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lncRNA full-sequence or partial sequence - (Mar/07/2013 )


I am going to study non-coding RNAs and their interaction with proteins.
I run some interaction software that gave me fragments with good predictions for interaction with my protein.
Now, my question is should I clone only this fragments and study the interaction with my protein or should I clone the full-lenght fragment?
Can anybody give me some advice on that?



I think you should clone the full length lncRNA. At this time any program cannot precisely predict how exactly lncRNA interacts with proteins. Just curious, how are you going to test the interaction next?


Well, the problem is that the lncRNAs are bigger than 10kb. I never had cloned such a big fragment.
So I thought that maybe I could start with a smaller fragments.

I am going to do pulldown experiments based on some papers I have read.