In a newly-explored deep-sea environment, several potentially new species of apparent bacteria have been discovered. In some of these single-celled life forms, a novel structure has been observed. The structure is apparently bound to the interior surface of the cell membrane and so does not float freely in the cytosol. Preliminary investigation indicates that this structure typically appears circular or ovoid in shape. It apparently consists of a long chain of nucleic acid wrapped around a tube of an unknown protein.
What approach would you use to isolate only cells that contain this new structure? What techniques could then be used to characterize the structure and composition of the structure?
I had to edit down your question a bit due to the number of questions involved. Since the DNA/protein structure is on the inside of the cell membrane, I do not think that there is any way to specifically target this structure without first rupturing the cell membrane. The cell membrane must first be ruptured and the best way to do this is to treat the cells with a surfactant, or a soap. This causes the lipids in the membrane to denature and break apart, thus freeing the target nucleic acid/protein structure from the cell membrane and exposing it. The surfactant can also help separate the nucleic acid from the protein but some additional mild enzymes might need to be added to accomplish this. Finally, adding alcohol will help the nucleic acid to precipitate from solution. There are several methods to identify a sequence of DNA. PCR (polymerase chain reaction) is a technique to replicate a piece of DNA to amplify its numbers for analysis. Then, techniques like Maxim-Gilbert or Sanger methods can be used to elucidate the exact nucleotide sequence of the DNA.
To work with the protein portion of the structure, the surfactant will also help the protein denature and unfold. You could then use a particular antibody that matches and binds with the protein to easily test for the presence of this new protein in new samples taken of the bacteria. Edman degradation is a standard method of analyzing the sequence of a polypeptide (protein) chain.