Dear   Maria

How big are the sequences for the targets you wish to raise?

Regards

Prash

Chapter Targeting of the HPV-16 E7 protein by RNA aptamers

80-400 nucleotides long

Thank you very much for your interest

Dear  Maria

There is indeed an in vitro selection but considering the fact that you could opt for "steps "  as desired:

1.  Collect, sample, pool and quantify RNA

2. Enrichment through RT/CDNA

3. Amplify the labeled pool of RNA and finally perhaps opt for online tools like Abcam, Basepairbio.com for finding the desired targets. 

Hope this helps

prash 

Hi Maria

I believe the most critical aspect is that you want to avoid selecting against sequences rather than structures. This means, if you go by a standrard SELEX protocol, you will finish with a seuqence that is a reverse complement of your target RNA. That would be an antisense probe, but not an aptamer. So what you need is to introduce counterselection steps to remove such sequences, and/or change your target RNA sequnce while mainting it structure - I do not know if that is feasible for you.

I know that the Mayer lab in Bonn is expert in these things, so I suggest you contact Günter Mayer:

http://www.mayerlab.de/

Regards, Mark

Many thanks Mark!

How can I pool RNA? By labelling? Sincerely grateful for your answers Prash!