CE-SELEX

Recently, Cell-SELEX, which deals with living cells, was developed (18, 19). Using this method, aptamers that specifically recognize a cell s surface were obtained. To improve the selection process, some researchers have used surface plasmon resonance (SPR) or capillary electrophoresis (CE) (20-22). By developing CE-SELEX, Krylov s group obtained a DNA aptamer by a non-SELEX technique that requires no cyclical processes (23). 

Browser et al. snggested a CE-based procednre for aptamer selection, termed CE-SELEX, which is similar to NECEEM-based SELEX bnt does not use the kinetic capabilities of NECEEM (Mendonsa and Bowser, 2004, 2005 Mosing et al., 2005). 

CE-SELEX Isolating Aptamers Using Capillary Electrophoresis... 

FIGURE 28.1 Secondary structure of a DNA aptamer selected using CE-SELEX to have affinity for neuropeptide Y. (From Mendonsa, S. D., Bowser, M. T., J. Am. Chem. Soc., 127, 9382-9383, 2005.)... 

Recently, the high resolution power of CE has been used to isolate high-affinity aptamers (see Table 28.1 and references therein). This process has been referred to as CE-SELEX. - The CE-SELEX process is illustrated in Figure 28.3. The target molecule is incubated with a nucleic... 

Comparison of Aptamers Selected Using CE-SELEX with Those Selected Using Conventional SELEX Protocols... 

Negative selections have not proven to be necessary in CE-SELEX selections. No aptamers have been identified that exhibit affinity for the capillary surface. This has been equally true for selections performed using uncoated or neutrally coated capillaries. This greatly simplifies the SELEX procedure and removes one of the significant pitfalls of aptamer selection. 

The affinity of the nucleic acid pool for the target is measured after every round of selection to monitor the progress of the enrichment. Affinity of the library for the target should increase as the selection progresses. Selection cycles should continue until no further improvement in affinity is observed between rounds. Dissociation constants in the low nM to pM range are typically observed at the completion of the CE-SELEX process. 

CE-SELEX has been used successfully to isolate aptamers for a variety of targets (see Table 28.1). While these initial proofs of concept experiments are promising, a more detailed study of the selection process is now needed. CE-SELEX has made the selection process dramatically faster. This will allow fundamental experiments assessing the effect of variables such as library concentration, target concentration, and incubation time to be performed for the first time. The 4-6 weeks that are necessary to complete a conventional selection have made these experiments unfeasible until now. 

Automated SELEX is just one example of the many modified SELEX procedures developed to improve aptamer selection. Other screening technologies have been developed to improve the selectivity of an aptamer, such as subtractive SELEX, negative SELEX, counter SELEX, and photo SELEX to create a more universal aptamer selection process with complex target SELEX, blended SELEX, and toggle SELEX and to improve the efficiency of obtaining aptamers such as non-SELEX and capillary electrophoresis (CE) SELEX. ... 

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