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Miscellaneous items => FAQs => Topic started by: xiangjun on March 20, 2012, 02:26:29 pm

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Title: How do I build an A- or B-form DNA model with a particular base sequence?
Post by: xiangjun on March 20, 2012, 02:26:29 pm

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.

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University