We have been using PEG-8000 (10%) and NaCl (0.5 M) precipitation for concentrating phage samples before ultracentrifugation and for some of them, we got a really viscous solution after PEG precipitation. Adding DNase I has not helped. Why this high viscosity and what to do to get rid of it? Using samples as they are for ultracentrifugation gives no visible virus bands.
With out knowing exactly what your samples are, it is a bit hard to say, but since you mention phage, I am guessing you are likely starting from some sort of bacterial culture? My inclination is that your thought is correct, and you are precipitating chromosomal DNA at the same time for some reason. PEG works via water exclusion, and basically causes large molecules to fall out of solution, possibly this has something to do with the NaCl you are using in the protocol that is causing DNA to ppt? I would start by disrupting your cells with whatever method you use... this should release the phage from within your cells, then I would spin down the prep to remove as much cellular debris as possible (including genomic DNA), once you have the clarified cell extract, I would adjust that to 10% PEG and continue from there.
Good luck
Ron
Bacteria and large bacterial fragments should be fully removed post-PEG precipitation. You can increase the volume to resuspend precipitate, or dialysis into some solutions without PEG， which may alleviate the problem. More sucrose gradient can be used in the density gradient centrifugation if you can`t find the visible virus bands. At the same time, you should avoid the mutual dissolution of sucrose with different concentrations to destroy the density gradient. At last, you can place a light source at the bottom of the centrifuge tube， which can help you get the virus band more easily.
Good luck
Guosong
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