How to determine copy number of a plasmid especially if isolating the plasmid from the organism remains a problem. I would also like to know if anyone has got a protocol for isolating plasmid from Deinococcus.

This article is a classic reference for copy number determination

Twigg, A. J., and D. Sherratt. 1980.
Trans-complementable copy-number mutants of plasmid ColEl. Nature (London) 283: 216-218.

This recent article describes the determination of plasmid copy number in bacteria using real time qPCR. The authors also compared their results with the agarose gel assay.

Lee, CL et al. Quantitative real-time polymerase chain reaction for determination of plasmid copy number in bacteria. Journal of Microbiological Methods, 65 (2006) 258-267.