Help:Ribosome Binding Sites/Shine-Dalgarno sequence
The binding of a bacterial ribosome to an mRNA is largely due to base-pairing between the mRNA and an RNA molecule that forms part of the bacterial ribosome (the 16s rRNA). The end of the 16s rRNA that is free to bind with the mRNA includes the sequence 5′–ACCUCC–3′. The complementary sequence 5′–GGAGGU–3′, named the Shine-Dalgarno sequence, is commonly found in whole or in part in bacterial mRNA. Very roughly speaking, ribosome binding sites with sequences close to the Shine-Dalgarno sequence will lead to high rates of translation initiation whereas sequences that are very different from the Shine-Dalgarno sequence will lead to low or negligible translation rates. However, since translation must initiate at a start codon, an mRNA with a sequence close to the Shine-Dalgarno sequence is not sufficient to provide high translation initiation rates. The Shine-Dalgarno sequence must be positioned approximately 6-7 nucleotides upstream of the start codon, this places the ribosome on the mRNA such that the start codon lines up with the initiator tRNA and translation can begin.