four stranded i-motif build and reconstruction

[sree]

Dear All,

I am working on i-motif, the four stranded loop structure (for eg: 1A83.pdb) and come across 3DNA software, is it possible to  build a four stranded i-motif structure using 3DNA or web3DNA software. Please advise if I miss anything.
I would like to look at different loop lengths for eg: CCCTTTCCCTTTCCCTTTCCCTTT, CCCTTTTCCCTTTTCCCTTTT, CCCTTTTTCCCTTTTTCCCTTTTT etc.
Many Thanks
Sree

[xiangjun]

Hi Sree,

Thanks for posting on the 3DNA Forum.

The PDB entry 1a83 you referred to has the sequence cCTTTCCTTTACCTTTCC. It has 2 Cs with looping nucleotides (mostly Ts) in between and a total 4 C+C intercalated pairs. The structures you want to model has 3 Cs with 3/4/5 etc Ts in between.

3DNA has no direct means to build such complicated four stranded i-motif structures. The 3DNA utility program mutate_bases, and the combination of find_pair (with the -s option), analyze, and rebuild may help in some aspects of such (heavily manual) modeling process. The NAB (Nucleic Acid Builder) from the David Case group at Rutgers may fit your needs better.

Xiang-Jun

[sree]

Thank you for your valuable advice. I will check if I can use  NAB software for this purposes.