Literature DB >> 25845592

Molecular crowding enhances facilitated diffusion of two human DNA glycosylases.

Shannen L Cravens1, Joseph D Schonhoft1, Meng M Rowland1, Alyssa A Rodriguez2, Breeana G Anderson1, James T Stivers3.   

Abstract

Intracellular space is at a premium due to the high concentrations of biomolecules and is expected to have a fundamental effect on how large macromolecules move in the cell. Here, we report that crowded solutions promote intramolecular DNA translocation by two human DNA repair glycosylases. The crowding effect increases both the efficiency and average distance of DNA chain translocation by hindering escape of the enzymes to bulk solution. The increased contact time with the DNA chain provides for redundant damage patrolling within individual DNA chains at the expense of slowing the overall rate of damaged base removal from a population of molecules. The significant biological implication is that a crowded cellular environment could influence the mechanism of damage recognition as much as any property of the enzyme or DNA.
© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Year:  2015        PMID: 25845592      PMCID: PMC4417188          DOI: 10.1093/nar/gkv301

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  45 in total

1.  The origins of high-affinity enzyme binding to an extrahelical DNA base.

Authors:  Daniel J Krosky; Fenhong Song; James T Stivers
Journal:  Biochemistry       Date:  2005-04-26       Impact factor: 3.162

2.  The effect of the presence of globular proteins and elongated polymers on enzyme activity.

Authors:  Barry K Derham; John J Harding
Journal:  Biochim Biophys Acta       Date:  2006-01-26

3.  Nucleic acid and protein mass mapping by live-cell deep-ultraviolet microscopy.

Authors:  Benjamin J Zeskind; Caroline D Jordan; Winston Timp; Linda Trapani; Guichy Waller; Victor Horodincu; Daniel J Ehrlich; Paul Matsudaira
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4.  Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase.

Authors:  J T Stivers; K W Pankiewicz; K A Watanabe
Journal:  Biochemistry       Date:  1999-01-19       Impact factor: 3.162

5.  Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited.

Authors:  G Xiao; M Tordova; J Jagadeesh; A C Drohat; J T Stivers; G L Gilliland
Journal:  Proteins       Date:  1999-04-01

6.  Protein-protein association in polymer solutions: from dilute to semidilute to concentrated.

Authors:  Noga Kozer; Yosef Yehuda Kuttner; Gilad Haran; Gideon Schreiber
Journal:  Biophys J       Date:  2006-12-22       Impact factor: 4.033

7.  Separating the contribution of translational and rotational diffusion to protein association.

Authors:  Yosef Yehuda Kuttner; Noga Kozer; Eugenia Segal; Gideon Schreiber; Gilad Haran
Journal:  J Am Chem Soc       Date:  2005-11-02       Impact factor: 15.419

8.  A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA.

Authors:  Paul C Blainey; Antoine M van Oijen; Anirban Banerjee; Gregory L Verdine; X Sunney Xie
Journal:  Proc Natl Acad Sci U S A       Date:  2006-04-03       Impact factor: 11.205

9.  Mechanism of poly(ethylene glycol) interaction with proteins.

Authors:  T Arakawa; S N Timasheff
Journal:  Biochemistry       Date:  1985-11-19       Impact factor: 3.162

10.  Electrostatic properties of complexes along a DNA glycosylase damage search pathway.

Authors:  Shannen L Cravens; Matthew Hobson; James T Stivers
Journal:  Biochemistry       Date:  2014-11-26       Impact factor: 3.162

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  19 in total

1.  Next-Generation DNA Curtains for Single-Molecule Studies of Homologous Recombination.

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Journal:  Methods Enzymol       Date:  2017-04-17       Impact factor: 1.600

2.  Macromolecular crowding induces compaction and DNA binding in the disordered N-terminal domain of hUNG2.

Authors:  Gaddiel Rodriguez; Benjamin Orris; Ananya Majumdar; Shridhar Bhat; James T Stivers
Journal:  DNA Repair (Amst)       Date:  2019-12-10

3.  AP-Endonuclease 1 Accelerates Turnover of Human 8-Oxoguanine DNA Glycosylase by Preventing Retrograde Binding to the Abasic-Site Product.

Authors:  Alexandre Esadze; Gaddiel Rodriguez; Shannen L Cravens; James T Stivers
Journal:  Biochemistry       Date:  2017-03-31       Impact factor: 3.162

4.  Distinguishing Specific and Nonspecific Complexes of Alkyladenine DNA Glycosylase.

Authors:  Erin L Taylor; Preethi M Kesavan; Abigail E Wolfe; Patrick J O'Brien
Journal:  Biochemistry       Date:  2018-07-16       Impact factor: 3.162

5.  Disordered N-Terminal Domain of Human Uracil DNA Glycosylase (hUNG2) Enhances DNA Translocation.

Authors:  Gaddiel Rodriguez; Alexandre Esadze; Brian P Weiser; Joseph D Schonhoft; Philip A Cole; James T Stivers
Journal:  ACS Chem Biol       Date:  2017-08-15       Impact factor: 5.100

6.  Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu.

Authors:  Pinki Dey; Arnab Bhattacherjee
Journal:  Biophys J       Date:  2019-11-29       Impact factor: 4.033

7.  Measurement of nanoscale DNA translocation by uracil DNA glycosylase in human cells.

Authors:  Alexandre Esadze; Gaddiel Rodriguez; Brian P Weiser; Philip A Cole; James T Stivers
Journal:  Nucleic Acids Res       Date:  2017-12-01       Impact factor: 16.971

8.  Comparative Effects of Ions, Molecular Crowding, and Bulk DNA on the Damage Search Mechanisms of hOGG1 and hUNG.

Authors:  Shannen L Cravens; James T Stivers
Journal:  Biochemistry       Date:  2016-09-07       Impact factor: 3.162

9.  Searching target sites on DNA by proteins: Role of DNA dynamics under confinement.

Authors:  Anupam Mondal; Arnab Bhattacherjee
Journal:  Nucleic Acids Res       Date:  2015-09-22       Impact factor: 16.971

10.  Processive searching ability varies among members of the gap-filling DNA polymerase X family.

Authors:  Michael J Howard; Samuel H Wilson
Journal:  J Biol Chem       Date:  2017-09-11       Impact factor: 5.157

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