- 16S ribosomal RNA
rRNAis 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 sequencewhich binds upstream to the AUG start codon on the mRNA.
* Interacts with 23S, aiding in the binding of the two ribosomal subunits (
* 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.
It is used for phylogenetic studies as it is highly conserved, in fact the
PCRprimers 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 CTTComparative analysis of 16S rRNA sequences from thousands of organisms has demonstrated the presence of oligonucleotide signature sequences.
Mitochondrial and chloroplastic rRNA is picked up, but not that of
Nanoarchaeota.cite journal |author=Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO |title=A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont |journal=Nature |volume=417 |issue=6884 |pages=63–7 |year=2002 |pmid=11986665 |doi=10.1038/417063a]
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 microbiologyas a rapid, accurate alternative to phenotypic methods of bacterial identification.
[http://depts.washington.edu/molmicdx/mdx/tests/bctseq.shtml University of Washington Laboratory Medicine: Molecular Diagnosis | Bacterial Sequencing]
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