Page "Southern blot" Paragraph 4

# If alkaline transfer methods are used, the DNA gel is placed into an alkaline solution ( typically containing sodium hydroxide ) to denature the double-stranded DNA.

The denaturation in an alkaline environment may improve binding of the negatively charged DNA to a positively charged membrane, separating it into single DNA strands for later hybridization to the probe ( see below ), and destroys any residual RNA that may still be present in the DNA.

The choice of alkaline over neutral transfer methods, however, is often empirical and may result in equivalent results.