Preventing nondesired RNA-primed RNA extension catalyzed by T7 RNA polymerase

Eur J Biochem. 2003 Apr;270(7):1458-65. doi: 10.1046/j.1432-1033.2003.03510.x.

Abstract

The transcription patterns of 64 linear double stranded DNA templates obtained with T7 RNA polymerase were investigated. These templates consisted of 17 nucleotide-long sequences under the control of the minimal bacteriophage T7 promoter and represented all possible combinations of nucleotides at positions +8, +10 and +11. Two clearly distinct types of template were identified, which produced the range of transcription patterns observed: (a) those that yielded 17-nucleotide-long RNA as the only detectable run-off product (only 15% of the total), and (b) templates that in addition to the expected full-length RNA, produced other products longer than 17 nucleotides. Self-complementarity analysis of the expected run-off transcripts showed that those obtained from the first type of template were able to form stable intermolecular duplexes with non-base-paired 3'-ends. However, the second type of template yielded RNAs able to generate energetically favorable intermolecular duplexes with 3'-end complementarity, therefore yielding an RNA-primed RNA-template. The gel-purified 17-nucleotide-long RNAs transcribed from the latter yielded longer products when incubated under in vitro transcription conditions in the absence of a DNA template. No extension was observed when assaying the 17-nucleotide RNA products resulting from the first type of template. We observed that just a single nucleotide change within the DNA template could convert the RNA product from an RNA-primed template into a nonextendible dimer thus leading to a drastic switch of the 17-nucleotide product yield from less than 10% to 100%. Further, two type B DNA templates were extended by two nucleotides at the 3'-end, to produce RNA transcripts theoretically unable to form 3'-end base-paired duplexes. The full-length products of these modified DNA templates were found to be nonextendible by T7 RNA polymerase under the standard in vitro transcription conditions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing
  • Catalysis
  • Cell-Free System
  • DNA / chemistry
  • DNA / metabolism
  • DNA-Directed RNA Polymerases / chemistry*
  • Gene Library
  • RNA / chemistry*
  • RNA / metabolism
  • RNA, Catalytic / chemistry
  • RNA, Catalytic / metabolism
  • RNA, Complementary / chemistry
  • RNA, Complementary / metabolism
  • Substrate Specificity
  • Templates, Genetic
  • Transcription, Genetic / physiology*
  • Viral Proteins

Substances

  • RNA, Catalytic
  • RNA, Complementary
  • Viral Proteins
  • RNA
  • DNA
  • bacteriophage T7 RNA polymerase
  • DNA-Directed RNA Polymerases