Cell-SELEX Identifies a "Sticky" RNA Aptamer Sequence.

Partha Ray,Rebekah R White

doi:10.1155/2017/4943072

Abstract

Cell-SELEX is performed to select for cell binding aptamers. We employed an additional selection pressure by using RNAse to remove surface-binding aptamers and select for cell-internalizing aptamers. A common RNA sequence was identified from independent cell-SELEX procedures against two different pancreatic cancer cell lines, indicating a strong selection pressure towards this sequence from the large pool of other available sequences present in the aptamer library. The aptamer is not specific for the pancreatic cancer cell lines, and a similar sequence motif is present in previously published internalizing aptamers. The identified sequence forms a structural motif that binds to a surface protein, which either is highly abundant or has strong affinity for the selected aptamer sequence. Deselecting (removing) this sequence during cell-SELEX may increase the probability of identifying aptamers against cell type-specific targets on the cell surface.

Highlights

Aptamers are nucleic acid polymers that are selected by Systematic Evolution of Ligands by Exponential enrichment (SELEX)
We incorporated an additional selection pressure in the SELEX protocol by using a cocktail of RNAse (RiboShredder, RS) that was first described by Magalhaes et al [11]
We performed cell-SELEX with the goal of identifying aptamers that bind to pancreatic cancer cells; an additional selection pressure was applied by using RNAse to remove surface-binding aptamers and select for cell-internalizing aptamers

Summary

Introduction

Aptamers are nucleic acid polymers that are selected by Systematic Evolution of Ligands by Exponential enrichment (SELEX). Positive selections are done against the cell type that is the desired target for aptamer binding. If one desires to generate an aptamer that would target certain cancer cell type, a corresponding normal cell type would be used as the negative selection target. The aptamers that binds to common targets that are shared between the positive and negative cells are removed from the selection, whereas aptamers that display specificity for the cancer cell targets are preferentially selected. Using this type of selection scheme, several aptamers have been generated that display high affinity and specificity against their targeted cells [4]

Methods

Results

Conclusion