depurination in southern blot

[kabuto]

hello,
In Southern Blot, we use HCl 0,25M to depurinate DNA in agarose gel before denaturing with NaOH 0,4M. The role of HCl was said to eliminate purines (A & G). But when purines were shot out, DNA will be cut in very small fragments with only pyrimidines (C & T) ! So the sequences died and how can they be hybrided with their probes ?