Environ Health Toxicol.  2014 ;29(1):e2014007. 10.5620/eht.2014.29.e2014007.

Characterization of denaturation and renaturation of DNA for DNA hybridization

• Wang X
• Lim HJ
• Son A

• KMID: 2380100
• DOI: http://doi.org/10.5620/eht.2014.29.e2014007

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.

Keyword

Beads mill; Dimethyl sulfoxide; DNA denaturation; DNA renaturation; Heating; Sonication

MeSH Terms

Baths
Dimethyl Sulfoxide
DNA*
Heating
Hot Temperature
Nucleic Acid Denaturation
Sodium Hydroxide
Sonication
DNA
Dimethyl Sulfoxide
Sodium Hydroxide