At low pHs, DNA begins to avidly bind silica and glass (at moderately acid pHs), and at lower pHs (pH 4 or lower), dupurination starts to occur, i.e. loss of purine bases from the backbone. The length of exposure to these conditions, and indeed the chemical background, governs the degree of depurination.

In contrast, high pHs prevent hydrogen bonding, thus the strands dentaure - which of course is the basis of alkaline lysis plasmid DNA preparation. If you switch rapidly from low pH to high, then you can induce non-enzymatic cleavage of the DNA at the positions of purine loss.

Hope that helps

Jim (MAD Scientist)