No. Other methods, such as alkaline unwinding, depend on the high pH to unravel the DNA molecules, starting at DNA breaks; the rate of unravelling depends on the frequency of breaks, and is assessed as the proportion of single-stranded DNA present after a certain unwinding time. But the comet assay is different.

The original comet paper (Östling and Johanson, 1984; BBRC 123, 291-298) used pH 10 (effectively neutral – certainly not high enough to unwind DNA), and reported the effect of low doses of ionising radiation. The dose range giving detectable damage was almost the same as that reported for the alkaline version by Singh et al. (1988; Exp. Cell Res. 175, 184-191).

The most likely explanation is in terms of supercoiling. The DNA in the nucleoids (the structures remaining after lysis with Triton X-100 and 2.5 M salt) is supercoiled in a negative sense. Imagine the DNA as a series of supercoiled loops, associated at their bases to the nuclear matrix (a scaffold of protein and RNA which supports the DNA). Comets from undamaged cells have tightly packed, supercoiled DNA and no tail. Damage that leads to DNA breaks relaxes the supercoiling in the loops with breaks; these loops relax, and are pulled into a tail under electrophoresis. A single-strand break is sufficient to relax supercoiling. So the neutral and the alkaline comet assays detect both single- and double-strand breaks, and it is impossible to distinguish between them.

"FAQ by Andrew Collins, Gunnar Brunborg and Jonas Nygren, 2006, NewGeneris FP7-project"