Monday, 11 May 2009

DNA

Ever since Jurassic Park we know that DNA looks pretty cool. Here is a piece of B-DNA.[1]

Or with thicker sticks:


In fact there is of course not so much space between the bases. Here is what it looks like when you draw the van der Waals spheres for the bases. It is actually quite difficult to model this stacking interaction because it is almost pure dispersion. From a computational point of view, dispersion is electron correlation. If the effect you are interested in is pure electron correlation, then you'd better model it really well. Hartree-Fock gives you zero dispersion. MP2 is great if you kind of want to include some electron correlation but it is not accurate enough in this case. What they are actually doing is high level coupled cluster CCSD(T) extrapolated to the complete basis set limit.


Another interesting question is how defects are propagated in such a framework: holes, electrons, or electron hole pairs. First of course you want to preserve the integrity of your genome. And second you want to make nano-robots. DNA is already a self-assembling structure with molecular recognition. If charge transport is better understood and conductive analogues are found, DNA will kick nanotubes' ass.

By the way: for printing out pymol graphics (see again [1]), the ray_trace_mode setting is nice. Especially:

set ray_trace_mode=1

Then you get some nice black frames instead of fuzzi ends in the print.




[1] from the crystal structure 1BNA. And drawn with pymol. Maybe I should eventually switch from pymol because they are becoming more and more commercial. But then I guess they would not mind me as a little personal user.

3 comments:

Ψ*Ψ said...

Definitely like the look of the black frames.
Seems like it wouldn't be all that difficult to make conductive DNA...I mean, those nucleic acids are nice and aromatic, and within nice pi-stacking range--IIRC, we've seen charge carrier mobility measurements on smaller things. Seriously doubt conducting DNA could compete with CNTs in terms of hole or electron mobility, though it might be much more soluble and easier to characterize...it would be awesome to see PCR done with semiconducting structures :)

Felix said...

i think that they are pretty sure that there is some kind of charge transport. Jaqueline Barton has for example tons of Nature papers about that: http://dx.doi.org/10.1038/382731a0

but it is still quite contradictory and it looks like they need some thorough computational support ...

maybe some analogues work better like expanded DNA bases (http://dx.doi.org/10.1126/science.1088334) or G tetramer structures

Geoff said...

I only came across this post today...

There's still debate about DNA conduction, but plenty of theory and computation -- see papers by Ratner, for example. From what I remember, some sequences do show transport (with G serving as a hop site), but "normal" DNA isn't very conductive.