Literature DB >> 25956222

RNA polymerase molecular beacon as tool for studies of RNA polymerase-promoter interactions.

Vladimir Mekler1, Konstantin Severinov2.   

Abstract

The molecular details of formation of transcription initiation complex upon the interaction of bacterial RNA polymerase (RNAP) with promoters are not completely understood. One way to address this problem is to understand how RNAP interacts with different parts of promoter DNA. A recently developed fluorometric RNAP molecular beacon assay allows one to monitor the RNAP interactions with various unlabeled DNA probes and quantitatively characterize partial RNAP-promoter interactions. This paper focuses on methodological aspects of application of this powerful assay to study the mechanism of transcription initiation complex formation by Escherichia coli RNA polymerase σ(70) holoenzyme and its regulation by bacterial and phage encoded factors.
Copyright © 2015 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Fluorescence spectroscopy; RNA polymerase; RNA polymerase–promoter interactions; Transcription initiation; Transcription regulation

Mesh：

Substances：

Year:  2015        PMID： 25956222      PMCID： PMC4577438          DOI： 10.1016/j.ymeth.2015.04.033

Source DB:  PubMed          Journal:  Methods        ISSN： 1046-2023            Impact factor:   3.608


  51 in total

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Review 2.  Protein-nucleic acid interactions during open complex formation investigated by systematic alteration of the protein and DNA binding partners.

Authors:  J D Helmann; P L deHaseth
Journal:  Biochemistry       Date:  1999-05-11       Impact factor: 3.162

3.  Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription.

Authors:  Anna Perederina; Vladimir Svetlov; Marina N Vassylyeva; Tahir H Tahirov; Shigeyuki Yokoyama; Irina Artsimovitch; Dmitry G Vassylyev
Journal:  Cell       Date:  2004-08-06       Impact factor: 41.582

4.  Structural basis for promoter-10 element recognition by the bacterial RNA polymerase σ subunit.

Authors:  Andrey Feklistov; Seth A Darst
Journal:  Cell       Date:  2011-12-01       Impact factor: 41.582

5.  A critical role of downstream RNA polymerase-promoter interactions in the formation of initiation complex.

Authors:  Vladimir Mekler; Leonid Minakhin; Konstantin Severinov
Journal:  J Biol Chem       Date:  2011-04-27       Impact factor: 5.157

6.  Mechanism of bacterial transcription initiation: RNA polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis.

Authors:  Ruth M Saecker; M Thomas Record; Pieter L Dehaseth
Journal:  J Mol Biol       Date:  2011-03-01       Impact factor: 5.469

7.  Molecular mechanism of transcription inhibition by phage T7 gp2 protein.

Authors:  Vladimir Mekler; Leonid Minakhin; Carol Sheppard; Sivaramesh Wigneshweraraj; Konstantin Severinov
Journal:  J Mol Biol       Date:  2011-09-21       Impact factor: 5.469

Review 8.  Analysis of RNA polymerase-promoter complex formation.

Authors:  Wilma Ross; Richard L Gourse
Journal:  Methods       Date:  2008-10-24       Impact factor: 3.608

9.  A new basal promoter element recognized by RNA polymerase core enzyme.

Authors:  Yulia Yuzenkova; Vasisht R Tadigotla; Konstantin Severinov; Nikolay Zenkin
Journal:  EMBO J       Date:  2011-07-26       Impact factor: 11.598

10.  Transcription initiation by mix and match elements: flexibility for polymerase binding to bacterial promoters.

Authors:  India G Hook-Barnard; Deborah M Hinton
Journal:  Gene Regul Syst Bio       Date:  2007
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  4 in total

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Journal:  Nat Chem Biol       Date:  2020-09-28       Impact factor: 16.174

2.  Novel Escherichia coli RNA Polymerase Binding Protein Encoded by Bacteriophage T5.

Authors:  Evgeny Klimuk; Vladimir Mekler; Darya Lavysh; Marina Serebryakova; Natalia Akulenko; Konstantin Severinov
Journal:  Viruses       Date:  2020-07-26       Impact factor: 5.048

3.  A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation.

Authors:  Wei-Yang Ooi; Yuko Murayama; Vladimir Mekler; Leonid Minakhin; Konstantin Severinov; Shigeyuki Yokoyama; Shun-Ichi Sekine
Journal:  Nucleic Acids Res       Date:  2018-01-09       Impact factor: 16.971

4.  Regulation of Gene Expression of phiEco32-like Bacteriophage 7-11.

Authors:  Daria Lavysh; Vladimir Mekler; Evgeny Klimuk; Konstantin Severinov
Journal:  Viruses       Date:  2022-03-08       Impact factor: 5.048
  4 in total

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