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 has several functions:

Like the large ribosomal RNA, it has a structural role, acting as a scaffold defining the positions of the ribosomal protein.
The 3' end contains the anti-Shine-Dalgarno sequence which binds upstream to the AUG start codon on the mRNA.
Interacts with 23S, aiding in the binding of the two ribosomal subunits (50S+30S).
Stabilizes correct codon-anticodon pairing in the A site, via a hydrogen bond formation between the N1 atom of Adenine (see image of Purine chemical structure) residues 1492 and 1943 and the 2'OH group of the mRNA backbone.

Genes VIII p 160 contains a detailed structural diagram.

1 Universal Primers
- 1.1 PCR applications
2 References
3 External links

[edit] Universal Primers

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

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]

[edit] PCR applications

In addition to highly conserved primer binding sites, 16s rDNA sequences contain hypervariable regions which can provide species-specific signature sequences useful for bacterial identification to species level. As a result, 16s rDNA sequencing has become prevalent in medical microbiology as a rapid, accurate alternative to phenotypic methods of bacterial identification.

[edit] References

^ Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A (2000). "Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution". Cell 102 (5): 615–23. doi:10.1016/S0092-8674(00)00084-2. PMID 11007480.
^ 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.