@ saira, its not micro RNA, its a 0.9kb fragment of in vivo ribosomal RNA..

You have several options but my first question is do you need to improve the efficiency? You can check to see if the transfer has been efficient by the following:

1. If you ran your RNA in a gel with ethidium then you can simply visualise the membrane after transfer as you would a normal ethidium stained agarose gel - the ethidium remains bound to the RNA during transfer and this allows you to see the RNA on the membrane. We do this during the UV cross linking step.

2. You can stain the RNA on the membrane using a methylene blue solution (0.005% (w/v) methylene blue in 0.3 M sodium acetate) for 30 seconds or so. Then destain the membrane with three washes (or more if needed) of 0.1X SSC and 1% SDS for 15 minutes each.

3. You can also check to see if there's any RNA remaining in the gel after your transfer by staining the gel with ethidium.

Totally agree with Daniel, these are the first things to check. As further suggestions,  If you are really concern about your semidry system, you may want to include a DNA molecular marker, to visualize how the bands of different sizes are transferred, so you have a rough idea if the time and voltage are adequate. Double check the membrane that you are using ( a positive charged one), I used hybond N+ with good results. Good luck!

Dear Daniel and Sara, I have attached here the pic of my membrane stained with methylene blue and the gel with Etbr to check if transfer was complete or not.You can clearly see that the transfer is inefficient.

For transfer I used 0.5X TBE, and transferred RNA at 20V for 3hrs in cold room.I dont know how to improve the efficiency of transfer.Please suggest something.The membrane I use is Gene Screen Plus hybridisation membrane from perkin elmer.