DNA toroids (1st of April 2010)
Rudi Podgornik is writing a book on DNA. It has an appropriate
title, "Physics of DNA" and should come out sometime next year (2011) if everything goes as planned.
There is a certain difference between science that is being written for books and papers. The papers (articles)
are expected to be quick and precise, to convey the information to experts without too much introduction, to not
digress unnecessarily and to be clear. But, the book is something else. The book is written for a rookie and its
purpose, besides exposing precisely the scientific information, is to be interesting, but also beautiful. I use the
word "beautiful" which is not often related to science, but is often related to books. Everyone likes a beautiful
book, with a beautiful and large enough font, with catchy illustrations and nice and shiny cover page. Of course,
this somehow "naturally" connects to the usefulness and clarity of what is being exposed, good distribution of
matter in chapters, a useful and detailed index and similar. Since one expects certain aesthetics from a
book on science, the authors starts thinking about showing a scientific information in the best possible light, to
make a useful, but also beautiful illustration of the matter that he writes about. And that's where this post
begins. With an illustration of toroidal DNA structures that I made for Rudi's book and which opens this post (above).
The technically and scientifically useful information are only green parts of the image, the cross-sections of toroids
(and only their upper halves). By rotating these cross-sections around the central axis one gets the whole structures.
Thus, the image that we are preparing for the (scientific) paper that we are working on is much less visually
pleasing, yet much more precise (the image below).
And now a bit on DNA toroids: DNA can condense in appropriate conditions (depending on the concentration of
multivalent salt ions) in the so-called "globules" in which the DNA strands wound like a piece of wire in a toroidal
hank. The illustration above shows how such DNA "hanks" look depending on the parameters of energy, in particular the
ratio of elastic energy of the wound DNA and the energy of DNA surface exposed to the surrounding (the toroid surface).
For different ratios one gets the solutions that are represented by the three toroids on the image that opened this
post. The total lengths of the DNA molecules (i.e. the number of bases) are the same in all the three solutions.
Rudi and I have worked previously on the problem of toroidal packing of the DNA in viruses that attack bacteria
(bacteriophages). In that case also I prepared a special graphics/illustration for the magazine of the European
physical society, Europhysics News (download
the highlight in question HERE). Namely, our paper was selected in the "Highlights" section of the magazine (which
is some kind of success or honor, one might say). One of the variant of the image that I made for the opportunity
is shown below.
In this case, the greenish part of the image that represents the protein coating of the bacteriophage is completely unnecessary with respect to the technical content of the information (the yellow- and magenta-colored cross-section through the virus), yet it can certainly draw attention of the uninformed reader and make her/him read the text that goes along with the image.
UPDATE: (22.11.2104.) In october 2014, with mag. phys. Sanjin Marion, I publised a paper "Ejecting Phage DNA against Cellular Turgor Pressure" (download HERE) which deals with ejecting DNA from viruses (bacteriophages) into bacteria. According to our calculations, a significant contribution to thermodynamics of this process is provided by condensation of DNA in bacteria, which we described within a framework of a toroidal shape and energetics (see above).
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Last updated on 22nd of November 2014.