Screening of DNA Signaling Aptamer from Multiple Candidates Obtained from SELEX with Next-generation Sequencing

Abstract

Here, we demonstrated a strategy for developing signaling aptamers, based on screening of signaling aptamers from multiple aptamer candidates obtained by SELEX with next generation sequencing. Among aptamer candidates labelled by 6-carboxyfluorescein and quencher at both end termini, there is the possibility of discovering a potent signaling aptamer. In this study, we discovered DNA signaling aptamers against VEGFR-1. This strategy has the potential for signaling aptamer discovery without the extremely laborious task of optimization of oligodeoxynucleotide modifications.

Novel Approach to Overcome Defects of Cell-SELEX in Developing Aptamers against Aspartate β-Hydroxylase

“… 33 , 34 Researchers have recently implemented deep sequencing to overcome the defects of traditional sequencing in the process of SELEX. 35 − 37 In agreement with the previous studies, 38 , 39 our obtained NGS data showed that the final enriched pools consist of a large number of oligomers, the top sequences of which only make up 0.5–3.6% of the total number of sequences ( Table 1 ), indicating that the conventional method of sequencing does not provide an authentic view of the enriched pool. Deep sequencing also enables us to track the evolution of ligands much sooner than the process is completed.…”

“…The traditional Sanger sequencing used frequently in various aptamer selection systems can merely visualize a small portion of all of the different sequences available in the enriched pools. , Researchers have recently implemented deep sequencing to overcome the defects of traditional sequencing in the process of SELEX. − In agreement with the previous studies, , our obtained NGS data showed that the final enriched pools consist of a large number of oligomers, the top sequences of which only make up 0.5–3.6% of the total number of sequences (Table ), indicating that the conventional method of sequencing does not provide an authentic view of the enriched pool. Deep sequencing also enables us to track the evolution of ligands much sooner than the process is completed. , Powerful owing to its harnessing of natural forms of target proteins, the routine Cell-SELEX procedure is quite time-consuming in practice.…”

Using a Biosensor Based on Surface-Enhanced Raman Scattering to Identify Influenza Viruses in Biological Fluids

“…Hundreds of aptamer sequences for different targets are currently known, including cells, viruses, proteins, and low-molecular-weight compounds. The number of aptamer sequences is growing along with the development of in vitro selection technologies, along with the use of next generation sequencing to identify leading candidates [ 3 ]. Aptamers as recognition elements are a more technological solution than the monoclonal or polyclonal antibodies widely used in marketed test systems and biosensors, since the aptamer structure can be adjusted.…”

Design strategy of antidote sequence for bivalent aptamer: Rapid neutralization of high‐anticoagulant thrombin‐binding bivalent DNA aptamer‐linked M08 with HD22

“…Compared with antibodies, DNA aptamers possess many advantages such as relatively small size, greater stability, potential for chemical modification, lower toxicity, and reduced immunogenicity 1 . Aptamers have been studied as smart biomolecules in numerous investigations for diagnostic 2 and therapeutic applications 3 . Recently, we developed the systematic evolution of ligands by exponential enrichment (SELEX) with microbead‐assisted capillary electrophoresis (MACE), referred to as MACE‐SELEX, which features a sophisticated separation step with high sensitivity based on capillary electrophoresis separation using target‐coupled microbeads 4 .…”