Identification of RNA aptamer which specifically interacts with PtdIns(3)P

The phosphinositide PtdIns(3)P plays an important role in autophagy; however, the detailed mechanism of its activity remains unclear. Here, we used a Systematic Evolution of Ligands by EXponential enrichment (SELEX) screening approach to identify an RNA aptamer of 40 nucleotides that specifically recognizes and binds to intracellular lysosomal PtdIns(3)P. Binding occurs in a magnesium concentration- and pH-dependent manner, and consequently inhibits autophagy as determined by LC3II/I conversion, p62 degradation, formation of LC3 puncta, and lysosomal accumulation of Phafin2. These effects in turn inhibited lysosomal acidification, and the subsequent hydrolytic activity of cathepsin D following induction of autophagy. Given the essential role of PtdIns(3)P as a key targeting molecule for autophagy induction, identification of this novel PtdIns(3)P RNA aptamer provides new opportunities for investigating the biological functions and mechanisms of phosphoinositides. •By SELEX screening, PtdIns(3)P binding RNA aptamer was identified.•PtdIns(3)P RNA aptamer binds specifically to PtdIns(3)P as magnesium concentration dependent and pH dependent manner.•PtdIns(3)P RNA aptamer can be used for monitoring the intracellular PtdIns(3)P.•PtdIns(3)P RNA aptamer inhibits autophagy, lysosomal acidification, cathepsin D activity, and cellular proliferation.•Identification of PtdIns(3)P RNA aptamer will have varieties of implication on the phosphoinositide related biology. SELEX screening identified an RNA aptamer that interacts with PtdIns(3)P to control autophagy.