Substitution of ribonucleotides in the T7 RNA polymerase promoter element

A systematic analysis was carried out to examine the effects of ribonucleotide substitution at various locations within the promoter element for T7 RNA polymerase. Ribonucleotides could be introduced at most positions without significantly decreasing transcription efficiency. A critical window of residues that were intolerant of RNA substitution was defined for both the nontemplate and template strands of the promoter. These residues are involved in important contacts with the AT-rich recognition loop, specificity loop, and beta-intercalating hairpin of the polymerase. These results highlight the malleability of T7 RNA polymerase in recognizing its promoter element and suggest that promoters with altered backbone conformations may be used in molecular biology applications that use T7 RNA polymerase for in vitro transcription.