The template RNAs of RNA polymerases can have compact secondary structure, formed by long double helices with partial violations of the complementarity.
A new method of contextual analysis was used to search the long non-random inverted repeats and the complementary palindromes in the genes of E. coli and T7 RNA polymerases. These genes were found to contain from 25% to 50% of all the nucleotides involved in such helices. The 5' -and 3' -ends of mRNA can be protected by neighbouring double helices from the nuclease attack. Some double helices are competing and very similar to the attenuator of E. coli trp-operon.
D001482:Base Composition; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D004926:Escherichia coli / Q000201:enzymology*; D009690:Nucleic Acid Conformation; D011336:Probability; D012329:RNA, Bacterial; D012333:RNA, Messenger; D012367:RNA, Viral; D013604:T-Phages / Q000201:enzymology*
D012329:RNA, Bacterial; D012333:RNA, Messenger; D012367:RNA, Viral; D012321:DNA-Directed RNA Polymerases