Dear all I have a technical question pertaining to molecular biology.
Can a RNA binding protein get detected in chromatin immunoprecipitation if the final PCR is designed about the same region in the DNA template in which the protein binds to RNA?
In other words, after cross-linking, fragmentation and pull-down, is there a chance that the RNA-protein complex is pulled down along with the the DNA-protein complex and finally, gives a band in PCR which is a false negative result indicating that the protein was actually bound to DNA?
Would be glad to hear some ideas.
After the pull down and the de-crosslinking, you usually have a DNA elution step, in which the RNA fraction (if it exists) is usually discarded.
I think is highly unlikely that you find RNA in your final eluted material.
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