Why does fixing of cells with something like formaldehyde disrupt the membrane enough for probes, antibodies, and dyes to get into the cell?

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    $\begingroup$ It doesn't. You generally also need to permeabilize with a detergent in order to do antibody staining. Fluorescent dyes are very small when compared to antibodies or large nucleic acids, and so can diffuse across the membrane or fit through very small pores created by (para)formaldehyde fixation. $\endgroup$ – MattDMo Sep 17 '15 at 20:27
  • $\begingroup$ In my experience, somehow antibodies are accessible to the inside of cells without permiabilization. But I do not know the explanation. $\endgroup$ – 243 Sep 17 '15 at 21:34
  • $\begingroup$ 243 is right, however fixing tissues with formaldehyde or PAF usually leads to the formation of methylen bridges cross linking proteins and potentially masking epitopes. Therefore in most of the cases you'll need an antigen retrieval step based on heat induced or proteolytic protocols to properly access to the antigens. While working with cell some chemical will at the same time fix and permeabilize your cells (like aceton) $\endgroup$ – Cobactan Sep 17 '15 at 21:43

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