ShineDalgarno

Shine-Dalgarno sequence, named after J. Shine and L. Dalgarno, is a ribosome binding site found in prokaryotic messenger RNAs that helps initiate translation. It is a purine-rich motif usually located a short distance upstream of the start codon, typically 5 to 9 nucleotides before the AUG in bacteria. The exact sequence varies by organism, but a commonly cited consensus is AGGAGG, with variations common in nature.

Mechanism: The sequence base-pairs with the complementary anti-Shine-Dalgarno sequence at the 3' end of the 16S rRNA, aligning the start codon with the ribosome's P site. This interaction facilitates correct initiation of translation in combination with initiation factors and the small ribosomal subunit.

Distribution and variation: SD sequences are widespread in bacteria and are also found in some archaeal transcripts and plastids, whereas many archaeal species use alternative initiation signals. In many genes, the strength of the SD interaction, the spacing to the start codon, and the local mRNA structure influence translation efficiency. Leaderless mRNAs, which lack a 5' untranslated region and SD sequence, rely on different initiation mechanisms.

History and significance: Shine and Dalgarno described the motif in 1975 as a basis for ribosome binding to mRNA. The SD sequence remains a central concept in prokaryotic gene expression, used in studies of translation regulation and in the design of expression constructs in biotechnology.