Mouse lipocalin‐2 aptamer: an RNA probe for molecular discrimination

High‐resolution molecular discrimination is a feature of aptamers that can be applied to molecular recognition. Aptamers can recognize molecules for which antibodies are lacking or confirm the molecular species recognized by existing antibodies. To develop the latter approach, an RNA aptamer was selected against mouse lipocalin‐2 (mLcn2) and found highly specific for mLcn2, not binding the human and chicken orthologs. The majority of bases in contact with the protein are located in the loop regions of the proposed aptamer structure as proved by sequence variants and RNA foot printing. Charged surface amino acids replaced by alanine did not change aptamer affinity for mLcn2, while mutation of three conservative basic core amino acids decreased or abolished the interaction. The mutants showed no evidence of global conformational changes as reflected by their unchanged Tm’s from the wild‐type protein. Sequence alignment with the human Lcn2 (hLcn2) showed that residues surrounding these three conserved amino acids are also conserved, which suggests that the molecular discrimination of the aptamer derives from an interaction with another feature of mLcn2 that differs in hLcn2. The high degree of molecular discrimination of this aptamer, a general characteristic of aptamers, will be applied to sharpening the discriminatory capabilities of antibody‐based analysis. This work was funded by Iowa State University.