Editing Shine–Dalgarno sequence (section)

===Translation start sites===
Using  a method developed by Hunt,<ref>{{cite journal | author = Hunt J A | year = 1970 | title = Terminal-sequence studies of high-molecular-weight ribonucleic acid. The 3'-termini of rabbit reticulocyte ribosomal RNA | journal = Biochemical Journal | volume = 120 | issue = 2| pages = 353–363 | doi=10.1042/bj1200353| pmid = 4321896 | pmc = 1179605}}</ref><ref>{{cite journal |author2-link=Lynn Dalgarno |vauthors=Shine J, Dalgarno L | year = 1973 | title = Occurrence of heat-dissociable ribosomal RNA in insects: the presence of three polynucleotide chains in 26S RNA from cultured Aedes aegypti cells | journal = Journal of Molecular Biology | volume = 75 | issue = 1| pages = 57–72 | doi=10.1016/0022-2836(73)90528-7| pmid = 4197338 }}</ref> Shine and Dalgarno showed that the nucleotide tract at the [[3' end]] of ''E. coli'' [[16S ribosomal RNA]] (rRNA) (that is, the end where [[translation]] begins) is [[Pyrimidine#Nucleotides|pyrimidine-rich]] and has the specific sequence {{tt|[[Nucleic acid notation|Y]]<u>ACCUCCU</u>UA}}. They proposed that these ribosomal nucleotides recognize the complementary purine-rich sequence {{tt|AGGAGGU}}, which is found upstream of the start codon AUG in a number of mRNAs found in viruses that affect ''E. coli''.<ref name=":0" /> Many studies have confirmed that base pairing between the Shine–Dalgarno sequence in mRNA and the 3' end of 16S rRNA is of prime importance for initiation of translation by bacterial ribosomes.<ref>{{cite journal | author = Dahlberg A E | year = 1989 | title = The functional role of ribosomal RNA in protein synthesis | journal = Cell | volume = 57 | issue = 4| pages = 525–529 | doi=10.1016/0092-8674(89)90122-0| pmid = 2655923 | s2cid = 36679385 }}</ref><ref>{{cite journal | author = Steitz J A, Jakes K | year = 1975 | title = How ribosomes select initiator regions in mRNA: base pair formation between the 3'-terminus of 16S rRNA and the mRNA during the initiation of protein synthesis in Escherichia coli | journal = Proc Natl Acad Sci USA | volume = 72 | issue = 12| pages = 4734–4738 | doi=10.1073/pnas.72.12.4734 | pmid=1107998 | pmc=388805| bibcode = 1975PNAS...72.4734S | doi-access = free }}</ref>

Given the complementary relationship between rRNA and the Shine–Dalgarno sequence in mRNA,  it was proposed that the sequence at the 3'-end of the rRNA determines the capacity of the prokaryotic ribosome to translate a particular gene in an mRNA.<ref>{{cite journal |vauthors=Shine J, Dalgarno L | year = 1975 | title = Determinant of cistron specificity in bacterial ribosomes | journal = Nature | volume = 254 | issue = 5495| pages = 34–38 | doi=10.1038/254034a0 | pmid=803646| bibcode = 1975Natur.254...34S | s2cid = 4162567 }}</ref> Base pairing between the 3'-end of the rRNA and the Shine–Dalgarno sequence in mRNA is a mechanism by which the cell can distinguish between initiator AUGs and internal and/or out-of-frame AUG sequences. The degree of base pairing also plays a role in determining the rate of initiation at different AUG initiator codons.