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Hi, I was wondering if it is possible to build a dsRNA helix using 3DNA that has non-Watson-Crick base-pairs. When using the fiber -r -s -seq=(arbitrary seq) command there doesn't seem to be a way to specify for non-Watson-Crock base-pairs, like the common U-G wobble.
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3DNA does not provide an automatic way to build a dsRNA with non-Watson-Crick base pairs, e.g., the G-U wobble pair. Nevertheless, it has the components that can could possibly be combined to get the job done, on a case-by-case basis. If you are specific about what you want to achieve, our discussions can be more concerete. Alternatively, you may try software tools developed from the laboratories of Eric Westhof or François Major, among other possible choices.
Xiang-Jun