I know there's a method to do that with RNase H. this enzyme cleaves at sites of double-strand RNA-DNA hybrid.

so you prepare an oligo that will anneal to the site where you want to cleave.

this paper has a protocol: http://nar.oxfordjournals.org/content/36/21/6728.long

Thanks Gal,i will try that. Is there any method which do not require binding of oligo, as i think that the pre-mRNA is having lots of secondary structures and is not accessible to the primers what i am using for cDNA synthesis and amplification ?

Are you denaturating RNA template before cDNA synthesis?

I do 10min 70celsius with Oligo's before synthesis.

Yes, i am using this step which is recommended by Sigma HSRT kit also. But i am not sure if this step is able to denature the 10 kb long fragnment ?

Tarun - If you just want non-specific fragments, then maybe sonication can work?

I know sonication is used to break genomic DNA to small fragments. However, I do not know how sonication affects RNA.

ok..thanks Gal