Nucleic acids (DNA and RNA)/nucleus often needs to be stained to identify cell types and cellular location for use in confocal imaging, LCM (laser capture microdissection), flow cytometry etc. Some of the commonly used fluorescent stains include propidium idodide (PI), DAPI, Hoechst 33342, Sybr Green, Sytox Green, Syto, To-Pro etc and visual stains such as Haematoxylin, Eosin Y, Periodic Acid Schiff (PAS) etc.
Do some/any of these stains affect downstream processes such as DNA/RNA extraction, RT, qPCR, RNA-Seq etc? Do these stained samples need to be treated in any special manner before proceeding with the said methods?
If you are staining the cells prior to a DNA/RNA extraction then you should be fine to go on with qPCR,sequencing, etc... Most of those dyes should not inhibit the solutions used in common DNA/RNA extraction kits from Qiagen/MoBIo/Promega or a phenol/chloroform extraction. The dyes will be removed during the precipitation and wash steps of the extraction leaving pure DNA for downstream applications.
At the time that you have isolated your bands from gels or PCR clean up by column is made, all staining is gone...you are not staining your nucleic acid before sending to sequencing...
If you are staining the cells prior to a DNA/RNA extraction then you should be fine to go on with qPCR,sequencing, etc... Most of those dyes should not inhibit the solutions used in common DNA/RNA extraction kits from Qiagen/MoBIo/Promega or a phenol/chloroform extraction. The dyes will be removed during the precipitation and wash steps of the extraction leaving pure DNA for downstream applications.
Just to endorse the above answers, we have hands-on experience with staining biopsy specimens with H&E. After LCM, isolation (TRIzol), and preparation (Ovation RNA-Seq system), the quality of the RNA/DNA was sufficient to perform sequencing on the GS FLX (454).
Here is a paper that refers to qPCR inhibition post DAB staining but I have not been able to find published data about other types of inhibition.
3,3′-Diaminobenzidine staining interferes with PCR-based ...
https://www.nature.com › scientific reports › articlesby C Dölle - 2018 - Cited by 6 - Related articlesJan 19, 2018 - DAB staining affects PCR-based quantitative DNA analysis in neurons. ... These results suggest that the observed reduction in qPCR signal is due to a direct effect on the DNA template derived from DAB-stained tissue, rather than inhibition of the polymerase or signal detection.
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