Efficient screening of anti-idiotype DNA aptamers that bind specifically to trastuzumab for bioanalytical applications

We have developed a novel aptamer discovery method that rapidly and efficiently yields anti-idiotypic DNA aptamers for trastuzumab using fast protein liquid chromatography (FPLC) separation and large amounts of DNA. The use of large amounts of oligo DNA allowed us to obtain more aptamer candidates without PCR amplification within only two days. Quartz crystal microbalance (QCM) measurements confirmed that the obtained anti-trastuzumab aptamer had a high affinity with a K_D of 120.0 nM and 97.7 nM at pH 6.0 and 7.4, respectively. Molecular docking simulations suggested that this sequence has high specificity and binding affinity to multiple sites in the complementarity-determining region of trastuzumab. The K_D increased to 11.4 nM due to avidity expression after dense immobilization in the QCM sensor cell, indicating that this anti-trastuzumab aptamer is applicable as a capture molecule in the ligand binding assay.