The typical way of detecting proteins by immunohistochemical staining involves a two-step process. A primary antibody is raised against the antigen, and then a second, fluorescently-labeled antibody is used to detect the first.
Evidently, a one-step staining method would be far simpler and quicker than the indirect method. However, until recently direct conjugation has been avoided because of problems in sensitivity and amplification of the signal. Factors influencing this include the sample size needed, low percentage of recovery and dilution. The indirect method has greater sensitivity, as the signal can be amplified through using several secondary antibodies, each specific to a different antigenic site on the primary protein. However, the procedure is tedious, requiring numerous incubation and wash steps. Using secondary proteins also means more likelihood of cross-over problems and non-specific binding.
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