In silico designed RNA aptamer against epithelial cell adhesion molecule for cancer cell imaging

Aptamers are short, single-stranded oligonucleotides that bind to their targets with high affinity and specificity. Usually, aptamers are selected experimentally using SELEX approach. Here, we describe a computational approach for selection of aptamers for proteins, which involves generation of a virtual library of sequences, modeling of their 3D-structures and selection of perspective aptamers through docking, molecular dynamics simulation, binding free energy calculations and finally estimating the experimental affinity. Using this method, a 15-mer RNA aptamer was designed for epithelial cell adhesion molecule. Flow cytometry and fluorescence microscopy results reviled that RNA1 aptamer interacts specifically with human cancer cells that express EpCAM, but not with the EpCAM negative cells. The binding affinity of the RNA1 aptamer to MCF-7 and MDA-MB-231 is approximately 21.8 and 96.9 nM respectively. This novel RNA aptamer will help in the future development of targeted therapeutics and molecular imaging. [Display omitted] •Specific aptamer was identified for EpCAM by in silico approach.•The binding affinity and specificity of aptamer was verified in vitro.•Endocytosis inhibition confirmed that the RNA1 aptamer is efficiently internalized upon binding to EpCAM positive cells.•RNA1 aptamer can be used for diagnostic, imaging and for therapeutic purposes.