create RNA sequence syn nucleosides

[amirtaghavi]

Hello,
 
I have a question and I was wondering if you could help.
I want to make a small RNA with the sequence 5' UCAA*GA with the complementary seq. as 3' AGUC*CA. I want to make all four possible combinations of this sequence with the starred  nucleosides (A* and C*) being in the syn-syn, syn-anti, anti-syn & anti-anti (which is the standard form with fiber).
Is there any way that I can create these systems with x3dna.

Thanks in forward.

Best regards,
Amir

[xiangjun]

Unfortunately, the answer is no within 3DNA. Nevertheless, you may use the 3DNA fiber program to generate a structure in the anti-anti form as a starting point. There exist interactive tools (e.g., PyMOL) to rotate the desired base by its glycosidic bond into the syn form.

Xiang-Jun