Characterization of denaturation and renaturation of DNA for DNA hybridization

Environ Health Toxicol. 2014 Sep 11:29:e2014007. doi: 10.5620/eht.2014.29.e2014007. eCollection 2014.

Abstract

Objectives: The present study was designed to systematically characterize the denaturation and the renaturation of double stranded DNA (dsDNA), which is suitable for DNA hybridization.

Methods: A series of physical and chemical denaturation methods were implemented on well-defined 86-bp dsDNA fragment. The degree of each denaturation was measured and the most suitable denaturation method was determined. DNA renaturation tendency was also investigated for the suggested denaturation method.

Results: Heating, beads mill, and sonication bath did not show any denaturation for 30 minutes. However probe sonication fully denatured DNA in 5 minutes. 1 mol/L sodium hydroxide (alkaline treatment) and 60% dimethyl sulfoxide (DMSO) treatment fully denatured DNA in 2-5 minutes.

Conclusions: Among all the physical methods applied, the direct probe sonication was the most effective way to denature the DNA fragments. Among chemical methods, 60% DMSO was the most adequate denaturation method since it does not cause full renaturation during DNA hybridization.

Keywords: Beads mill; DNA denaturation; DNA renaturation; Dimethyl sulfoxide; Heating; Sonication.