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RNA fragmentation


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#1 rimal

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Posted 31 August 2010 - 05:23 PM

Dear all,

I have long RNA more than , I need to use it in EMSA assay but I need to fragment it to get small size RNA's , is restriction digestion in specific sites, can any body explain how to chose the sites?

#2 blaszcz

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Posted 02 September 2010 - 07:06 AM

Restriction digestion of RNA's? Its impossible. You have to amplify smaller DNA templates. Next you can use it for generation of shorter RNA constructs.

#3 rimal

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Posted 02 September 2010 - 05:06 PM

Restriction digestion of RNA's? Its impossible. You have to amplify smaller DNA templates. Next you can use it for generation of shorter RNA constructs.


I am sorry I didn't mean RNA, I ment DNA plasmid, so if I have long plasmid for RNA can I digest the areas that I need with restriction enzyme, and then I can use T7 for transcription of this fragmnets?

#4 blaszcz

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Posted 03 September 2010 - 01:07 AM

Of course you can do it but there is big probability that you will not find a restriction enzyme that cuts precisely. So you can get then a fragment of interest with for egzample extra 20nt. I think that better method is to amplify your desire constructs from plasmid using PCR and set of primers because you have a certain that your construcst are exactly as you want.




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