Novel insight into the patterns of in vitro short abortive RNA release by Escherichia coli RNA polymerase
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Date
2020-05Author
Kadaster, Artun
Advisor(s)
Record, M. Thomas Jr
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Show full item recordAbstract
E. coli RNA polymerase (RNAP) catalyzes prokaryotic transcription with the σ70 specificity factor,
which directs the binding of RNAP to promoter DNA. RNAP operates on the promoter to form an open
complex. In transcription initiation, complementary ribonucleotide triphosphates (NTP) bind stepwise to
the template DNA in the active site and RNAP catalyzes phosphodiester bond formation. After each NTP
addition, the RNA-DNA hybrid translocates into the active site cleft while maintaining promoter contacts.
In productive complexes, free energy buildup from translocation allows RNAP to break its specific contacts
and escape from the promoter to transcribe full-length RNA. Nonproductive complexes stall before escape,
release a short RNA, and re-initiate a cycle of abortive (short RNA) transcription. Dinucleotide RNA is the
shortest possible abortive product. Experimental evidence and a thermodynamic rationale are presented
indicating that most of the RNA synthesized by nonproductive complexes in vitro for the conditions
investigated is 3-mer or longer.