What is an Aptamer?
The term “Aptamer” was coined by Andy Ellington. It stems from the Latin terms “aptus,” meaning to fit, and “meros,” meaning part. Aptamers are single-stranded DNA or RNA (ssDNA or ssRNA) molecules. Aptamers assume a variety of shapes due to their tendency to form helices and single-stranded loops. Hence, they are extremely versatile and bind targets with high selectivity and specificity. Common targets include proteins, peptides, carbohydrates, small molecules and many other compounds. Rather than primary sequence, aptamer binding is determined by its tertiary structure. Target recognition and binding involve three dimensional, shape-dependent interactions as well as hydrophobic interactions, base-stacking, and intercalation. Aptamers bind because they “fit” their targets.
SELEX Aptamer Selection
Aptamers with affinity for a desired target are selected from a large oligonucleotide library through a process called SELEX, which stands for Sequential Evolution of Ligands by Exponential Enrichment. Through an iterative process, non-binding aptamers are discarded and aptamers binding to the proposed target are expanded. Initial positive selection rounds are sometimes followed by negative selection. This improves the selectivity of the resulting aptamer candidates. Base Pair maintains several proprietary oligonucleotide libraries for use in aptamer selection. Base Pair has also patented a multiplex format of SELEX. Learn more about multiplex SELEX.
- Targets are immobilized
- Aptamer library is applied and allowed to bind
- Weak binders are washed away
- Bound aptamers are eluted and amplified using PCR
- The pool of amplified aptamers is reapplied to the targets
- Process is repeated multiple times under increasing stringency
The SELEX process yields ~106 aptamer sequences. Identifying the best candidates is a specialized process employing a variety of analytical techniques at Base Pair. See the Custom Aptamer Discovery page for more information on aptamer characterization, optimization, and application. Acknowledgements: The following programs were utilized to generate the IL-7 aptamer structure:  T. Macke and D.A. Case. Modeling unusual nucleic acid structures. In Molecular Modeling of Nucleic Acids, N.B. Leontes and J. SantaLucia, Jr., eds. (Washington, DC: American Chemical Society, 1998), pp. 379-393. . Visual Molecular Dynamics.