Three modes of operation are available for chromatographic analysis of nucleic acids, depending on the temperature of the column. They are nondenaturing, partially denaturing, and completely denaturing modes.
Each mode of operation serves a different purpose in nucleic acid analysis. In brief, the nondenaturing condition is applied to the size-dependent separation of double strand (ds) DNA molecules. The partially denaturing condition is used for screening of putative SNPs or detection of unknown mutations.
The third operation mode performed under completely denaturing condition is used for the analysis of short DNA fragments such as products of primer extensions and synthetic oligonucleotides, as well as RNA.
Nucleic acid chromatography is most widely used under partially or completely denaturing conditions, and hence is frequently called denaturing HPLC (DHPLC).