Denaturating HPLC and gel electrophoresis: As these techniques separates the samples on the basis of parameters like how long the sample takes to run through the column, therefore the sample can be separated after denaturation of DNA in homozygous and heterozygous bases.

Denaturing high performance liquid chromatography (DHPLC) uses reversed-phase HPLC for identification of SNP and it has differential affinity for single and double stranded DNA. In this process, the DNA molecule is first denatured and then reannealed. These reannealed DNA fragments have specific melting temperature which determines their time to be retained in the column. Two types of DNA fragments are generated i.e. target DNA containing the SNP polymorphic site and an allele-specific DNA sequence. This second fragment is identical to the target DNA except the diffeernce at the SNP polymorphic site. The fragments are denatured and then allowed to gradually reanneal. After reannealing, the DNA fragments are added to the DHPLC column. In case of normal DNA sequence, perfect matching will take place leading to formation of homoduplex during annealing process, whereas if SNP will be there, it will form heteroduplex DNA.The mismatched heteroduplexes will have a different melting temperature than the homoduplexes and will pass through the column fastly. This generates the difference in separation of normal DNA fragments and SNP bearing DNA sequence. The eluted DNA is detected by UV absorption. DHPLC is easily automated as no labeling or purification of the DNA fragments is needed. The method is also relatively fast and has a high specificity. One major drawback of DHPLC is that the column temperature must be optimized for each target in order to achieve the right degree of denaturation.