In silico selection against progesterone receptor DNA-binding domain.

Progesterone receptor is one of the markers used in antibody-based immunohistochemistry for the diagnostics of breast cancer. The shortcomings of antibodies raise the need to focus on alternative molecular recognition. Aptamers are chosen due to their many advantages as compared to antibodies. However, the rigor of conventional SELEX intensifies the efforts to select DNA aptamers using in silico-docking approach. In this study, we performed in silico selection and experimental validation of DNA aptamers against the progesterone receptor DNA binding domain (PR DBD) using the ssDNA sequences derived from human progesterone response elements (PREs). Firstly, a library of sixty-four different ssDNA was subjected to secondary and tertiary structural determination prior to docking using PatchDock. PRDBDapt17 appeared to be the best candidate, with the highest docking scores of 11334. Molecular dynamic simulation also substantiates PRDBDapt17 as the most potent aptamer. This aptamer, PRDBDapt17 was validated by using direct ELASA. Direct ELASA demonstrated a limit of detection of 3.91 nM while the equilibrium dissociation constant was estimated at 366.6 nM. As PRDBDapt17 also interacts with estrogen receptor and androgen receptor, it can also be a potential universal binder of steroid hormone receptors. PRDBDapt17 can be used in the diagnostics of breast cancer.