Electronic control of DNA polymerase binding and unbinding to single DNA molecules

ACS Nano

Volumn 3, Issue 4, 2009, Pages 995-1003

  Wilson, Noah A ^a   Abu Shumays, Robin ^a   Gyarfas, Brett ^a   Wang, Hongyun ^a   Lieberman, Kate R ^a   Akeson, Mark ^a   Dunbar, William B ^a  

^a University of California Santa Cruz   (United States)

Author keywords

Active control; Alpha hemolysin; Dna binding proteins; Klenow fragment; Nanopore; Single molecule

Indexed keywords

ACTIVE CONTROL; ALPHA-HEMOLYSIN; DNA-BINDING PROTEINS; KLENOW FRAGMENT; SINGLE MOLECULE;

AVIATION; BLOOD; CATALYSTS; CONTROL SYSTEM ANALYSIS; DNA; ELECTRIC POTENTIAL; ELECTRONICS INDUSTRY; ENZYMES; ESCHERICHIA COLI; GENES; MOLECULES; NANOPORES; POLYMERS; POWER ELECTRONICS; RNA; SUBSTRATES; VOLTAGE REGULATORS;

NUCLEIC ACIDS;

BACTERIAL TOXIN; DNA; DNA DIRECTED DNA POLYMERASE; DNA DIRECTED DNA POLYMERASE BETA; HEMOLYSIN; NANOMATERIAL; STAPHYLOCOCCAL ALPHA-TOXIN; STAPHYLOCOCCUS ALPHA TOXIN;

ARTICLE; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; MACROMOLECULE; METABOLISM; MOLECULAR GENETICS; NANOTECHNOLOGY; NUCLEOTIDE SEQUENCE; STATIC ELECTRICITY;

BACTERIAL TOXINS; BASE SEQUENCE; DNA; DNA POLYMERASE I; DNA-DIRECTED DNA POLYMERASE; HEMOLYSIN PROTEINS; MACROMOLECULAR SUBSTANCES; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NANOSTRUCTURES; NANOTECHNOLOGY; STATIC ELECTRICITY;

EID: 66949130341     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn9000897     Document Type: Article

References (18)

1. Joyce, C. M.; Steitz, T. A. Function and Structure Relationships in DNA Polymerases. Anal. Rev. Bio Chem. 1994, 63, 777-822.
2. Joyce, C. M.; Benkovic, S. J. DNA Polymerase Fidelity: Kinetics, Structure, and Checkpoints. Biochemistry 2004, 43, 14317-24.
3. Brautigam, C. A.; Steitz, T. A. Structural and Functional Insights Provided by Crystal Structures of DNA Polymerases and their Substrate Complexes. Curr. Opin. Struct. Biol. 1998, 8, 54-63.
4. Joyce, C. M.; Potapova, O.; Delucia, A.; Huang, X.; Basu, V.; Grindley, N. D. F. Fingers-Closing and Other Rapid Conformational Changes in DNA Polymerase I (Klenow Fragment) and Their Role in Nucleotide Selectivity. Biochemistry 2008, 47, 6103-16.
5. Doublie, S.; Tabor, S.; Long, A. M.; Richardson, C. C.; Ellenberger, T. Crystal Structure of a Bacteriophage T7 DNA Replication Complex at 2.2 Å Resolution. Nature (London) 1998, 391, 251-8.
6. Johnson, S. J.; Taylor, J. S.; Beese, L. S. Processive DNA Synthesis Observed in a Polymerase Crystal Suggests a Mechanism for the Prevention of Frameshift Mutations. Proc. Natl. Acad. Sci. USA. 2003, 100, 3895-900.
7. Li, Y.; Korolev, S.;Waksman, G. Crystal Structures of Open and Closed Forms of Binary and Ternary Complexes of the Large Fragment of Thermus Aquaticus DNA Polymerase I: Structural Basis for Nucleotide Incorporation. EMBO J. 1998, 17, 7514-25.
8. Cockroft, S. L.; Chu, J.; Amorin, M.; Ghadiri, M. R. A Single-Molecule Nanopore Device Detects DNA Polymerase Activity with Single-Nucleotide Resolution. J. Am. Chem. Soc. 2008, 130, 818-20.
9. Benner, S.; Chen, R. J. A.; Wilson, N. A.; Abu-Shumays, R.; Hurt, N.; Lieberman, K. R.; Deamer, D. W.; Dunbar, W. B.; Akeson, M. Sequence-Specific Detection of Individual DNA Polymerase Complexes in Real Time Using a Nanopore. Nat. Nanotechnol. 2007, 2, 718-24.
10. Hornblower, B.; Coombs, A.; Whitaker, R.; Kolomeisky, A.; Picone, S.; Meller, A.; Akeson, M. Single-Molecule Analysis of DNA-Protein Complexes Using Nanopores. Nat. Methods 2007, 4, 315-7.
11. Abbondanzieri, E. A.; Greenleaf, W. J.; Shaevitz, J. W.; Landick, R.; Block, S. M. Direct Observation of Base-Pair Stepping by RNA Polymerase. Nature (London) 2005, 438, 460-5.
12. Vercoutere, W.; Akeson, M. Biosensors for DNA Sequence Detection. Curr. Opin. Chem. Biol. 2002, 6, 816-22.
13. Song, L.; Hobaugh, M. R.; Shustak, C.; Cheley, S.; Bayley, H.; Gouaux, J. E. Structure of Staphylococcal Alpha-Hemolysin, a Heptameric Transmembrane Pore. Science 1996, 274, 1859-66.
14. Tropini, C.; Marziali, A. Multi-Nanopore Force Spectroscopy for DNA Analysis. Biophys. J. 2007, 92, 1632-7.
15. Hurt, N.; Wang, H.; Akeson, M.; Lieberman, K. R. Specific Nucleotide Binding and Rebinding to Individual DNA Polymerase Complexes Captured on a Nanopore. J. Am. Chem. Soc. 2009, 131, 3772-78.
16. Dahlberg, M. E.; Benkovic, S. J. Kinetic Mechanism of DNA Polymerase I (Klenow Fragment) : Identification of a Second Conformational Change and Evaluation of the Internal Equilibrium Constant. Biochemistry 1991, 30, 4835-43.
17. Gill, A. Introduction to the Theory of Finite-state Machines; McGraw-Hill: New York, 1962.
18. Trimberger, S. M. Field-Programmable Gate Array Technology; Springer: New York, 1994.