Free energy periodicity in E. coli coding

Sequences upstream from coding regions in E. coli commonly possess significant complementarity to the exposed part of the 16S rRNA. This region is known as the Shine-Dalgarno sequence. Free energy calculations for binding between homologous sequences suggest that this region is used as a landing site for construction of the ribosome around the mRNA. While strong upstream binding appears to be a condition for translation, it may not be sufficient. The authors´ research suggests that the 16S has a continuing role throughout translation, particularly in ribosomal synchronization with the reading frame. The authors consider the entire E. coli genome of over 2000 forward coding sequences. Presence of strong upstream binding is confirmed, and a definite three-base periodic signal is observed. The distribution of bases parallels that needed to produce a signal of the type observed