Free energy periodicity and memory model for genetic 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. This research suggests that the 16S has a continuing role throughout translation, particularly in ribosomal synchronization with the reading frame. This work considers translational free energy calculations for 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 signal is ostensibly not the result of base or codon preferences within coding sequences. This work develops a new ribosomal memory model to capture the persistence of the observed synchronization signal present in E. coli coding sequences. Additionally, this work produces a very simple decision mechanism for distinguishing coding from noncoding regions of the genome. The simple mechanism demonstrates the potential for building a highly accurate decision mechanism based on energy periodicity within open reading frames. The energy calculations and the memory model may also be able to predict transgenic translation efficiency, as evidenced both by examination of two coding sequences containing known frameshifts, and the high capture rate of experimentally verified starts by the simple decision mechanism.