Related Experiment Video
Updated: Sep 15, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Limited resolution of 16S rDNA DGGE caused by melting properties and closely related DNA sequences
1Umeå Marine Sciences Center, Umeå University, Norrbyn, SE-910 20, Hörnefors, Sweden.
Abstract:
The phylogenetic affiliation of 91 operational taxonomic units, randomly sampled from three aquatic microcosm experiments, was investigated by two PCR based and one culture dependent method. The occurrence of multiple melting domains and poor coupling between Tm and DGGE retardation was demonstrated to cause poor resolution at the species level in PCR-DGGE analysis of microbial communities. We also showed that the problem of multiple melting domains was particularly prone for brackish water bacterioplankton in the Flavobacterium genus, providing characteristic band morphology for this genus. Banding patterns from DGGE analysis may therefore be misinterpreted in terms of the species richness in natural bacterial communities, when using commonly applied universal primers.
Related Concept Videos
Fixing Double-strand Breaks
Homologous Recombination
Sanger Sequencing
Next-generation Sequencing
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Restriction Enzymes
The host bacteria protect their own genomic DNA from these enzymes by methylating these sites. Some...
Maxam-Gilbert Sequencing
Challenges of the Maxam-Gilbert Method
The...

