16S ribosomal RNA

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Atomic structure of the 30S Subunit from Thermus thermophilus. Proteins are shown in blue and the single RNA strand in orange.[1]

The 16S rRNA is a 1542 nt long component of the small prokaryotic ribosomal subunit (30S) and is known to interact with the 50S subunit in both P and A site. The 3' end contains the anti-Shine-Dalgarno sequence which binds upstream to the AUG start codon on the mRNA.

Universal Primers

It is used for phylogenetic studies as it is highly conserved, in fact the primers are called universal (or quasi-universal as it does not pick up some recently discovered hydrothermal archaea species though).

16S rRNA Forward AGA GTT TGA TCC TGG CTC AG

16S rRNA Reverse ACG GCT ACC TTG TTA CGA CTT

Mitochondrial and chloroplastic rRNA is picked up, but not that of Nanoarchaeota.[2]

  1. Schluenzen F, Tocilj A, Zarivach R; et al. (2000). "Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution". Cell. 102 (5): 615–23. PMID 11007480. Unknown parameter |month= ignored (help)
  2. Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO (2002). "A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont". Nature. 417 (6884): 63–7. doi:10.1038/417063a. PMID 11986665. Unknown parameter |month= ignored (help)

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