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Author Topic: How do I build an A- or B-form DNA model with a particular base sequence?  (Read 2457 times)

Offline xiangjun

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The easiest way to build a canonical double helical structure of specific sequence is to use the fiber program. The default option is structure #4, which corresponds to the calf thymus B-DNA double helix due to Struther Arnott. To build the A-form, the user should choose structure #1. Coordinates of these two structures are taken from Struther Arnott: "Polynucleotide secondary structures: an historical perspective", pp. 1-38 in "Oxford Handbook of Nucleic Acid Structure", edited by Stephen Neidle (Oxford Press, 1999).

For example, to build an A-DNA structure of sequence 'AAGCTTTC', one can do the following:
Code: [Select]
fiber -a -seq=AAGCTTTC fa.pdb
Note the -seq option is added as of v2.1.
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.