5th June 2019
One of the key benefits to using aptamers instead of antibodies is how you store and use the reagent. Over this past 60 years the stability of oligonucleotides has been rigorously studied and well defined.
Most provides of synthetic oligonucleotides recommend storing the suspended DNA at in a neutral buffer, free from divalent metal ions (e.g Tris EDTA) at -20°C. Stored like this, most manufacturers guarantee a shelf life of 2 years. However even at 37°C it is estimated that the oligonucleotide would be stable for in excess of 6 weeks (IDT 2014).
As it is becoming more commonplace, to see oligonucleotide-based therapeutics and diagnostics; it is therefore important to understand the stability of oligonucleotides in vivo and how we can manipulate their chemistry to suit your needs.
Typically, DNA has a very short half-life in vivo (30-60 minutes) (Sago et al 2018). This is due to the abundance of endogenous nucleases. Prolonging the stability in vivo is often done by modifying the oligonucleotide backbone; removing or replacing functional groups involved in enzymatic degradation. One of the most widely known examples of the application of stabilising modifications are the use of 2’Fluoro and 2’O-Methyl nucleotides in the drug Macugen (White, Sullenger, Rusconi, 2000). Using these modifications has been shown to increase the half-life of the aptamers from minutes (for unmodified RNA) to days (Hassler et al 2018).
Other methods (often used in combination with backbone modifications) include the addition of dTdT or an inverted nucleotide cap on one end of the aptamer (Hassler et al). These caps inhibit endonucleases as they block the binding region on the 5’ or 3’ end. When used in conjunction with backbone modification is it common to see 5-10 fold increases in stability (Prakash et al 2016).
However, not every application of aptamers requires stability for days. When used in diagnostic applications, working with different matrixes or in shorter assay times, DNA-based sensing platforms are perfectly suitable, which we will discuss more next time.
By understanding different characteristics of nucleic acids, we are able to design the perfect solution for you application; whatever the challenge.
If you would like more information or would like to discuss how we can develop aptamers for your application then please get in touch with us using the contact form below or email email@example.com.
Integrated DNA Technologies, Oligonucleotide Stability Study, 2014, https://sfvideo.blob.core.windows.net/sitefinity/docs/default-source/technical-report/stability-of-oligos.pdf?sfvrsn=c6483407_10
Hassler, M. R., Turanov, A. A., Alterman, J. F., Haraszti, R. A., Coles, A. H., Osborn, M. F., Echeverria, D., Nikan, M., Salomon, W. E., Roux, L., Gofihno, B. M. D. C., Davis, S. M., Morrissey, D. V., Zamore, P. D., Karumanchi, S. A., Moore, M. J., Aronin, N., Khvorova, A., Comparison of partiallay and fully chemically-modified siRNA in conjugate-mediated delivery in vivo, Nucleic Acids Research, Volume 46, Issue 5, 16 March 2018, Pages 2185–2196
Prakash, T. P., Kinberger, G. A., Murray, H. M., Chappell, A., Riney, S., Graham, M. J., Lima, W. F., Swayze, E. E., Seth, P. P., Synergistic effect of phosphorothioate, 5′-vinylphosphonate and GalNAc modifications for enhancing activity of synthetic siRNA, Bioorganic & Medicinal Chemistry Letters, Volume 26, Issue 12, 15 June 2016, Pages 2817-2820
Sago, C. D., Kalathoor, S., Fitzgerald, J. P., Lando, G. N., Djeddar, N., Bryksin, A. V., Dahlman, J. E., Barcoding chemical modifications into nucleic acids improves drug stability in vivo, Journal of Materials Chemistry B, Issue 44, 2018
White, R. R., Sullenger, B. A., Rusconi, C. P., Developing aptamers into therapeutics, The Journal of Clinical Investigation, 2000 Oct 15; 106(8); 929-934