Hi, Bharti.

I don't know if this will address your issue, but your description reminds me of the RNA Design Problem: given a secondary structure, find sequences that would fold in such a way.

Here is a short and incomplete list of publications addressing the RNA Design Problem, aka RNA inverse folding problem.

• Eastman, P., Shi, J., Ramsundar, B. & Pande, V. S. Solving the RNA design problem with reinforcement learning. PLoS Comput Biol 14, e1006176 (2018).
• Anderson-Lee, J. et al. Principles for Predicting RNA Secondary Structure Design Difficulty. - PubMed - NCBI. J Mol Biol 428, 748–757 (2016).
• Zhou, Y. et al. Flexible RNA design under structure and sequence constraints using formal languages. in 229–238 (ACM Press, 2007). doi:10.1145/2506583.2506623
• Taneda, A. Multi-objective genetic algorithm for pseudoknotted RNA sequence design. Front Genet 3, 36 (2012).
• Waldispühl, J., Devadas, S., Berger, B. & Clote, P. Efficient algorithms for probing the RNA mutation landscape. PLoS Comput Biol 4, e1000124 (2008).
• Andronescu, M., Fejes, A. P., Hutter, F., Homann, H. H. & Condon, A. A new algorithm for RNA secondary structure design. J Mol Biol 336, 607–624 (2004).

You could look for instance at RNAinverse from the Vienna package/services:

• http://rna.tbi.univie.ac.at
• http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAinverse.cgi

Hope this helps.

All the best with your project!

Marcel

Thank you Marcel Turcotte for the informative response.

Here, I am not trying to predict RNA folding. I can already predict the hairpin structures and folding by using Oligo-analyzer tool from IDT (vendor). As there analyzer predicts certain number of folds that this stretch of RNA can acquire, I was trying to know if there is some way to get RNA synthesized commercially in a particular fold.

Thanks for additional help.

Regards

Bharti Singal

the RNA (t) has secondary structure giving it a semi-clover appearance, it is transcribed by polymerase III in the nucleoplasm. in order to modify its secondary structure you would have to alter the activity of the polymerase by making a change in the gene that encodes it; finally I recommend using the CRISPR / CAS 9 technique.