Aptamer, from the Latin aptus

Here at CiteAb we’re always interested to hear of any new developments in the world of affinity reagents and this week we’re taking a look at aptamers.

While aptamers aren’t exactly new arrivals to the affinity reagent party, we are now beginning to see companies pop up that provide catalogue aptamers rather than custom designed reagents. For this reason we thought it a good time to find out a little bit more about what they are and why you might use them.

So without further ado…

Spiegelmer

What are Aptamers?

Aptamers, from the Latin aptus, to fit and the Greek meros for “a bit of a thing” are a group of affinity reagents used in much the same way as antibodies. Like antibodies, and as you would expect from an affinity reagent they bind with high affinity to specific targets. Unlike antibodies however, aptamers are created in vitro and can come in a number of different formats: nucleic acid (RNA/DNA/XNA) or peptide based.

Like proteins, nucleic acids are capable of folding to form complex tertiary structures and participate in a wide array of biological processes[1]. It was this realisation that drove research into the functional capabilities of nucleic acids[2] and the subsequent development of  in vitro selection procedures that would eventually isolate nucleic acid aptamers.

The first iteration of these selection procedures were originally described in 1990 by several researchers working independently and focused on the identification of RNA based aptamers[3,4]. Soon after, driven by the excitement around functional RNA structures, the race was on to identify their DNA counterparts and the first functionally active DNA enzyme was generated in 1994[5].

Following on from the discovery of nucleic acid aptamers, their protein counterparts were soon developed and can often be referenced to by a number of different names; peptide aptamers, affibodies, paptamers[6]. Peptide aptamers as we’ll continue to refer to them, are artificial proteins: a stable protein scaffold into the coding sequence of which random oligonucleotides are inserted, which when expressed will act as a binding motif[6,7]. Conceptually peptide aptamers are similar to antibodies in the way that the heavy and light chains of the variable region come together to support the epitope binding region and actualy have dissociation constants comparable to antibodies[6].

When would I use an aptamer?

Sefah et al. 2010

Aptamers, unsurprisingly given their functional similarity to antibodies can be used in many of the same applications and are offered with many of the same conjugations. A search of the literature shows their use in flow cytometry[8], histochemistry[9], Western blotting and ELONA[10] (Enzyme Linked OligoNucleotide Assays and Aptamer Linked ImmunoSorbent Assays are functional equivalents of ELISA that use aptamers rather than antibodies in either the capture or detection of antigen).

Why Pay Attention to Aptamers?

So why as a researcher should you pay attention to aptamers?
In bypassing the need for biological systems, manufacturers are able to minimise batch to batch variation, an issue that may be more noticeable in polyclonal antibodies.
Aptamers to novel proteins can be developed more quickly than antibodies[11]
The constant region of an antibody is designed to facilitate intracellular interactions and can result in background signal[7]

So there we have it, an introduction to aptamers!

What are your opinions on Aptamers? Do you currently use them in your research or even manufacture them? We’d love to hear from you – leave a message below or send us a tweet to @CiteAb!

– Matt and the CiteAb team.

 


Image Credits

First image: Spiegelmer, from Wikipedia
Second image: Confocal images of aptamers staining with cultured DLD-1 (A–F) and HCT 116 (G–J), modified from FIGURE 7 Sefah K, Meng L, Lopez-Colon D, Jimenez E, Liu C, et al. (2010) DNA Aptamers as Molecular Probes for Colorectal Cancer Study. PLoS ONE 5(12): e14269. doi:10.1371/journal.pone.0014269)


References

1 – McKeague M, Derosa MC. Challenges and Opportunities for Small Molecule Aptamer Development. J Nucleic Acids. 2012; 2012: 748913.

2 – Weigand JE1, Suess B. Aptamers and riboswitches: perspectives in biotechnology. Appl Microbiol Biotechnol. 2009 Nov;85(2):229-36.

3 – Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 1990 Aug 3;249(4968):505-10.

4 – Ellington AD, Szostak JW. In vitro selection of RNA molecules that bind specific ligandsNature. 1990 Aug 30;346(6287):818-22.

5 – Abc (see draft) – Mok W, Li Y. Recent Progress in Nucleic Acid Aptamer-Based Biosensors and Bioassays. Sensors (Basel). Nov 2008; 8(11): 7050–7084.

6 – Crawford M, Woodman R, Ko Ferrigno P. Peptide aptamers: tools for biology and drug discovery. Brief Funct Genomic Proteomic. 2003 Apr;2(1):72-9.

7 – Straw et al. Proof of concept study to identify candidate biomarkers of fibrosis using high throughput peptide aptamer microarray and validate by enzyme linked immunosorbant assay J. Biomedical Science and Engineering, 2013, 6, 32-42.

8 – Liu J1, Liu H, Sefah K, Liu B, Pu Y, Van Simaeys D, Tan W. Selection of aptamers specific for adipose tissue. PLoS One2012;7(5):e37789. doi: 10.1371/journal.pone.0037789. Epub 2012 May 25.

9 – Sefah K, Meng L, Lopez-Colon D, Jimenez E, Liu C, et al. (2010) DNA Aptamers as Molecular Probes for Colorectal Cancer Study. PLoS ONE 5(12): e14269. doi:10.1371/journal.pone.0014269

10 – Martín ME1, García-Hernández M, García-Recio EM, Gómez-Chacón GF, Sánchez-López M, González VM. DNA aptamers selectively target Leishmania infantum H2A protein. PLoS One. 2013 Oct 21;8(10):e78886. doi: 10.1371/journal.pone.0078886. eCollection 2013.

11 – Song Q, Stadler LK, Peng J, Ko Ferrigno P. Peptide aptamer microarrays: bridging the bio-detector interface. Faraday Discuss. 2011;149:79-92; discussion 137-57.

 


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