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I've only solved NMR structure of globular proteins (actually in a complex with a short stretch of DNA), but never a structure of nucleic acid alone. What are (are there?) the major differences in the approaches when working on a structure of nucleic acid - in terms of choice of the NMR technique, maybe specific parameters and structure simulation? Are distance restraints alone sufficient to obtain structure of DNA or RNA? Thank you in advance! |
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The sequential assignments can be cumbersome due to loads of overlapping but is needed to make sure you have the type of DNA you want (B or A-form), and to map interactions upon complexation if that's your purpose. Two dimensional experiments with high resolution usually suffice (NOESY, TOCSY, COSY) and avoid symmetrization. The NOESY should be run in different mixing times (50 to 300 ms, or make a buildup curve to find the saturation point). Run short simulations with NOE-constraints from 50 ms mixing time first, and then add the contrainsts with the longest time (250-300ms). Give more flexibility in the penalty functions to the methyl constraints in your input file. That's what I can remember now... |
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I think these books will help you a lot: Protein NMR Spectroscopy, Second Edition: Principles and Practice by John Cavanagh, Wayne J. Fairbrother, Arthur G. Palmer III, Nicholas J. Skelton, Mark Rance Fundamentals of Protein NMR Spectroscopy (Focus on Structural Biology) by Gordon S. Rule, T. Kevin Hitchens) Or you can visit my site to get more information about protein analysis by NMR. |
