i like this post (click again to cancel)
i dont like this post (click again to cancel) remove favorite mark from this question (click again to restore mark)

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!

asked Feb 26 '10 at 14:04

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev

updated Mar 08 '10 at 09:45

2 Answers:
i like this answer (click again to cancel)
i dont like this answer (click again to cancel)

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...


answered Mar 07 '10 at 02:27

dyeison's gravatar image


i like this answer (click again to cancel)
i dont like this answer (click again to cancel)

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.


answered Jun 27 '16 at 19:27

Justin%20Frank's gravatar image

Justin Frank

Your answer
Please start posting your answer anonymously - your answer will be saved within the current session and published after you log in or create a new account. Please try to give a good answer, for discussions, please use comments and please do remember to vote (login to vote)
toggle preview

powered by CNPROG