Free energy based analysis of the coding region of Saccharomyces cerevisiae

In Prokaryotes, free energy based calculations of the binding interaction between their 16S rRNA tail end and their underlying mRNA has been used to analyze the translation process. There have been examinations of the free-energy interaction between the 16S rRNA and mRNA with focus on the leader region. The focus on the leader region has revealed an important feature of the prokaryotic ribosome tail; it has a strong affinity to an identifier called the Shine-Dalgarno sequence, roughly 13 bases upstream of the start codon. An important issue in today's research is predicting the protein-coding region for eukaryotic genes by detecting the splicing sites accurately. Proposed by previous work in prokaryotes, in the current work the interaction between the 3' tail end of the 18S rRNA and the underlying mRNA were investigated using the free-energy calculations which is then used as a tool for identifying the protein-coding region from non-coding region. In this paper, the yeast Saccharomyces cerevisiae is used for our analysis. It was observed that there is no upstream lock for yeast genes as opposed to what is observed in prokaryotes. The study shows that the binding energy between 3' tail end of 18S rRNA with the underlying mRNA from 135 genes confirms the existence of the ensemble synchronization signal as observed in prokaryotes. The frequency of this signal, as confirmed by the power spectra density, is one-third cycles per nucleotides and there appears to be no significant signal in the non-coding regions. The changes in the magnitude and phase characteristics of the cumulative synchronization signal in individual genes can help in identification of intron-exon splicing sites.