The formation and breaking of hydrogen bonds between nucleic acid bases is dependent on temperature. High GC content of organisms was surmised to be an adaptation for high temperature survival because of the thermal stability of G:C pairs. However, a survey of genomic GC% and optimum growth temperature (OGT) of several prokaryotes revoked any direct relation between them. Significantly high purine (R = A or G) content in mRNAs is also seen as a selective response for survival among thermophiles. Nevertheless, the biological relevance of thermophiles loading their unstable mRNAs with excess purines (R-loading) is not persuasive. Here, we analyzed the mRNA sequences of 168 prokaryotes with their OGTs ranging from -5°C to 100°C to verify the relation between R-loading and OGT. Our analysis fails to demonstrate any correlation between R-loading of the mRNA pool and OGT of a prokaryote. The percentage of purine-loaded mRNAs in prokaryotes is found to be in a rough negative correlation with the genomic GC% (r2 = 0.655, slope = -1.478, P < 000.1). We conclude that GC% and bias against certain combinations of nucleotides drive the mRNA-synonymous (sense) strands of DNA towards variations in R-loading.