Literature DB >> 23412360

Speed-stability paradox in DNA-scanning by zinc-finger proteins.

Junji Iwahara1, Yaakov Levy.   

Abstract

Extensive contact with DNA via multiple zinc fingers allows highly specific DNA-binding of zinc-finger-class transcription factors, but can also slow the target search process. Here we introduce recent insights into how zinc-finger proteins can rapidly scan DNA. Potential application of the new knowledge to the zinc-finger-based technology is also discussed.

Keywords:  DNA-scanning; dynamics; gene control; kinetics; target search; zinc-finger nucleases; zinc-finger transcription factors

Mesh：

Substances：

Year:  2013        PMID： 23412360      PMCID： PMC3646054          DOI： 10.4161/trns.23584

Source DB:  PubMed          Journal:  Transcription        ISSN： 2154-1272


  27 in total

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Authors:  Bruno Bozon; Sabrina Davis; Serge Laroche
Journal:  Neuron       Date:  2003-11-13       Impact factor: 17.173

Review 2.  How do site-specific DNA-binding proteins find their targets?

Authors:  Stephen E Halford; John F Marko
Journal:  Nucleic Acids Res       Date:  2004-06-03       Impact factor: 16.971

3.  Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential.

Authors:  Michael Slutsky; Leonid A Mirny
Journal:  Biophys J       Date:  2004-10-01       Impact factor: 4.033

4.  Asymmetrical roles of zinc fingers in dynamic DNA-scanning process by the inducible transcription factor Egr-1.

Authors:  Levani Zandarashvili; Dana Vuzman; Alexandre Esadze; Yuki Takayama; Debashish Sahu; Yaakov Levy; Junji Iwahara
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-06       Impact factor: 11.205

5.  Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A.

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Journal:  Science       Date:  1991-05-10       Impact factor: 47.728

Review 6.  Facilitated target location in biological systems.

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Journal:  J Biol Chem       Date:  1989-01-15       Impact factor: 5.157

7.  Egr-1, a master switch coordinating upregulation of divergent gene families underlying ischemic stress.

Authors:  S F Yan; T Fujita; J Lu; K Okada; Y Shan Zou; N Mackman; D J Pinsky; D M Stern
Journal:  Nat Med       Date:  2000-12       Impact factor: 53.440

8.  Regulation of the endogenous VEGF-A gene by exogenous designed regulatory proteins.

Authors:  Kiyoshi Tachikawa; Oliver Schröder; Gerhard Frey; Steven P Briggs; Takashi Sera
Journal:  Proc Natl Acad Sci U S A       Date:  2004-10-08       Impact factor: 11.205

9.  Egr-1-induced endothelial gene expression: a common theme in vascular injury.

Authors:  L M Khachigian; V Lindner; A J Williams; T Collins
Journal:  Science       Date:  1996-03-08       Impact factor: 47.728

10.  Independent cellular processes for hippocampal memory consolidation and reconsolidation.

Authors:  Jonathan L C Lee; Barry J Everitt; Kerrie L Thomas
Journal:  Science       Date:  2004-04-08       Impact factor: 47.728
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  10 in total

1.  Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble.

Authors:  Levani Zandarashvili; Alexandre Esadze; Dana Vuzman; Catherine A Kemme; Yaakov Levy; Junji Iwahara
Journal:  Proc Natl Acad Sci U S A       Date:  2015-08-31       Impact factor: 11.205

2.  DNA Shape versus Sequence Variations in the Protein Binding Process.

Authors:  Chuanying Chen; B Montgomery Pettitt
Journal:  Biophys J       Date:  2016-02-02       Impact factor: 4.033

3.  The Role of Noncognate Sites in the 1D Search Mechanism of EcoRI.

Authors:  Sadie C Piatt; Joseph J Loparo; Allen C Price
Journal:  Biophys J       Date:  2019-05-08       Impact factor: 4.033

4.  Targeted DNA demethylation in human cells by fusion of a plant 5-methylcytosine DNA glycosylase to a sequence-specific DNA binding domain.

Authors:  Jara Teresa Parrilla-Doblas; Rafael R Ariza; Teresa Roldán-Arjona
Journal:  Epigenetics       Date:  2017-02-23       Impact factor: 4.528

5.  Kinetic origin of nucleosome invasion by pioneer transcription factors.

Authors:  Anupam Mondal; Sujeet Kumar Mishra; Arnab Bhattacherjee
Journal:  Biophys J       Date:  2021-10-30       Impact factor: 4.033

6.  Positive and negative impacts of nonspecific sites during target location by a sequence-specific DNA-binding protein: origin of the optimal search at physiological ionic strength.

Authors:  Alexandre Esadze; Catherine A Kemme; Anatoly B Kolomeisky; Junji Iwahara
Journal:  Nucleic Acids Res       Date:  2014-05-16       Impact factor: 16.971

7.  Protein plasticity driven by disorder and collapse governs the heterogeneous binding of CytR to DNA.

Authors:  Sneha Munshi; Soundhararajan Gopi; Sandhyaa Subramanian; Luis A Campos; Athi N Naganathan
Journal:  Nucleic Acids Res       Date:  2018-05-04       Impact factor: 16.971

8.  CTCF confers local nucleosome resiliency after DNA replication and during mitosis.

Authors:  Nick Owens; Thaleia Papadopoulou; Nicola Festuccia; Alexandra Tachtsidi; Inma Gonzalez; Agnes Dubois; Sandrine Vandormael-Pournin; Elphège P Nora; Benoit G Bruneau; Michel Cohen-Tannoudji; Pablo Navarro
Journal:  Elife       Date:  2019-10-10       Impact factor: 8.140

9.  Tunable order-disorder continuum in protein-DNA interactions.

Authors:  Sneha Munshi; Soundhararajan Gopi; Gitanjali Asampille; Sandhyaa Subramanian; Luis A Campos; Hanudatta S Atreya; Athi N Naganathan
Journal:  Nucleic Acids Res       Date:  2018-09-28       Impact factor: 16.971

10.  Influence of quasi-specific sites on kinetics of target DNA search by a sequence-specific DNA-binding protein.

Authors:  Catherine A Kemme; Alexandre Esadze; Junji Iwahara
Journal:  Biochemistry       Date:  2015-11-02       Impact factor: 3.162
  10 in total

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