3DNA Forum

Welcome => Feature requests => Topic started by: sree on August 15, 2016, 11:50:47 am

Title: four stranded i-motif build and reconstruction
Post by: sree on August 15, 2016, 11:50:47 am: 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
Title: Re: four stranded i-motif build and reconstruction
Post by: xiangjun on August 15, 2016, 01:29:45 pm: Hi Sree,

Thanks for posting on the 3DNA Forum.

The PDB entry 1a83 (http://www.rcsb.org/pdb/explore/explore.do?structureId=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) (http://casegroup.rutgers.edu) from the David Case group at Rutgers may fit your needs better.

Xiang-Jun
Title: Re: four stranded i-motif build and reconstruction
Post by: sree on August 15, 2016, 02:02:32 pm: Thank you for your valuable advice. I will check if I can use NAB software for this purposes.