Peter Slickers (slickers at imb-jena.de) wrote:
[deleted]
: DOES anybody knows if there is any recommendation for the naming of the
: two phosphate oxygens OP1 and OP2 according to their position in
: relation to the central P ?
To the best of my knowledge, nobody makes the distinction between these
substituents because there is rarely a reason to do so. At least I can't
think of any right now. They are chemically equivalent. Just out of
curiosity, why do you want to distinguish between them?
: The structural meaning of this would be, whether OP1 is pointing towards
: the minor or the major groove in a DNA double helix.
That suggestion works fine for a static structure. Since the backbone
torsions are flexible, the positions of the phosphate oxygens and C5'
hydrogens with respect to the grooves can reverse. I don't know if this
is standard, but in many nucleic acid drawings that I've seen the right-
hand rule is used for numbering. If you wrap your right hand around the
sugar-phosphate backbone at the phosphate and C5' positions with your
thumb pointing 5' to 3' you'll get consistent numbering.
It's easy to draw a distinction between the H2' and H2'' atoms of the
sugar; one will always be above the ring (i.e., on the same side as the
C5') and one will always be below.
Hope this helps.
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