The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: Implications for transcription start-site selection

The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: Implications for transcription start-site selection

Show other versions (1)

Bacterial transcription is initiated after RNA polymerase (RNAP) binds to promoter DNA, melts ~ 14 bp around the transcription start site and forms a single-stranded "transcription bubble" within a catalytically active RNAP-DNA open complex (RPo). There is significant flexibility in the tr...

Full description

Bibliographic Details
Main Authors:	Robb, N, Cordes, T, Hwang, L, Gryte, K, Duchi, D, Craggs, T, Santoso, Y, Weiss, S, Ebright, R, Kapanidis, A
Format:	Journal article
Language:	English
Published:	2013

Similar Items

The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection.
by: Robb, N, et al.
Published: (2013)

Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes
by: Duchi, D, et al.
Published: (2017)

RNA polymerase pausing during initial transcription
by: Duchi, D, et al.
Published: (2016)

Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism.
by: Kapanidis, A, et al.
Published: (2006)

Sensing DNA opening in transcription using quenchable Forster resonance energy transfer.
by: Cordes, T, et al.
Published: (2010)

New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB.
by: Lagrange, T, et al.
Published: (1998)

Single-Molecule Studies of Transcription Initiation using a Vesicle Approach
by: Llumigusin, D, et al.
Published: (2012)

The rate-limiting step of DNA synthesis by DNA polymerase occurs in the fingers-closed conformation
by: Evans, GW, et al.
Published: (2021)

Translocation of sigma(70) with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA.
by: Mukhopadhyay, J, et al.
Published: (2001)

Single-molecule studies of transcription initiation
by: Duchi Llumigusin, D, et al.
Published: (2014)

Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis.
by: Kapanidis, A, et al.
Published: (2005)

Structural transitions in transcription initiation: Kinetic and single molecule kinetic analyses
by: Mukhopadhyay, J, et al.
Published: (2001)

PHYS 293-Single-molecule analysis of transcription
by: Ebright, R, et al.
Published: (2007)

The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp
by: Duchi, D, et al.
Published: (2018)

DNA polymerase conformational dynamics and the role of fidelity-conferring residues: Insights from computational simulations
by: Meli, M, et al.
Published: (2016)

The topology of transcription by immobilized polymerases.
by: Iborra, F, et al.
Published: (1996)

Fluorescence resonance energy transfer (FRET) in analysis of transcription-complex structure and function.
by: Mukhopadhyay, J, et al.
Published: (2003)

RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding
by: Mazumder, A, et al.
Published: (2021)

Transcription by an immobilized RNA polymerase from bacteriophage T7 and the topology of transcription.
by: Cook, P, et al.
Published: (1992)

Exon-Mediated Activation of Transcription Starts
by: Fiszbein, Ana, et al.
Published: (2021)

Exon-Mediated Activation of Transcription Starts
by: Fiszbein, Ana, et al.
Published: (2022)

Transcription termination by RNA Polymerase II
by: White, E
Published: (2012)

Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes.
by: Margeat, E, et al.
Published: (2006)

Structural basis of transcription inhibition by fidaxomicin (lipiarmycin A3)
by: Lin, W, et al.
Published: (2018)

Real-time transcription initiation by E. coli RNA polymerase in vitro and in vivo
by: Plochowietz, A, et al.
Published: (2015)

Transcription initiation at a consensus bacterial promoter proceeds via a 'bind-unwind-load-and-lock' mechanism
by: Mazumder, A, et al.
Published: (2021)

Fixing the model for transcription: the DNA moves, not the polymerase.
by: Papantonis, A, et al.
Published: (2011)

Exon tethering in transcription by RNA polymerase II.
by: Dye, M, et al.
Published: (2006)

Alternative transcription cycle for bacterial RNA polymerase
by: Harden, Timothy T, et al.
Published: (2021)

ACTIVE POLYMERASES FIXED IN REPLICATION AND TRANSCRIPTION FACTORIES
by: Hassan, B, et al.
Published: (1994)

Disengaging polymerase: terminating RNA polymerase II transcription in budding yeast.
by: Mischo, H, et al.
Published: (2013)

Closing and opening of the RNA polymerase trigger loop
by: Mazumder, A, et al.
Published: (2020)

Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei.
by: Jackson, D, et al.
Published: (1998)

Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei
by: Jackson, D, et al.
Published: (1998)

Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion.
by: Hohlbein, J, et al.
Published: (2013)

Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase
by: Craggs, T, et al.
Published: (2019)

Multiple transcript cleavage precedes polymerase release in termination by RNA polymerase II.
by: Dye, M, et al.
Published: (2001)

Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin.
by: Vasiljeva, L, et al.
Published: (2008)

DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts
by: Kuś, K, et al.
Published: (2025)

Interplay between chromatin conformation and transcription in eukaryotes
by: Bhardwaj, S
Published: (2013)