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Peng, Y. Transcription Bubble. Encyclopedia. Available online: https://encyclopedia.pub/entry/60956 (accessed on 02 November 2026).
Peng Y. Transcription Bubble. Encyclopedia. Available at: https://encyclopedia.pub/entry/60956. Accessed November 02, 2026.
Peng, Yu. "Transcription Bubble" Encyclopedia, https://encyclopedia.pub/entry/60956 (accessed November 02, 2026).
Peng, Y. (2026, October 14). Transcription Bubble. In Encyclopedia. https://encyclopedia.pub/entry/60956
Peng, Yu. "Transcription Bubble." Encyclopedia. Web. 14 October, 2026.
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Transcription Bubble
EditA transcription bubble is a localized region of separated DNA strands within a transcription complex, exposing a template for RNA synthesis. During bacterial initiation, promoter binding and DNA opening produce an RNA-polymerase complex positioned to initiate the transcript [1]. Regulatory proteins can alter promoter recognition and the transitions leading to productive initiation [2]. In an elongating complex, the template strand enters the polymerase active site, where the growing RNA forms a short hybrid with DNA before emerging from the enzyme [3][4]. The displaced nontemplate strand follows a separate path. Structural elements of RNA polymerase coordinate the two bubble boundaries, with downstream strand separation and upstream strand reannealing accompanying progression of the transcription complex along the DNA [5].
RNA polymerase
DNA strand separation
open promoter complex
RNA–DNA hybrid
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References
- Douglas F. Browning; Stephen J. W. Busby; The Regulation of Bacterial Transcription Initiation. Nat. Rev. Microbiol. 2004, 2, 57-65. [CrossRef]
- Douglas F. Browning; Stephen J. W. Busby; Local and Global Regulation of Transcription Initiation in Bacteria. Nat. Rev. Microbiol. 2016, 14, 638-650. [CrossRef]
- Christopher O. Barnes; Monica Calero; Indranil Malik; Brian W. Graham; Henrik Spahr; Guowu Lin; Aina E. Cohen; Ian S. Brown; Qiangmin Zhang; Filippo Pullara; Michael A. Trakselis; Craig D. Kaplan; Guillermo Calero; Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble. Mol. Cell 2015, 59, 258-269. [CrossRef]
- Patrick Cramer; Organization and Regulation of Gene Transcription. Nature 2019, 573, 45-54. [CrossRef]
- Andreas U. Mueller; James Chen; Mengyu Wu; Courtney Chiu; B. Tracy Nixon; Elizabeth A. Campbell; Seth A. Darst; A General Mechanism for Transcription Bubble Nucleation in Bacteria. Proc. Natl. Acad. Sci. 2023, 120, e2220874120. [CrossRef]
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