Stepping Library-Based Post-SELEX Strategy Approaching to the Minimized Aptamer in SPR

Analytical Chemistry
Xiaoqin HeJianwei Xie

Abstract

When evolved from SELEX (systematic evolution of ligands by exponential enrichment), aptamers are generally about 70-130 nucleotides in length and needed to be effectively truncated for further diagnosis or therapeutic uses. Post-SELEX optimization is then aroused to simplify the aptamer sequence and improve the affinity property. In this work, we report a new post-SELEX strategy based on a stepping library for the first time. With a hypothesis that one nucleobase can influence the whole binding affinity through its adjacent base stacking and potential steric hydrogen bonding interaction, we designed a stepping library composed of all probable nucleotide truncation directions. We employed an aptamer 807-39nt toward EPO-α as a model, and surface plasmon resonance (SPR) as an efficient screening and evaluation method to optimize all label-free sequences in the library. We have successfully picked out In27 as the minimized aptamer from a mini library of only 35 sequences. Aptamer In27 has a sole loop, without the original stem portion of the initial aptamer, but retains the whole binding affinity. We have also defined the key nucleotide contribution by site mutagenesis with natural bases, and finally produced a degenerated sequenc...Continue Reading

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Citations

Jul 14, 2017·Biomedicines·David E Volk, Ganesh L R Lokesh
Jul 13, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Alexander Eisold, Dirk Labudde
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Feb 19, 2020·Analytical Biochemistry·Hirotaka MinagawaIwao Waga
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Jul 3, 2019·ACS Combinatorial Science·Hasan KurtMeral Yüce
Nov 30, 2018·Journal of the American Chemical Society·Linlin WangDihua Shangguan

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