Hi,
I'm working with an RNA which has many nonstandard nucleotides. The
2' position of the pyrimidines is fluorinated, the 2' position of (all
but two of the) purines is methylated and the 3' termini has Thymine
linked backwards (via its 3' O).
I have a pdb for this molecule, which I can post if it would help.
I'm having problems deciding how to get this molecule into Analysis in
a manner which will minimize headaches later. I could treat the
molecule as a standard RNA (completely neglect the modifications), but
we anticipate (and indeed see) NOEs involving the 2' methyls.
Does anyone have any suggestions on how to deal with this sort of molecule?
Thanks,
Justin
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