I have a doubt regarding the designing of the RNA probe. What is the ideal length of the RNA probe for RNA FISH and will it be okay if I have a fluorescent modification (Cy5 labelling ) on either 5' or on 3' end of the probe or it will effect the hybridization of the probe with RNA?
Mª Angeles Zorrilla Lopez-Perea Thank you for your reply. Actually, I am looking for What are the things that I have to consider while designing an RNA Probe Like length of the Probe, fluorescence labelling (5'or 3') ,recommended fluorophores (Cy5 or Cy3),and concentration of the probe (100um or 100nm) , kindly help me with this.
Thank you in advance.
I would a second opinion on this,sorry I totally misread the question. What I meant is there are online software to build probes, and I wanted to suggest the above. I would say a length 5-10,but in an approximate way. You may use a fluorescent labelling,maybe it would be slightly unstable (it is not the same to just label one side),which would be 5' with Cy5. The concentration 100um (maybe I have been to generous). Hope this is fine.
Mª Angeles Zorrilla Lopez-Perea No problem, at least you gave me some suggestions.
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