Introduction Methods Gene Organisms
Introduction
DNA degradation (which results in a smear pattern) occurs with some bacterial strains during pulsed-field gel electrophoresis (PFGE), like Streptomyces lividans 1326. The DNA degradation (Dnd) phenotype is also frequently determinated by PCR with activated TAE buffer.
Fig. 1. DNA degradation (Dnd) phenotype under normal agarose gel electrophoresis. Lane 1, 6, 7 and 8 display the intact DNA after treatment with the activated TAE buffer, whereas Lane 2, 3, 4, 5 and 9 show the Dnd phenotype after treatment.
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Methods
Protocol for the Dnd phenotype determination with activated TAE buffer, in the MS Word file (.doc) or in the Adobe PDF document (.pdf).
Protocol of pulsed-field gel electrophoresis (PFGE) at protocol-online.
A liquid chromatography-coupled tandem quadrupole mass spectrometry approach was descriped in the paper of Wang, et al. (2011).
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Analysis of dndABCDE genes responsible for The DNA degradation (Dnd) system in Streptomyces lividans 1326
Mutations in dndA ,dndC, dndD and dndE in wide-type Streptomyces lividans 1326 all abolished the Dnd phenotype while mutation in dndB only aggravates the Dnd phenotype.
Fig. 2. Streptomyces lividans 1326 and its dnd mutants. [Xu et al., BMC Microbiol. 2009 Feb 20;9(1)]
Fig. 3. (A) All of the DNA samples were proven to be stable in normal agarose gel electrophoresis buffer with added thiourea. (B) Genomic DNA from wide-type Streptomyces lividans 1326 and its dndB mutant XTG2 both undergo degradation (streaking in the lane) during gel electrophoresis in Tris-containing buffer. [Xu et al., BMC Microbiol. 2009 Feb 20;9(1)]
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Reported organisms with Dnd phenotype under agarose gel electrophoresis
The file containing NCBI taxonomy IDs: NCBI_Taxon_ID_200812_442.txt
iTOL can generate the phylogenetic tree based on NCBI taxonomy IDs provided.

No. Organism Description Dnd phenotype Reference