Amplified Ribosomal DNA Restriction Analysis

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The amplified rDNA restriction analysis (in German 'amplified ribosomal DNA restriction analysis', ARDRA) is a molecular biological method for DNA analysis , more precisely for the detection of polymorphisms in a gene that encodes part of the rRNA of the ribosome . ARDRA is a variant of RFLP in the 16S rRNA gene of bacteria .

principle

The ARDRA combines an amplification of the gene of the bacterial 16S rRNA (approx. 1500 base pairs ) with a restriction (sequence-specific enzymatic cleavage by AluI , HaeIII , TaqI, etc.) of the amplificates and a separation of the generated restriction fragments by gel electrophoresis . This creates a pattern in the gel that is characteristic of a certain species . To ensure a sufficient number of cleavage sites in the rDNA, a restriction enzyme with a comparatively short recognition sequence of four base pairs is usually used. The patterns characteristic of the respective species can be grouped to create a cladogram .

As an alternative to ARDRA, RFLP , SSCP or DNA sequencing can be used for typing .

history

ARDRA was originally developed in 1993 by M. Vaneechoutte and others for typing mycobacteria and was later expanded for other species.

Individual evidence

  1. ↑ a b M. Vaneechoutte, H. De Beenhouwer, G. Claeys, G. Verschraegen, A. De Rouck, N. Paepe, A. Elaichouni, F. Portaels: Identification of Mycobacterium species by using amplified ribosomal DNA restriction analysis. In: Journal of clinical microbiology. Volume 31, Number 8, August 1993, ISSN  0095-1137 , pp. 2061-2065, PMID 8396586 , PMC 265696 (free full text).
  2. ↑ AC Cihan: Taxonomic classification of Anoxybacillus isolates from geothermal regions in Turkey by 16S rRNA gene sequences and ARDRA, ITS-PCR, Rep-PCR analyzes. In: Polish journal of microbiology / Polskie Towarzystwo Mikrobiologów = The Polish Society of Microbiologists. Volume 62, Number 2, 2013, ISSN  1733-1331 , pp. 149-163, PMID 24053018 .
  3. ↑ MY Sklarz, R. Angel, O. Gillor, MI Soares: Evaluating amplified rDNA restriction analysis assay for identification of bacterial communities. In: Antonie van Leeuwenhoek. Volume 96, Number 4, November 2009, ISSN  1572-9699 , pp. 659-664, doi : 10.1007 / s10482-009-9380-1 , PMID 19777364 , PMC 2764076 (free full text).
  4. ↑ M. Vaneechoutte, L. Dijkshoorn, I. Tjernberg, A. Elaichouni, P. de Vos, G. Claeys, G. Verschraegen: Identification of Acinetobacter genomic species by amplified ribosomal DNA restriction analysis. In: Journal of clinical microbiology. Volume 33, Number 1, January 1995, ISSN  0095-1137 , pp. 11-15, PMID 7699025 , PMC 227870 (free full text).
  5. ↑ T. Stakenborg, J. Vicca, P. Butaye, D. Maes, T. De Baere, R. Verhelst, J. Peeters, A. de Kruif, F. Haesebrouck, M. Vaneechoutte: Evaluation of amplified rDNA restriction analysis ( ARDRA) for the identification of Mycoplasma species. In: BMC infectious diseases. Volume 5, 2005, ISSN  1471-2334 , p. 46, doi : 10.1186 / 1471-2334-5-46 , PMID 15955250 , PMC 1177949 (free full text).