Naming of phosphate oxygens in nucleotides

Henry Gabb gabb at europa.lif.icnet.uk
Wed Nov 22 12:39:12 EST 1995


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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|  Henry Gabb                                 (gabb at icrf.icnet.uk)   |
|  Imperial Cancer Research Fund                                     |
|  44 Lincoln's Inn Fields                                           |
|  London WC2A 3PX                                                   |
|  United Kingdom                                                    |
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