Predicting Shine–Dalgarno Sequence Locations Exposes Genome Annotation Errors
Figure 6
An Overview of How ΔG ° Values Are Calculated in Each TIR
For each base in each initiation region, we simulated the change in free energy required for the 3′ 16S rRNA tail to hybridize with the mRNA. A minimum of two consecutive bases need to pair, and for the binding to occur spontaneously require a change more negative than −4.08 kcal/mol [13], the value for ΔGinit °, In this example, the initiation region from E. coli's gene hcaF, alignment 1 is set to zero because the change in free energy required to bring together a single complementary double is not favorable. Alignment 2 and 71 are set to zero because there are no complementary doublets. Alignment 6 is set to −16.5 because it requires −16.5 kcal/mol less than −4.08 kcal/mol to hybridize.