We demonstrate the use of surface-immobilized, orientedpeptide aptamers for the detection of specific targetproteins from complex biological solutions. These peptideaptamers are target-specific peptides expressed within aprotein scaffold engineered from the human proteaseinhibitor stefin A. The scaffold provides stability to theinserted peptides and increases their binding affinityowing to the resulting three-dimensional constraints. Aunique cysteine residue was introduced into the proteinscaffold to allow orientation-specific surface immobilization of the peptide aptamer and to ensure exposure of thebinding site to the target solution. Using dual-polarizationinterferometry, we demonstrate a strong relationshipbetween binding affinity and aptamer orientation anddetermine the affinity constant
KD for the interactionbetween an oriented peptide aptamer ST
and thetarget protein CDK2. Further, we demonstrate the highselectivity of the peptide aptamer STM
pep9 by exposingsurface-immobilized ST
to a complex biological solution containing small concentrations of the target proteinCDK2.