Initial bubble collapse plays a key role in the transition to elongation in T7 RNA polymerase.

The Journal of Biological Chemistry
Peng GongC T Martin

Abstract

RNA polymerases bind to specific sequences in DNA, melt open duplex DNA around the start site, and start transcription within the initially melted bubble. The initially transcribing complex is relatively unstable, releasing short abortive products. After synthesis of a minimal length of RNA (approximately 10-12 bases in the T7 system), RNA polymerases complete the transition to a processive (highly stable) elongation phase and lose the initial promoter contacts. The current study strongly supports a model for T7 RNA polymerase in which initial bubble collapse from position -4 to position +3 is responsible for initiating RNA displacement in the transition process. More specifically, collapse of the bubble from position -4 to position -1 indirectly and energetically facilitates the direct strand invasion offered by collapse at positions +1 to +3. Parallel work shows that promoter release, another key event occurring during this stage of transcription, begins after translocation to position +8 and is largely complete upon translocation to about position +12. The timing of promoter release agrees with the timing of initial bubble collapse determined by our previous fluorescence studies, suggesting that these two events are closely ...Continue Reading

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Citations

Jul 23, 2011·Biochemistry·Ankit V Vahia, Craig T Martin
Dec 19, 2009·Proceedings of the National Academy of Sciences of the United States of America·Guo-Qing TangSmita S Patel
Oct 23, 2009·The Journal of Biological Chemistry·Xiaoqing Liu, Craig T Martin
Nov 18, 2006·Science·Achillefs N KapanidisRichard H Ebright
Apr 16, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jean GuillerezMarc Dreyfus
Jan 27, 2016·Analytical Chemistry·Tamaki EndohNaoki Sugimoto
Apr 4, 2008·Journal of Molecular Biology·Xiao-chuan XueZhong-can Ou-Yang
Jun 20, 2006·Journal of Molecular Biology·Rajiv P BandwarSmita S Patel
Jul 1, 2014·Journal of Molecular Biology·Vadim MolodtsovWilliam T McAllister
Feb 23, 2012·Biochimica Et Biophysica Acta·Aishwarya P Deshpande, Smita S Patel
Feb 16, 2005·The Journal of Biological Chemistry·Qing Guo, Rui Sousa
Jun 23, 2006·The Journal of Biological Chemistry·Peng Gong, Craig T Martin
Aug 17, 2020·Communications Biology·Thomas ConradSascha Sauer

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