the cells, tissues etc is that the aptamers can be directed to their target as it is presented in ‘the real world’ e.g. cell surface. This avoids issues with potentially isolating aptamers against domains that are not accessible in the cell e.g. transmembrane domains.

As with aptamer selection against protein targets; counter-selection steps can be included to ensure that we isolate aptamers which discriminate between cell or tissue types.

These processes are therefore especially useful for generating novel reagents for use in Immunohistochemistry (IHC), fluorescence imaging, flow cytometry and Fluorescence-activated cell sorting (FACS), etc.

Our small molecule aptamers offer:

  • Over 85% success
  • Enhanced specificity
  • Complete control over binding / sample conditions
  • Readily integrated into common assay formats
  • Gain of Signal response

Our protein selections offer:

  • 90% success rate
  • Complete control of conditions
  • Discriminate between PTMs or point mutations

Our cell and tissue selections offer:

  • Over 90% success
  • Strategies for cell internalisation and tissue penetration
  • Unbiased selection techniques