Capillary Electrophoresis (CE) for Rapid Aptamer Selection

Aptamers are ribonucleic acids (RNA) or single-stranded DNA (ssDNA) molecules that demonstrate high affinity and specificity for a wide range of targets.  These molecules possess several advantages such as good tissue penetration and are easily modified for increased stability and combination therapy.  Consequently, aptamers are used as drugs and diagnostic tools. Bioimaging, analytical reagents, and toxin/hazardous chemical detection are only a few of the other applications of aptamers.

Despite the wide application of aptamers, they are identified through an iterative process termed SELEX (Systematic Evolution of Ligands by Exponential enrichment).  The SELEX process is used to select aptamers from a large oligonucleotide library with high specificity for targets. Conventional SELEX uses affinity chromatography and filtration methods to separate desired nucleotide sequences from unwanted ones. However, this is difficult, takes time, and is prone to biases. Recently, there has been an increased adaptation of Capillary Electrophoresis (CE) for selecting aptamers known as CE-SELEX. In CE-SELEX, bound nucleic acids undergo a mobility shift and migrate differently from the unbound sequences, allowing them to be collected at different fractions. High resolving power combined with the flexibility of CE, significantly reduces the selection time of SELEX from weeks to days.  This seminar will discuss details of the conventional SELEX mechanism and highlight the analytical mechanism, instrumentation, and data collection in CE that pertains to aptamer selection.

Selected Literature

1. Mendonsa, S. D.; Bowser, M. T., In Vitro Selection of High-Affinity DNA Ligands for Human IgE Using Capillary Electrophoresis. Analytical Chemistry 2004, 76 (18), 5387-5392.

2. Yang, J.; Bowser, M. T., Capillary Electrophoresis–SELEX Selection of Catalytic DNA Aptamers for a Small-Molecule Porphyrin Target. Analytical Chemistry 2013, 85 (3), 1525-1530.

3. Boussebayle, A.;  Groher, F.; Suess, B., RNA-based Capture-SELEX for the selection of small molecule-binding aptamers. Methods 2019, 161, 10-15.

4. Rodriguez, E. L.;  Poddar, S.;  Iftekhar, S.;  Suh, K.;  Woolfork, A. G.;  Ovbude, S.;  Pekarek, A.;  Walters, M.;  Lott, S.; Hage, D. S., Affinity chromatography: A review of trends and developments over the past 50 years. Journal of Chromatography B 2020, 1157, 122332.

5. Harstad, R. K.;  Johnson, A. C.;  Weisenberger, M. M.; Bowser, M. T., Capillary Electrophoresis. Analytical Chemistry 2016, 88 (1), 299-319.