[phenixbb] DNA sugar pucker

Laura Murray ljw7 at duke.edu
Sun Oct 26 14:22:07 PDT 2008

Hi. I'm one of the Richardsons' people. I have more experience with RNA, but
have looked at DNA some as well.
1. On C2'-endo and C3'-exo being equivalent: no, not quite equivalent, but
related. If you do have C1', C4', and O4' in the plane, then "popping" C2'
out on one side or C3' out on the other is relatively similar (sort of) and
there's a recognized "twist" conformation where you've got them both out of
plane a bit. However, you can really get C3' mostly in-plane with the other
three and have a conformation that's distinctly a C2' endo pucker rather
than looking like it could be either one. If you're building ideal B-form
DNA, it would be better to use a real C2'-endo pucker than the twist, and
certainly better than using the C3'-exo.

2. I'm afraid I don't know the appropriate format for use with PHENIX, but
there are pucker-specific parameters available on the Nucleic Acid Database
site: http://ndbserver.rutgers.edu -- specifically, here:
http://ndbserver.rutgers.edu/standards/parameter.html -- these are set up
for XPLOR, but the values should help. At any rate, these files distinguish
the dihedrals for C2'-endo and C3'-endo sugar puckers. (The set for higher
resolution also provides slightly different bond lengths and angles for
them, since the ring strains are a bit different.) And I don't think they
make a habit of turning up C3'-exo.

Laura Murray
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