Protocol Online logo
Top : New Forum Archives (2009-): : siRNA, microRNA and RNAi

optimal size for 3'UTR cloning - miRNA and 3'UTR cloning (Apr/19/2011 )

Hi all,
I understand that the field of miRNA is very emerging and there is a lot of data which is being added each day to add to the existing knowledge and maybe add to a paradigm shift in our understanding of non-coding RNAs. Since I'm new to this field and am following experimental systems in the literature, can anybody help me in understanding how people report success with 3'UTR assays when they say they have cloned in part as opposed to the complete 3'UTR?
Would really appreciate your suggestions and inputs



I don't think there is consensus regarding what kind of 3UTR reporter assay is more accurate. Several strategies have been used in the literature:

full-length 3'UTR cloning
partial 3' UTR cloning
cloning of a single miRNA target site with a few flanking bases
cloning multiple miRNA targets in tandem

There are pros and cons for each method. For example, the full-length 3UTR reporter assay should in theory provide the most accurate readout, in the same time it complicates the assay by exposing other potential target sites to miRNA targeting.


Thanks for your helpful inputs

I'm beginning with partial 3'UTR cloning...lets see how that goes!!