I just had a lively discussion with the guy in the next office about whether the single-stranded DNA that enters a bacterial cell by conjugation becomes double-stranded before it recombines into the chromosome. The textbook he's using to teach his new bacterial molecular genetics course say yes, but this seems rather improbable to me.
Another faculty member found a paper from about 10 years ago that concludes that the DNA becomes double-stranded before it recombines. But I don't think this double-strandedness was necessitated by the findings of their experiments; rather it seems to be mainly driven by the assumptions of the researchers.
The paper had another surprise. It showed the DNA being transferred into the recipient cell as a loop, with the 'leading' end being held back in the 'donor' cell, and the loop being pushed into the recipient. I've only seen it represented differently, with the leading end moving into the recipient cell as if it was pulling the DNA strand along behind it. But now I think more carefully, the protein attached to the leading end isn't expected to have any power to 'pull' anything once it's in the recipient cell, so the DNA must be being transported just by the machinery in the membrane of the 'donor'.
I'm putting 'donor' in quotes, because that's how most people think of the process of conjugation. They've been taught to think of the cell that has a plasmid kindly donating a copy of it to a cell that lacks the plasmid; if the plasmid is attached to chromosomal DNA the recipient cell is blessed with a copy of part of the donor's chromosome. But plasmids are genetic parasites, and the 'donation' is really an infection. The recipient is passive, and the plasmid DNA is forcibly inserted into it by the 'donor'. To do this the plasmid uses the proteins it codes for, and proteins already produced by its cell.
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