Physics of DNA packaging and ejection in viruses
Bacteriophage, viruses that attack bacteria, are amazing examples of natural nanotechnology. A single bacteriophage, roughly 50 nm across, consists of nothing more than a protein capsid enclosing a single piece of DNA. When added to a bacterial culture, this little machine quickly attaches itself to a bacterium and injects its DNA. The DNA contains instructions for the bacterium to build proteins which automatically assemble into new capsids, powerful nano-motors for packaging the DNA into the capsids, and many copies of the DNA. Together, these parts assemble several hundred new copies of the bacteriophage. Within an hour, the bacterium dies and the new copies are released. Each attaches itself to another bacterium, and the infection proceeds until every cell has been killed.
The bacteriophage DNA must be stored under a very high pressure to fit within a capsid. When stretched out to its full extent, the DNA is around 10 um long, 200 times the size of the capsid, so the DNA must be severely bent and wrapped around itself several hundred times. The total volume of the DNA is about half of that of the capsid, so there is very little space left between the DNA strands. Since DNA is a highly charged molecule, the strands repel each other. Polyvalent ions such as Mg2+ are necessary to diminish this repulsion. If they are not present, the capsid simply explodes. Even under normal, non-explosive conditions, the pressure in a bacteriophage is thought to be as high as 20 or 40 atm. This pressure may power the injection of DNA into cells, and it is thought that some bacteriophage motors can sense the increase in pressure as the DNA becomes fully packaged, using it as a signal to halt the packaging process.
We are using theoretical mechanics to predict the pressure inside bacteriophage capsids and checking the results experimentally. Our theoretical models assume a regular spool conformation for the DNA (see figure). We add the elastic and electrostatic energies of each DNA loop to get the total energy for particular values of the DNA length and interstrand spacing. Minimizing the energy by varying the spacing gives us the most favorable conformation of the DNA, and differentiating the energy with respect to the capsid size gives us the internal pressure. The internal pressure, packaging force, and interstrand spacing computed with this model can all be compared to experimental values. In our laboratory we are currently collaborating with Alex Evilevitch, Chuck Knobler, and William Gelbart of UCLA to make use of their technique of measuring the capsid pressure during DNA ejection. We are applying the technique to lambda bacteriophage with varying genome lengths and also to bacteriophage phi29. By studying the workings of these biological nanomachines, we hope to learn useful techniques for future nanotechnology.
Protocols used in the experiments can be found on our lab info page.
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