Characterization of Single-Stranded DNA Aptamers Against Carcinoembryonic Antigen

Cancer biomarkers play a crucial role in the development of diagnostics tools for cancer detection. Carcinoembryonic antigen (CEA) is a well-known cancer biomarker that is a cell surface glycoprotein, critical in fetal development. Its expression in adult healthy cells is highly associated with colorectal carcinoma and metastasis. Colorectal cancer (bowel cancer or colon cancer) is the third death causing type of cancer, both worldwide and in Kazakhstan. Therefore, there is an urgent need to develop diagnostic assays where aptamers can be employed. Aptamers are artificial recognition agents that have advantages over antibodies because of smaller size, simpler to synthesize and incorporation of modifications, and higher stability allowing high selectivity during detection. Previously, single stranded DNA (ssDNA) aptamers against CEA were selected by SELEX method (Systematic Evolution of Ligands by Exponential enrichment). As a result of twelve SELEX cycles, six aptamer candidates were selected from a pool of ssDNA library with a central 40 nt random region. Predicted secondary structures of selected six aptamers showed similarities in structure between some of them as well as distinct structures. In this study, aptamers against CEA were evaluated based on the binding of the ssDNA aptamers against CEA using ELONA. Obtained results show that the selected aptamers showed a solid specificity and sensitivity values comparing to the non-target proteins (IL-6 and HSA) as well as controls. Future work will be concentrated on the SPR protocol optimization to improve the data regarding affinity. In the case of low signal, aptamers could be modified easily with self-assembled monolayers (SAMs), such as HS groups or magnetic/gold nanoparticles or any other fluorescent reporting molecules. These could be further used in the application of characterized aptamers in the electrochemical impedance spectroscopy (EIS) based aptasensor for the detection of cancer biomarkers. In addition, CEA aptamers on CEA spiked human serum samples will be tested in order to observe how a protein rich medium can affect the detection of the target