In silico post-SELEX screening and experimental characterizations for acquisition of high affinity DNA aptamers against carcinoembryonic antigen

Abstract

DNA aptamers against carcinoembryonic antigen (CEA) have been identified through the systematic evolution of ligands by exponential enrichment (SELEX) technique, but their affinity needs to be improved. In this study, an in silico approach was firstly used to screen the mutation sequences of a reported DNA aptamer (the parent aptamer, denoted as P) against CEA. The affinities of several high-score DNA mutants were determined by the biolayer interferometry technique. Finally, the newly obtained aptamers were verified in an aptasensor application. For the in silico approach, Mfold and RNA Composer were combined to generate the 3D RNA structures of the DNA mutants. The RNA structures were then modified to 3D DNA structures with the Write program. The docking model and binding ability of the 3D DNA structures with CEA were simulated and predicted with the ZDOCK program. Two mutation sequences (P-ATG and GAC-P) exhibited significantly higher ZDOCK scores than P. The dissociation constant of P-ATG and GAC-P to CEA was determined to be 4.62 and 3.93 nM respectively, obviously superior to that of P (6.95 nM). The detection limit of the P-ATG and GAC-P based aptasensors was 1.5 and 1.2 ng mL⁻¹, respectively, markedly better than that based on P (3.4 ng mL⁻¹). The consistency between the in silico and the experimental results indicates that the developed in silico post-SELEX screening approach is feasible for improving DNA aptamers. The P-ATG and GAC-P aptamers found in this study could be used for future CEA aptasensor design and fabrication, promisingly applicable for highly sensitive CEA detection and early cancer diagnosis.