SSCP

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Under SSCP (English single beach conformation polymorphism ) is meant a molecular detection method, which characterizes the composition and changes in microbial communities. It is one of the "DNA fingerprint" methods.

principle

Procedure : A DNA extraction is carried out with a sample , whereby the DNA of the community is preserved. A polymerase chain reaction with universal primers for the 16S rRNA is carried out with this. This is on the one hand a universal reverse primer with phosphate group and on the other hand a universal forward primer. The DNA double strands produced in the PCR are digested with a lambda exonuclease so that only single DNA strands without a phosphate group remain. Gel electrophoresis now takes place with the single strands . After staining (e.g. silver staining ) the DNA in the gel, individual bands can be cut out of the gel, cloned and sequenced.

Advantages of molecular "fingerprint" methods:

  • Ability to analyze a large number of samples simultaneously
  • Complex population dynamics of microorganisms can be recorded

Disadvantage of molecular "fingerprint" methods:

  • Only groups of microorganisms whose DNA content makes up more than 10% of the original sample are recorded

Individual evidence

  1. ^ A. Schmalenberger, CC Tebbe: Profiling the diversity of microbial communities with single-strand conformation polymorphism (SSCP). In: Methods in molecular biology. Volume 1096, 2014, pp. 71-83, ISSN  1940-6029 . doi : 10.1007 / 978-1-62703-712-9_6 . PMID 24515361 .
  2. ↑ P. Kozlowski, WJ Krzyzosiak: Economical protocol for combined single-strand conformation polymorphism and heteroduplex analysis on a standard capillary electrophoresis apparatus. In: Methods in molecular biology. Volume 653, 2010, pp. 181-192, ISSN  1940-6029 . doi : 10.1007 / 978-1-60761-759-4_10 . PMID 20721743 .
  3. ↑ SR Hiibel, A. Pruden, B. Crimi, KF Reardon: Active community profiling via capillary electrophoresis single-strand conformation polymorphism analysis of amplified 16S rRNA and 16S rRNA genes. In: Journal of microbiological methods. Volume 83, Number 3, December 2010, pp. 286-290, ISSN  1872-8359 . doi : 10.1016 / j.mimet.2010.10.002 . PMID 20940021 .