title: Probing single nanometer-scale pores with polymeric molecular rulers.
abstract: We previously demonstrated that individual molecules of single-stranded DNA can be driven electrophoretically through a single Staphylococcus aureus alpha-hemolysin ion channel. Polynucleotides thread through the channel as extended chains and the polymer-induced ionic current blockades exhibit stable modes during the interactions. We show here that polynucleotides can be used to probe structural features of the alpha-hemolysin channel itself. Specifically, both the pore length and channel aperture profile can be estimated. The results are consistent with the channel crystal structure and suggest that polymer-based "molecular rulers" may prove useful in deducing the structures of nanometer-scale pores in general.
authors.affiliation: Semiconductor Electronics Division, NIST, Bldg. 225, Room B326, Gaithersburg, Maryland 20899-8120, USA.
authors.forename: Sarah E
authors.initials: SE
authors.lastname: Henrickson
authors.forename: Edmund A
authors.initials: EA
authors.lastname: DiMarzio
authors.forename: Qian
authors.initials: Q
authors.lastname: Wang
authors.forename: Vincent M
authors.initials: VM
authors.lastname: Stanford
authors.forename: John J
authors.initials: JJ
authors.lastname: Kasianowicz
mesh_terms: D001692:Biological Transport; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000378:metabolism*; D006460:Hemolysin Proteins / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008968:Molecular Conformation; D015335:Molecular Probes / Q000737:chemistry / Q000378:metabolism*; D049329:Nanostructures / Q000737:chemistry*; D016062:Porosity
chemical_list: D004277:DNA, Single-Stranded; D006460:Hemolysin Proteins; D015335:Molecular Probes
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Feb;63(2 Pt 1):021115
references.pmid: 11308476
references.citation: Biophys J. 1993 Jan;64(1):16-25
references.pmid: 7679295
references.citation: EMBO J. 1996 Apr 15;15(8):1857-64
references.pmid: 8617232
references.citation: J Biol Chem. 2005 Oct 7;280(40):34056-62
references.pmid: 16087661
references.citation: Biochemistry. 1998 Mar 17;37(11):3941-8
references.pmid: 9521715
references.citation: Biophys J. 2008 Aug;95(3):1157-64
references.pmid: 18645196
references.citation: Microbiol Rev. 1991 Dec;55(4):733-51
references.pmid: 1779933
references.citation: Curr Opin Chem Biol. 1999 Oct;3(5):525-9
references.pmid: 10508669
references.citation: Phys Rev Lett. 2001 Apr 9;86(15):3435-8
references.pmid: 11327989
references.citation: Proc Natl Acad Sci U S A. 1994 Dec 20;91(26):12828-31
references.pmid: 7809129
references.citation: J Membr Biol. 1995 Oct;147(3):233-9
references.pmid: 8558589
references.citation: Proc Natl Acad Sci U S A. 1972 Dec;69(12):3561-6
references.pmid: 4509315
references.citation: Anal Chem. 2001 May 15;73(10):2268-72
references.pmid: 11393851
references.citation: Nano Lett. 2005 Jul;5(7):1193-7
references.pmid: 16178209
references.citation: Membr Cell Biol. 1997;11(4):497-505
references.pmid: 9553937
references.citation: Macromolecules. 1976 Jan-Feb;9(1):182-5
references.pmid: 1249988
references.citation: Nat Mater. 2003 Sep;2(9):611-5
references.pmid: 12942073
references.citation: Proc Natl Acad Sci U S A. 1997 Mar 4;94(5):2045-9
references.pmid: 9050902
references.citation: Nature. 1986 Sep 4-10;323(6083):36-9
references.pmid: 2427958
references.citation: Biophys J. 2002 Jan;82(1 Pt 1):160-9
references.pmid: 11751305
references.citation: Biophys J. 1999 Dec;77(6):3023-33
references.pmid: 10585924
references.citation: Cell. 1992 May 15;69(4):677-84
references.pmid: 1375130
