Denaturing Gradient Gel Electrophoresis (DGGE) is a powerful genetic analysis technique that can be used for detecting single base changes and polymorphisms in genomic, cloned, and PCR amplified DNA. Two of the most valuable uses for DGGE in human and microbial genetics are in directly detecting single base changes that cause disease and in detecting polymorphisms with DNA probes for genetic-linkage analysis. In DGGE, conformational transitions of multiple nucleic acid complexes are induced by an increasing concentration of solvent (urea/formamide) at a constant temperature. Clinical applications of DGGE include a rapid and effective method for screening samples for genetic mutations and variants. Also, DNA fragment melting points can be determined using perpendicular DGGE. In contrast to DGGE, CDGE (Constant Denaturant Gel Electrophoresis) uses a single solvent percentage to induce partial melting of DNA fragments as they enter the gel. The disadvantage of CDGE is that only a single melting
domain can be interrogated.

Destabilisation of nucleic acid complexes can be studied using acrylamide gels that contain a uniform solvent concentration as in CDGE, but with an increasing temperature gradient. Since the temperature of the entire gel is uniformly raised over a period of time, this technique has been termed Temporal Temperature Gradient Electrophoresis (TTGE). This technique incorporates many improvements over DGGE/CDGE especially when studying multiple melting domains.

Single Strand Conformational Polymorphism (SSCP) reveals differences in electrophoretic mobility between normal and mutant single strands of DNA. In SSCP, normal and mutant duplex DNA are denatured to form single stranded molecules of equal length. These molecules can re-anneal onto themselves and based on the varying degree of intrastrand base pairing, form different three-dimensional structures. These structures, differ in electrophoretic mobility and can be separated on a chilled non-denaturing polyacrylamide gel.