16S ribosomal RNA



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. Genes VIII p 160 contains a detailed structural diagram

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 (Huber, H., Hohn, M. J., Rachel, R., Fuchs, T., Wimmer, V. C. & Stetter, K. O. (2002) Nature (London) 417, 63-67).