references.citation: Phys Rev Lett. 1996 Jul 22;77(4):783-786
references.pmid: 10062901
references.citation: FEMS Microbiol Immunol. 1992 Sep;5(1-3):93-100
references.pmid: 1384601
references.citation: Biophys J. 2004 Sep;87(3):2086-97
references.pmid: 15345583
references.citation: Biophys J. 1999 Dec;77(6):3227-33
references.pmid: 10585944
references.citation: Biosci Rep. 1995 Dec;15(6):503-14
references.pmid: 9156580
references.citation: Phys Rev Lett. 1993 Apr 12;70(15):2352-2355
references.pmid: 10053539
references.citation: Proc Natl Acad Sci U S A. 1999 Jun 22;96(13):7262-4
references.pmid: 10377402
references.citation: Electrophoresis. 2002 May;23(10):1417-20
references.pmid: 12116151
references.citation: Proc Natl Acad Sci U S A. 1996 Nov 26;93(24):13770-3
references.pmid: 8943010
references.citation: Nano Lett. 2005 Oct;5(10):1883-8
references.pmid: 16218703
references.citation: J Chem Phys. 2004 Feb 15;120(7):3460-6
references.pmid: 15268503
references.citation: Nat Mater. 2004 Jun;3(6):355-6
references.pmid: 15173852
references.citation: Electrophoresis. 2002 Aug;23(16):2697-703
references.pmid: 12210174
references.citation: Cell. 1991 May 3;65(3):371-80
references.pmid: 1902142
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2005 May;71(5 Pt 1):051903
references.pmid: 16089567
references.citation: Biophys J. 1995 Jul;69(1):94-105
references.pmid: 7545444
references.citation: Nat Struct Biol. 2003 Jan;10(1):13-8
references.pmid: 12459720
references.citation: Phys Rev Lett. 2001 Apr 2;86(14):3188-91
references.pmid: 11290139
references.citation: Biophys J. 1999 Oct;77(4):1824-38
references.pmid: 10512806
references.citation: Phys Rev Lett. 2002 Dec 30;89(27):276106
references.pmid: 12513225
references.citation: Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 Jul;62(1 Pt B):927-39
references.pmid: 11088550
references.citation: Gen Physiol Biophys. 1993 Apr;12(2):95-111
references.pmid: 7691679
references.citation: Biophys J. 1999 Feb;76(2):837-45
references.pmid: 9929485
references.citation: Science. 1992 Oct 9;258(5080):307-10
references.pmid: 1384130
references.citation: Biophys J. 2005 Jun;88(6):3745-61
references.pmid: 15764651
references.citation: Nano Lett. 2005 Oct;5(10):1905-9
references.pmid: 16218707
references.citation: Science. 1996 Dec 13;274(5294):1859-66
references.pmid: 8943190
references.citation: Biophys J. 2004 Oct;87(4):2905-11
references.pmid: 15326034
references.citation: J Membr Biol. 1976 Dec 28;30(2):99-120
references.pmid: 1011248
references.citation: J Membr Biol. 1986;90(2):177-90
references.pmid: 2425095
references.citation: Phys Rev Lett. 2000 Oct 2;85(14):3057-60
references.pmid: 11006002
references.citation: J Biol Chem. 1997 Oct 3;272(40):25275-82
references.pmid: 9312144
references.citation: Biofizika. 2000 Jan-Feb;45(1):69-78
references.pmid: 10732213
references.citation: Angew Chem Int Ed Engl. 2004 Jun 7;43(23):3063-7
references.pmid: 15188482
references.citation: Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10445-50
references.pmid: 16020525
references.citation: Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 Nov;62(5 Pt B):7536-9
references.pmid: 11102127
references.citation: Biochem Soc Trans. 1998 Aug;26(3):S193
references.pmid: 9765912
references.citation: Science. 1998 Apr 3;280(5360):69-77
references.pmid: 9525859
references.citation: Langmuir. 2004 Feb 3;20(3):898-905
references.pmid: 15773121
references.citation: Nature. 1994 Jul 28;370(6487):279-81
references.pmid: 7518571
references.citation: J Struct Biol. 1998;121(2):110-22
references.pmid: 9615434
references.citation: Nature. 2001 Jul 12;412(6843):166-9
references.pmid: 11449268