Tuesday 29 March 2011

DNA close up

I wanted to look a little bit more at the details of the DNA structure. In part motivated by James Watson's book (described here). Some time ago I showed pictures of the helix, but now I want to show some molecular details.[1]

This is the backbone of DNA in its B-form. The phosphate is in front. The 2-deoxyribose is the vertical 5-ring. Its anomeric center is bonded to the nitrogen of the base and the oxygen closing the furanose ring. The 3' oxygen bonds to the next phosphate group. The 5' oxygen leading to the other side is bonded to the carbon outside of the ring.

In principle a pentose has five active groups. In DNA all are saturated and no OH groups remain. Why?
1' bonded to the nitrogen
2' that's the "deoxy" in "deoxy-ribonucleic acid"
3' bonded to phosphate
4' forming the ring
5' bonded to phosphate

What happens if we put an OH group at the 2' position?

The new OH groups is shown with its full van-der-Waals radius. There is clearly not enough room for the extra oxygen atom, considering for example that the other oxygen atoms should be just as big. It is in fact not possible to push the atoms out of the way in any simple manner. Therefore RNA does not form a B-helix.

The structures were created with the nucleic functionality of Tinker. The pictures were drawn with pymol.

[1] One thing I really learned in science is quoting myself ...

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