Deciphering aptamer-protein interactions for bovine sperm sorting through in silico and in vitro studies

In recent years, aptamers have emerged as versatile molecular tools with promising applications in various fields, including diagnostics and therapeutics. In livestock reproduction, their application holds promise for improving the sorting and identification of X and Y chromosome-bearing sperm cells, which is essential for increasing productivity in the dairy and beef industries.

This study utilized seven rounds of Cell-SELEX using bovine X and Y sperm cells to isolate specific aptamers that target these cells. A comprehensive in-silico analysis was conducted to evaluate the binding interactions between the selected aptamer sequences and the differentially expressed plasma membrane proteins of X and Y sperm cells.

The analysis identified the aptamer sequences APT1X, APT2X, and APT5X as having the most stable interactions with the X sperm surface proteins TLR8 (Toll-like receptor 8), CLRN3, and TLR7 (Toll-like receptor 7), respectively. APT2Y exhibited a relatively high affinity for the protein SCAMP1, a Y-sperm-specific protein. Aptamer‒protein interactions are characterized by hydrogen bonds and hydrophobic contacts. Notably, APT1X formed the greatest number of hydrogen bonds with the polar residues of TLR8, whereas TLR7-APT5X interactions exhibited the greatest number of hydrophobic contacts.

The use of in-silico analysis for evaluating the interaction between candidate aptamer sequences and differentially expressed X and Y bovine sperm proteins provides valuable insights. This approach might facilitate the sorting of bovine X and Y sperm cells, contributing to advancements in livestock reproduction strategies.