Oligonucleotides known as "aptamers" are powerful reagents that bind target ligands with affinities comparable to antibodies. Aptamers are gaining increasing interest since they have been used as ligands in applications ranging from biosensors to targeted therapeutics.
Knight and coworkers (2009) - using the CustomArray platform - produced aptamers on-chip with high affinity and specificity to the fluorescent protein allophycocyanin (APC). They started with a relatively small initial library size (6000 sequences), and used a genetic algorithm (GA) to optimize the binding strength. The ability to systematically generate aptamers through this method is likely to be dependent on the sequence binding profile of the target aptamer.
A study by Platt et al (2009) demonstrated the on-chip evolution of aptamers for fluorescently tagged protein targets (also using the CustomArray platform). The authors were able to demonstrate a rapid process for identification of aptamers against Thrombin using “on-chip” synthesized 30mer oligos. Using no prior information from existing aptamers, and with an initial library size of only 4.6 x 104 30mers, the population was optimized within four evolutionary cycles (each taking 24 hours), producing a final population of aptamers which exhibited nanomolar (nM) affinity.
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Knight, C.G. ,Platt, M., Rowe, W., Wedge, D.C., Khan, F., Day, P.J., McShea, A., Knowles, J. and Kell D.B. (2009) “Array-based evolution of DNA aptamers allows modelling of an explicit sequence–fitness landscape” Nucleic Acids Res. 37; e6.
Platt, M., Rowe, W., Wedge, DC, Kell, DB, Knowles, J. and Day, PR. (2009) “Aptamer evolution for array-based diagnostics” Analytical Biochemistry 390; 203–205