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Urea and formamide are used as denaturants in Denaturing Gradient Gel Electrophoresis (DGGE). In DGGE, urea and formamide denature the DNA fragments by disrupting the Hydrogen bonding between the nitrogenous base pairs. As shown in the figure above, urea and formamide form Hydrogen bond with nitrogenous bases that is why DNA fragments get denatured. Urea provides three Hydrogen bonding sites while formamide provides two H-bonding sites
Denaturing Gradient Gel Electrophoresis is an analytical tool that is most commonly used in the analysis of microbial community. DGGE is used to separate DNA fragments based on their mobility under the increasing denaturing conditions created by different concentrations of urea and formamide. DGGE is applicable to separate DNA and RNA fragments but not the polypeptide chains. It is used to analyze the 16S ribosomal DNA of bacterial sample during the study of the microbial population from a community.
DNA fragments having the same length of base pairs but different CG composition are called as DNA sequence variants. DNA fragments may have same lengths of base pairs but they may have the different composition of base pairs. The variance contributed by the differences in the composition of CG base pairs is the main basis that is considered during the DGGE analysis of these sequence variants.
DNA sequence variants have different melting points because they have different CG content and thus they migrate differently in Denaturing Gradient Gel Electrophoresis. It is assumed that each sequence variants of the same length of base pairs are from the different bacterial population within a community. So, if we see more than one band in DGGE then we should consider that there is more than one population within that community.