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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
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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
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Thank you for your valuable advice. I will check if I can use NAB software for this purposes.
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.