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Author Topic: Pauling's triplex model of DNA and RNA  (Read 715 times)

Offline xiangjun

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Pauling's triplex model of DNA and RNA
« on: November 17, 2016, 11:26:31 am »
As of v2.3-2016nov16, the 3DNA fiber program has added the --pauling option. This new feature is intended for easy generation of DNA/RNA triplex models based on the historical paper of Pauling and Corey in 1953, titled "A proposed structure for the nucleic acids". Combined with the existing --sequence option, 3DNA users can now construct a Pauling triplex model with arbitrary base sequence.

The basic usage is very straightforward, as illustrated in the following list of examples. There are also other variants as well, which may be useful for advanced users.

Code: [Select]
fiber -pauling triplex-C10C10C10.pdb        # default: 10 Cs per strand
fiber -pauling -seq=AAA triplex-A3A3A3.pdb  # 3 As per strand
fiber -pauling -seq=AAAA:CCCC:GGGG Pauling-triplex-A4C4G4.pdb
fiber -pauling -seq=ACGGUU,UUGGAC,GGAACC  Pauling-triplex-mixed.pdb
fiber --pauling-dna -seq=ACGGTT,TTGGAC,GGAACC  Pauling-triplex-DNA.pdb

A sample 3D image for the mixed sequence (last one in the above list, Pauling-triplex-DNA.pdb) is shown below:



See my blogpost titled "Pauling's triplex model of nucleic acids is available in 3DNA" for further information.
« Last Edit: November 17, 2016, 03:02:02 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.