Minimally, I believe you want to use P and C1'.
(This has been done by others, including Pabo and Pabo & Nekludova,
J.Mol. Biol., 301:597-694 (2000).
I actually prefer to use all backbone atoms: P O5' C5' C4' O3' C3' C2'
C1' O1'
Barry Finzel
Medicinal Chemistry Department
2-160C Weaver-Densford
Tel: (612) 626-5979
Lab: (612) 626-5226
Fax: (612) 624-0139
finze...@umn.edu
On Jan 22, 2013, at 9:00 AM, Alan Cheung wrote:
Dear all - is there a convention for superposing nucleic acids
duplexes of unrelated sequence?
i.e. which atoms should be superposed : C4' of the sugar, P of the
backbone, O3'/O5' of the backbone, or some combination thereof?
Alan
--
Alan Cheung
Gene Center
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: che...@lmb.uni-muenchen.de
