Diego Duchi
University of Oxford
8 Papers
132 Citations
Diego Duchi is an academic researcher from University of Oxford. The author has contributed to research in topics: RNA polymerase & Promoter. The author has an hindex of 6, co-authored 8 publications.
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Papers
Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3)
Wei Lin,Kalyan Das,David Degen,Abhishek Mazumder,Diego Duchi,Dongye Wang,Yon W. Ebright,Richard Y. Ebright,Elena V. Sineva,Matthew Gigliotti,Aashish Srivastava,Sukhendu Mandal,Yi Jiang,Yu Liu,Ruiheng Yin,Zhening Zhang,Edward T. Eng,Dennis Thomas,Stefano Donadio,Haibo Zhang,Changsheng Zhang,Achillefs N. Kapanidis,Richard H. Ebright +22 more
TL;DR: A cryo-EM structure of Mycobacterium tuberculosis RNAP holoenzyme in complex with Lpm at 3.5-Å resolution shows that Lpm binds at the base of the RNAP "clamp."
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RNA Polymerase Pausing during Initial Transcription.
Diego Duchi,David L.V. Bauer,Laurent Fernandez,Geraint Evans,Nicole C. Robb,Ling Chin Hwang,Kristofer Gryte,Alexandra I. Tomescu,Pawel Zawadzki,Zakia Morichaud,Konstantin Brodolin,Achillefs N. Kapanidis +11 more
TL;DR: This work revealed a long pause (“initiation pause,” ∼20 s) after synthesis of a 6-mer RNA; such pauses can serve as regulatory checkpoints in a model for initial transcription, in which pausing is controlled by a complex set of determinants that modulate the transition from a6- to a 7-nt RNA.
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The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp
Diego Duchi,Abhishek Mazumder,Abhishek Mazumder,Anssi M. Malinen,Richard H. Ebright,Achillefs N. Kapanidis +5 more
TL;DR: It is shown that the clamp in RNAP holoenzyme populates three distinct conformational states and interconvert between these states on the 0.1–1 s time-scale, raising the possibility that ppGpp controls promoter opening by modulating clamp dynamics.
Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes
Diego Duchi,Kristofer Gryte,Nicole C. Robb,Zakia Morichaud,Carol Sheppard,Konstantin Brodolin,Sivaramesh Wigneshweraraj,Achillefs N. Kapanidis +7 more
TL;DR: The results revealed the existence of two stable states within RNAP–DNA complexes in which the promoter DNA appears to adopt closed and partially open conformations, and support a bend-load-open model for the sequence of transitions leading to bubble opening during open complex formation.
E. Coli RNA Polymerase Pauses during Initial Transcription
TL;DR: This work has revealed that RNA polymerase pauses after producing a 6-mer RNA, and that the pause can serve as a regulatory checkpoint, and identifies a structural region of the polymerase, σ3.2, which contains a loop blocking the RNA-exit channel, as a pausing determinant.
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