denaturing vs non denaturing gels

[Nick Jacobsen]

Hi,
  denaturing gels will contain a DNA denaturant e.g. urea which will keep 
your DNA fully denatured throughout the gel run. Non-denaturing gels 
obviously do not contain urea and promote renaturation of DNA and 
secondary structure formation within ssDNA - hence its use in SSCP when 
you are looking for single base changes that alter secondary structure. 
This leads (in an ideal situation) to differing conformer profiles for 
wild type and mutant. (N.B. prior to loading you heat samples to 95 C for 
five minutes in formamide loading buffer in order to initially denature 
the strands)

hope this helps

Nick.