Literature DB >> 28474797

A mechanistic study of helicases with magnetic traps.

Samar Hodeib1,2, Saurabh Raj1,2, Maria Manosas3,4, Weiting Zhang1,2, Debjani Bagchi1,2, Bertrand Ducos1,2, Francesca Fiorini5, Joanne Kanaan2, Hervé Le Hir2, Jean-François Allemand1,2, David Bensimon1,2,6, Vincent Croquette1,2.   

Abstract

Helicases are a broad family of enzymes that separate nucleic acid double strand structures (DNA/DNA, DNA/RNA, or RNA/RNA) and thus are essential to DNA replication and the maintenance of nucleic acid integrity. We review the picture that has emerged from single molecule studies of the mechanisms of DNA and RNA helicases and their interactions with other proteins. Many features have been uncovered by these studies that were obscured by bulk studies, such as DNA strands switching, mechanical (rather than biochemical) coupling between helicases and polymerases, helicase-induced re-hybridization and stalled fork rescue.
© 2017 The Protein Society.

Entities:  

Keywords:  DNA unwinding; Holliday junction migration; active unwinding; ds-DNA fork; fork regression; helicase/polymerase coupling; helicases; magnetic traps; polymerase; primase; primosome; replisome; strand annealing

Mesh:

Substances:

Year:  2017        PMID: 28474797      PMCID: PMC5477542          DOI: 10.1002/pro.3187

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  90 in total

Review 1.  A general model for nucleic acid helicases and their "coupling" within macromolecular machines.

Authors:  P H von Hippel; E Delagoutte
Journal:  Cell       Date:  2001-01-26       Impact factor: 41.582

Review 2.  Single-molecule views of protein movement on single-stranded DNA.

Authors:  Taekjip Ha; Alexander G Kozlov; Timothy M Lohman
Journal:  Annu Rev Biophys       Date:  2012-02-23       Impact factor: 12.981

3.  Highly parallel magnetic tweezers by targeted DNA tethering.

Authors:  Iwijn De Vlaminck; Thomas Henighan; Marijn T J van Loenhout; Indriati Pfeiffer; Julius Huijts; Jacob W J Kerssemakers; Allard J Katan; Anja van Langen-Suurling; Emile van der Drift; Claire Wyman; Cees Dekker
Journal:  Nano Lett       Date:  2011-10-27       Impact factor: 11.189

4.  Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase.

Authors:  Daniel S Johnson; Lu Bai; Benjamin Y Smith; Smita S Patel; Michelle D Wang
Journal:  Cell       Date:  2007-06-29       Impact factor: 41.582

5.  NS3 helicase actively separates RNA strands and senses sequence barriers ahead of the opening fork.

Authors:  Wei Cheng; Sophie Dumont; Ignacio Tinoco; Carlos Bustamante
Journal:  Proc Natl Acad Sci U S A       Date:  2007-08-20       Impact factor: 11.205

6.  Reconstruction of bacterial transcription-coupled repair at single-molecule resolution.

Authors:  Jun Fan; Mathieu Leroux-Coyau; Nigel J Savery; Terence R Strick
Journal:  Nature       Date:  2016-08-03       Impact factor: 49.962

7.  Escherichia coli helicase II (urvD gene product) translocates unidirectionally in a 3' to 5' direction.

Authors:  S W Matson
Journal:  J Biol Chem       Date:  1986-08-05       Impact factor: 5.157

Review 8.  RNA helicases at work: binding and rearranging.

Authors:  Eckhard Jankowsky
Journal:  Trends Biochem Sci       Date:  2011-01       Impact factor: 13.807

9.  Protein structure. Engineering of a superhelicase through conformational control.

Authors:  Sinan Arslan; Rustem Khafizov; Christopher D Thomas; Yann R Chemla; Taekjip Ha
Journal:  Science       Date:  2015-04-17       Impact factor: 47.728

10.  DNA unwinding step-size of E. coli RecBCD helicase determined from single turnover chemical quenched-flow kinetic studies.

Authors:  Aaron L Lucius; Alessandro Vindigni; Razmic Gregorian; Janid A Ali; Andrew F Taylor; Gerald R Smith; Timothy M Lohman
Journal:  J Mol Biol       Date:  2002-11-29       Impact factor: 5.469

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  7 in total

Review 1.  Approaches for measuring the dynamics of RNA-protein interactions.

Authors:  Donny D Licatalosi; Xuan Ye; Eckhard Jankowsky
Journal:  Wiley Interdiscip Rev RNA       Date:  2019-08-20       Impact factor: 9.957

2.  Three-Dimensional Tracking of Tethered Particles for Probing Nanometer-Scale Single-Molecule Dynamics Using a Plasmonic Microscope.

Authors:  Guangzhong Ma; Zijian Wan; Yunze Yang; Wenwen Jing; Shaopeng Wang
Journal:  ACS Sens       Date:  2021-11-17       Impact factor: 7.711

3.  Sequence-dependent mechanochemical coupling of helicase translocation and unwinding at single-nucleotide resolution.

Authors:  Andrew H Laszlo; Jonathan M Craig; Momčilo Gavrilov; Ramreddy Tippana; Ian C Nova; Jesse R Huang; Hwanhee C Kim; Sarah J Abell; Mallory deCampos-Stairiker; Jonathan W Mount; Jasmine L Bowman; Katherine S Baker; Hugh Higinbotham; Dmitriy Bobrovnikov; Taekjip Ha; Jens H Gundlach
Journal:  Proc Natl Acad Sci U S A       Date:  2022-08-29       Impact factor: 12.779

Review 4.  Determining translocation orientations of nucleic acid helicases.

Authors:  Himasha M Perera; Michael A Trakselis
Journal:  Methods       Date:  2021-11-07       Impact factor: 4.647

Review 5.  Insight into the biochemical mechanism of DNA helicases provided by bulk-phase and single-molecule assays.

Authors:  Piero R Bianco
Journal:  Methods       Date:  2021-12-08       Impact factor: 4.647

6.  The mechanism of DNA unwinding by the eukaryotic replicative helicase.

Authors:  Daniel R Burnham; Hazal B Kose; Rebecca B Hoyle; Hasan Yardimci
Journal:  Nat Commun       Date:  2019-05-14       Impact factor: 14.919

7.  A conserved structural element in the RNA helicase UPF1 regulates its catalytic activity in an isoform-specific manner.

Authors:  Manjeera Gowravaram; Fabien Bonneau; Joanne Kanaan; Vincent D Maciej; Francesca Fiorini; Saurabh Raj; Vincent Croquette; Hervé Le Hir; Sutapa Chakrabarti
Journal:  Nucleic Acids Res       Date:  2018-03-16       Impact factor: 16.971

  7 in total

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