title: Molecular crowding enhances facilitated diffusion of two human DNA glycosylases.
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.
authors.affiliation: Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA.
authors.forename: Shannen L
authors.initials: SL
authors.lastname: Cravens
authors.affiliation: Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA.
authors.forename: Joseph D
authors.initials: JD
authors.lastname: Schonhoft
authors.affiliation: Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA.
authors.forename: Meng M
authors.initials: MM
authors.lastname: Rowland
authors.affiliation: Department of Chemistry and Biochemistry, The University of San Diego, 5998 Alcalá Park, San Diego, CA 92110, USA.
authors.forename: Alyssa A
authors.initials: AA
authors.lastname: Rodriguez
authors.affiliation: Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA.
authors.forename: Breeana G
authors.initials: BG
authors.lastname: Anderson
authors.affiliation: Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA jstivers@jhmi.edu.
authors.forename: James T
authors.initials: JT
authors.lastname: Stivers
mesh_terms: D004247:DNA / Q000378:metabolism; D045647:DNA Glycosylases / Q000378:metabolism*; D004260:DNA Repair; D055459:Facilitated Diffusion; D006801:Humans; D011092:Polyethylene Glycols; D021381:Protein Transport; D051981:Uracil-DNA Glycosidase / Q000378:metabolism*
chemical_list: D011092:Polyethylene Glycols; D004247:DNA; D045647:DNA Glycosylases; D051981:Uracil-DNA Glycosidase; C479058:oxoguanine glycosylase 1, human
references.citation: Biochemistry. 1985 Nov 19;24(24):6756-62
references.pmid: 4074726
references.citation: Biochemistry. 2014 Dec 9;53(48):7680-92
references.pmid: 25408964
references.citation: Biochemistry. 1999 Jan 19;38(3):952-63
references.pmid: 9893991
references.citation: Proteins. 1999 Apr 1;35(1):13-24
references.pmid: 10090282
references.citation: Biochemistry. 2005 Apr 26;44(16):5949-59
references.pmid: 15835884
references.citation: J Am Chem Soc. 2005 Nov 2;127(43):15138-44
references.pmid: 16248654
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 11;103(15):5752-7
references.pmid: 16585517
references.citation: Biochim Biophys Acta. 2006 Jun;1764(6):1000-6
references.pmid: 16720113
references.citation: Biophys J. 2007 Mar 15;92(6):2139-49
references.pmid: 17189316
references.citation: Nat Methods. 2007 Jul;4(7):567-9
references.pmid: 17546037
references.citation: Nature. 2007 Sep 27;449(7161):433-7
references.pmid: 17704764
references.citation: Proteins. 2008 Apr;71(1):320-35
references.pmid: 17932929
references.citation: Annu Rev Biophys. 2008;37:375-97
references.pmid: 18573087
references.citation: Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10791-6
references.pmid: 18669665
references.citation: Biochemistry. 2008 Nov 4;47(44):11434-45
references.pmid: 18839966
references.citation: Faraday Discuss. 2009;141:131-44; discussion 175-207
references.pmid: 19227355
references.citation: Nature. 2000 Feb 24;403(6772):859-66
references.pmid: 10706276
references.citation: Arch Biochem Biophys. 2000 May 1;377(1):1-8
references.pmid: 10775435
references.citation: J Biol Chem. 2001 Apr 6;276(14):10577-80
references.pmid: 11279227
references.citation: Trends Biochem Sci. 2001 Oct;26(10):597-604
references.pmid: 11590012
references.citation: Biopolymers. 2001 Nov;59(6):427-33
references.pmid: 11598877
references.citation: Biochemistry. 2002 Sep 17;41(37):11236-47
references.pmid: 12220189
references.citation: J Biol Chem. 1981 Dec 10;256(23):12108-17
references.pmid: 7298647
references.citation: J Biol Chem. 1983 May 10;258(9):5710-5
references.pmid: 6853541
references.citation: Nucleic Acids Res. 2009 Jun;37(11):3493-500
references.pmid: 19339520
references.citation: Biophys J. 2009 Aug 5;97(3):875-85
references.pmid: 19651046
references.citation: Nat Struct Mol Biol. 2009 Dec;16(12):1224-9
references.pmid: 19898474
references.citation: Biochim Biophys Acta. 2010 Jun;1804(6):1231-64
references.pmid: 20117254
references.citation: Proc Natl Acad Sci U S A. 2010 May 4;107(18):8183-8
references.pmid: 20404210
references.citation: Chem Rev. 2009 Mar 11;109(3):839-60
references.pmid: 19196002
references.citation: Biochemistry. 2010 Jun 22;49(24):4957-67
references.pmid: 20469926
references.citation: Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14609-14
references.pmid: 20639465
references.citation: Phys Chem Chem Phys. 2010 Sep 21;12(35):10154-60
references.pmid: 20714607
references.citation: Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12699-704
references.pmid: 21742980
references.citation: Nat Chem Biol. 2012 Feb;8(2):205-10
references.pmid: 22231272
references.citation: Biochemistry. 2012 Jul 31;51(30):6028-38
references.pmid: 22784353
references.citation: Biophys J. 2012 Sep 5;103(5):1011-9
references.pmid: 23009850
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D801-7
references.pmid: 23161693
references.citation: Biopolymers. 2013 Apr;99(4):239-44
references.pmid: 23348671
references.citation: Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):E448-57
references.pmid: 23341616
references.citation: Biochemistry. 2013 Apr 16;52(15):2526-35
references.pmid: 23506309
references.citation: Cytometry A. 2013 Jun;83(6):540-51
references.pmid: 23504822
references.citation: Chem Rev. 2014 Jul 9;114(13):6661-714
references.pmid: 24901537
references.citation: Nucleic Acids Res. 2014 Aug;42(14):9295-303
references.pmid: 25016526
references.citation: Nucleic Acids Res. 1998 Aug 15;26(16):3837-44
references.pmid: 9685503