10th May 2017
AptaBasics: ‘What is an Aptamer’?
An aptamer is a sequence of single strand nucleic acid (DNA or RNA) with a variable region of about 40 nucleotide bases. This variable sequence confers each aptamer with a unique 3 dimensional structure and potential ligand binding capability. These factors make aptamers high affinity and specific binding molecules, able to differentiate between targets that differ by only one functional group. It is because of this that aptamers are often called ‘nucleic acid antibodies’.
Aptamer/target binding is achieved mainly through electrostatic interactions, so the variability in aptamer sequences is what gives them their versatility. The way aptamers fold, the order of the nucleic acids and the conditions of the matrix they are in, all contribute to binding a target.
To bind to a small molecule, it is common for an aptamer to engulf the target (see diagram, left and centre). This type of binding will cause a structural switch, changing the aptamers structure, a feature that can be utilised for detection methods. When binding to a large molecule, an aptamer will usually only able to interact with an external surface.
Aptamers are selected in an appropriate matrix in vitro and so are not limited to functioning in only physiological conditions. They are also manufactured in vitro, and it is possible to modify aptamers with specific groups, such as fluorescent labels or biotin tags. Consequently, aptamer production is well controlled and reproducible with very low batch to batch variation.
In addition to small and large molecules, aptamers have been successfully identified as binding molecules for whole cells, viruses and tissues. This range of potential targets makes them ideal for many applications. They can be used in any instance where traditionally an antibody is used; however aptamers are not limited to these. Uses for aptamers include: biomarker discovery, drug discovery, diagnostics and therapeutics.
If you are interested in how aptamers could be used in your research, discovery and development projects, then please call us on +44 (0) 1904 567 790 or email email@example.com.
Next week we will discuss what an aptamer library is and why it is so large.