how to design a northen blot probe? - (May/07/2008 )

Hi friends,
I am trying to design a probe general enough to tag different members of a gene family in northern blot. I am thinking of designing this probe as a quick check to see if the pattern of expression of the members of gene family changes as a result of my treatment. So, I am not thinking of designing RT-PCR primers at this stage.

Does somebody have any piece of advise about steps that I have to take?
Thanks

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I am not sure what exact advise you are looking for. Here are some, feel free to ask specific questions:

1. Designing RT-PCR strategy would save you a lot of time.
2. When designing the probe make sure that it does not hybridize with anything other than the gene (family) of your interest. Do that particular organism genome blast.
3. Choose the part of gene that is highly conserved within the gene family.
4. Keep it 300-400 bp long.
5. Make sure there are no common repeat or repeat-like regions in the probe sequence.
6. You may need to keep the hybridization temp a little low in order to fish out all members of the family.


hth/

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