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Review
. 2016 Dec 10;9(4):76.
doi: 10.3390/ph9040076.

Applications of High-Throughput Sequencing for In Vitro Selection and Characterization of Aptamers

Nam Nguyen Quang  1   2 , Gérald Perret  3 , Frédéric Ducongé  4   5
Affiliations
Review

Applications of High-Throughput Sequencing for In Vitro Selection and Characterization of Aptamers

Nam Nguyen Quang et al. Pharmaceuticals (Basel). .

Abstract

Aptamers are identified through an iterative process of evolutionary selection starting from a random pool containing billions of sequences. Simultaneously to the amplification of high-affinity candidates, the diversity in the pool is exponentially reduced after several rounds of in vitro selection. Until now, cloning and Sanger sequencing of about 100 sequences was usually used to identify the enriched candidates. However, High-Throughput Sequencing (HTS) is now extensively used to replace such low throughput sequencing approaches. Providing a deeper analysis of the library, HTS is expected to accelerate the identification of aptamers as well as to identify aptamers with higher affinity. It is also expected that it can provide important information on the binding site of the aptamers. Nevertheless, HTS requires handling a large amount of data that is only possible through the development of new in silico methods. Here, this review presents these different strategies that have been recently developed to improve the identification and characterization of aptamers using HTS.

Keywords: SELEX; aptamers; evolution; fitness landscape; high-throughput sequencing.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Improvements of aptamers identification and characterization with the use of High-Throughput Sequencing. HTS analysis can investigate faster the enrichment of (sub-)sequences or predicted (sub-)structures. Variants of a same family sequence can be compared in order to extract mutants with higher affinity than the most abundant sequence. It is possible to more precisely characterize the interaction between aptamers and their targets by analyzing different conditions of selection (for instance, incubation with target’s variants or varying the composition of binding buffer). It is also possible to find aptamers specific for a defined condition. Finally, the impact of each selection parameter can be studied which could help to improve the SELEX experiments in the future.
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