SPR TRIS or PBS buffer
I presume the aptamer is biotinylated; if not, that’s a likely reason for the outcome.
Have you used a biotinylated positive control to confirm the surface is functional with PBS? I understand you want to buffer exchange to Tris, but this positive control in PBS buffer is important.
Amine coupling involves covalent attachment of the 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) to carboxylate on the chip surface, followed by replacement of this adduct with N-hydroxysuccinimide (NHS), thus creating an active surface to crosslink primary amines at slightly acidic pH. Then the unreacted active surface is quenched with ETH. Residual active surface would react with Tris that contains a primary amine.
Perhaps the ethanolamine blocking agent may not have completely inactivated the active surface following streptavidin amine coupling, enabling crosslinking of Tris buffer to that surface and impacting the ‘Protein’ capture?
Other possible reasons: Binding of the aptamer to streptavidin may sterically hinder binding of the 'Protein.' Also, the loss of the proper secondary structure of the aptamer may impact the 'Protein' binding. Perhaps refolding the aptamer prior to streptavidin capture may help?
Edit: Differences in pH and ionic strength may impact 'Protein' binding to aptamer when tested in Tris versus PBS buffers.