In earlier posts, I alluded to what might make DNA wind into a left or a right-handed helix. Here I switch the magnification of our structural microscope up a notch to take a look at some more inner secrets.
The 3D coordinates of this fragment were obtained by taking a crystal structure of a Z-d(CGCG)2 containing oligomer, editing (to remove water, and superfluous bases) and subjecting it to ωB97XD/6-311G(d,p)/SCRF=water geometry refinement. This should be accurate enough to recover dispersion attractions, and various electronic and electrostatic interactions. Z-d(CGCG)2 was then reduced to the fragment you see above, which is large enough to capture the essence of the Z-helical wind, but small enough to be able to spot things which a larger fragment might overwhelm.To complete the present analysis, I include an ELF diagram. This can locate lone-pairs (as monosynaptic basins) as well as bond pairs (disynaptic basins) and so is useful for visualising the anti-periplanar anomeric effects between a lone pair and a bond (connecting a mono and a disynaptic basin if you like). Some of the interactions described in the list above are shown below with dotted lines (note that some of the lone pairs appear as two basins, distributed either face of the aromatic base).
Well, cranking up the magnification on a microscope will always reveal new details. You might ask if these new details matter? Well, since DNA is such a very long polymer, repeating even a very weak (but predictable) interaction millions of times is bound to have some sort of cumulative effect. Who knows which of the ones above might play an important role in the super-winding of DNA, or its packing into a cell, or interaction with proteins, and so on. I do wonder how many of the terms I have identified above have been previously considered for such roles. Anyone know?Postscript: Shown below is a non-covalent-analysis (NCI, see earlier post). A reminder that the interaction surface is colour coded with orange or red tinge if repulsive, blue if attractive, and green for weaker interactions. These surfaces pretty much recapitulate what it itemised above, adding also other interactions not listed above (labelled 8 in diagram).
This post has DOI: 10.14469/hpc/12767
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