Is it possible to implement an unnatural nucleotide?

[zikriehsb]

Hello,

I am currently using a synthetic DNA that has two unnatural nucleotides, Cu(II)-DPA and dSpacer (DPA and DSP, pdbs attached). In my DNA, these two nucleotides are paired to each other as shown in the following.

5'-AAT ATT AXA GAT ATC TYT TTA TAA-3'
3'-TTA TAA TYT CTA TAG AXA AAT ATT-5'

where X is DPA and Y is DSP.

Is it possible to submit the unnatural Cu(II)-DPA and dSpacer PDB into the 3DNA software for building my synthetic DNA? I understand that one can edit the baselist.dat file to have a modified base in the library. However, i assume that modified bases are possible due to their commonalities with the canonical nucleotides and their ability to form hydrogen bonds for their pairing. Because my nucleotides are not based on the canonical nucleotides, I suspect that 3DNA might not be able to take my unnatural nucleotides' PDB and model my synthetic DNA. However, I would double check if it is impossible for me to model my synthetic DNA.

Regards,
Zikri

[xiangjun]

Hi Zikri,

Thanks for your interest in using 3DNA and for posting your questions on the Forum.

Regarding DPA and DSP, you are correct in saying that 3DNA is not able to model them. From the PDB files you attached, 3DNA (reasonably) does not take DPA and DSP as nucleotides at all. Other tools may help. If you find any, please share with us.

Thanks,

Xiang-Jun