The impact of immobilized metal affinity chromatography (IMAC) resins on DNA aptamer selection

E Kowalska,K Pels,F Bartnicki,W Strzalka

doi:10.1007/s00216-014-7937-y

E Kowalska, K Pels + Show 2 more

Open Access

https://doi.org/10.1007/s00216-014-7937-y

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Journal: Analusis	Publication Date: Jun 13, 2014
Citations: 24	License type: CC BY 4.0

Affiliation: Jagiellonian University

Abstract

DNA aptamers are single-stranded oligonucleotides which can form various secondary and tertiary structures. They can recognize a broad range of targets ranging from small molecules, such as ions, vitamins, antibiotics, to high molecular weight structures, including enzymes and antibodies. DNA aptamers are extensively studied as a potential source of new pharmaceutical drugs due to their inexpensive synthesis, low immunogenicity, and high specificity. The commonly used aptamer selection procedure is systematic evolution of ligands by exponential enrichment (SELEX) where the target molecule is immobilized on an appropriate chromatography resin. For peptide/protein targets, immobilized metal affinity chromatography (IMAC) resins are frequently used. There is a broad range of commercially available resins which can be used for IMAC. They are characterized by different metal ions, linker types, and bead materials. In this study, we tested the impact of different IMAC resins on the DNA aptamer selection process during eight SELEX cycles. A histidine-tagged 29 amino acid peptide corresponding to the interdomain connecting loop of human proliferating cell nuclear antigen was used as a selection target. Different resin materials containing the same metal ion (Co2+) were tested. Simultaneously, agarose resins containing identical linkers, but different metal ions (Co2+, Cu2+, Ni2+, and Zn2+) were analyzed. The results of this study clearly demonstrated the impact of the metal ion and resin material on the DNA aptamer selection progress. The presented data indicate that for successful IMAC resin-based SELEX, the determination of the optimal resin might be crucial.

Highlights

DNA or RNA aptamers are short single-stranded molecules, from 40 to 100 nucleotides in length, which are able to form unique secondary and tertiary structures
We have shown that immobilized metal affinity chromatography (IMAC) resin material and metal ions (Co2+, Cu2+, Ni2+, and Zn2+) may have an important impact on DNA aptamer selection
Taking into account this fact, we studied whether the results of IMAC resin-based systematic evolution of ligands by exponential enrichment (SELEX) might be dependent on carrier properties

Summary

Introduction

DNA or RNA aptamers are short single-stranded molecules, from 40 to 100 nucleotides in length, which are able to form unique secondary and tertiary structures. They can recognize many different targets, starting from small molecules such as metal ions and amino acids to large protein complexes or even whole viruses and cells, and bind them with high affinity and specificity [1]. Immobilized metal affinity chromatography (IMAC) resinbased SELEX [5] is often used for the selection of DNA aptamers against peptide/protein targets which are bound to resins through a short histidine tag. We have shown that IMAC resin material and metal ions (Co2+, Cu2+, Ni2+, and Zn2+) may have an important impact on DNA aptamer selection

Materials and methods

Results and discussion

Conclusions