Modified Selection against EGFR Using Known Aptamer E07 to Optimize SELEX Efficiency

Modified Selection against EGFR Using Known Aptamer E07 to Optimize SELEX Efficiency

Marc St. Cyr

               Aptamer research provides a wealth of possibilities for therapeutic, diagnostic, and drug delivery purposes but the methods are constantly evolving and being optimized. It is very difficult to stay updated with the most current and innovative techniques and procedures. However, it is possible to, from time to time, perform selection with positive controls and varying conditions in order to determine the optimum conditions that should be used while performing a Systematic Evolution of Ligands by Exponential Enrichment (SELEX). There are many aspects of the SELEX procedure that can be optimized but the most crucial for these purposes are the time-based and nucleic acid recovery components (Stoltenburg 2007). Reducing the amount of time spent on one round of selection allows for faster results, which lead to expedited aptamer identification. The most effective way to optimize experiments is by comparing the results provided by reagents known to work with current conditions and conditions proposed to be faster, more effective, or otherwise helpful.

The aptamer E07 was successfully selected against epidermal growth factor receptor (EGFR) (Li 2011). Using this aptamer in the SELEX procedure to replace the randomized RNA pool will allow for the optimization of certain aspects of selection. The same reagents provided in the published aptamer paper will be used while the conditions of the selection itself will be varied and analyzed by assaying reactions, incubations, etc. to provide data or comparisons (Avutu 2010).

Specific Aim 1: Provide the FRI Aptamer Lab with optimized selection conditions with the goal of producing more efficient results when using the SELEX method of aptamer selection. This can include a wide and varying range of suggestions from shorter incubation times, new procedures, or preferred versions of already established procedures.

Figure 1. Overall outline of the SELEX method of selection of LNA against a target, including binding, washing, and amplification steps.

References:

1)      Stoltenburg R, Reinemann C, Strehlitz B (2007) SELEX- A (R)evolutionary Method to Generate High-Affinity Nucleic Acid Ligands. Biomedical Engineering 24(4): 381-403.

2)      Li N, Nguyen HH, Byrom M, Ellington AD (2011) Inhibition of Cell Proliferation by an Anti-EGFR Aptamer. PLoS ONE 6(6): e20299. doi:10.1371/journal.pone.0020299

3)      Avutu V (2010) Avidity Effects of MinE07, an anti-EGFR Aptamer, on Binding to A431 Cells <http://repositories.lib.utexas.edu/handle/2152/13407?show=full>

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