One of the major points is the validation, which usually is assay specific. For example, one of the companies I buy antibodies from write about the validation procedure for western blot application:
Validation Steps Include:
1) Examination of several cell lines and/or tissues of known expression levels allows accurate determination of species cross-reactivity and verifies specificity.
2)Treatment of cell lines with growth factors, chemical activators or inhibitors, which induce or inhibit target expression, verifies specificity. Phosphatase treatment confirms phospho-specificity.
3)The use of siRNA transfection or knockout cell lines verifies target specificity.
And I ask myself, is the companies who are making aptamers at the moment, are doing this type of validation? I know they are selecting on specificity, and they are determining the binding constant, but are their commercial aptamers that one can buy that are validated in the same way as aptamers are?
I am rather sure, that customers of aptamer development companies are doing validation for their application, but I have the feeling that 'off the shelf aptamers' have not gone through these procedures, and maybe this is one of the reasons aptamers are not replacing antibodies as fast as they could.