Probing mercury(II)-DNA interactions by nanopore stochastic sensing

Journal of Physical Chemistry B

Volumn 117, Issue 17, 2013, Pages 4763-4769

  Wang, Guihua ^a   Zhao, Qitao ^b   Kang, Xiaofeng ^c   Guan, Xiyun ^a  

^a Illinois Institute of Technology   (United States)

^b UNIVERSITY OF TEXAS AT ARLINGTON   (United States)

^c NORTHWEST UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

LEAD; MERCURY COMPOUNDS; METAL IONS; NANOPORES; SENSORS;

DETECTION LIMITS; DNA INTERACTION; HAIRPIN STRUCTURES; ION CHANNEL; MERCURIC IONS; MERCURY DETECTION; ORDERS OF MAGNITUDE; STEM LENGTH;

DNA;

EID: 84877077146     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp309541h     Document Type: Article

References (60)

1. Weaver, D. T.; DePamphilis, M. L. The Role of Palindromic and Non-palindromic Sequences in Arresting DNA Synthesis in Vitro and in Vivo J. Mol. Biol. 1984, 180, 961-986
2. Ma, H.; Wan, C.; Wu, A.; Zewail, A. H. DNA Folding and Melting Observed in Real Time Redefine the Energy Landscape Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 712-716
3. Dai, X.; Greizerstein, M. B.; Nadas-Chinni, K.; Rothman-Denes, L. B. Supercoil-Induced Extrusion of a Regulatory DNA Hairpin Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 2174-2179
4. Schoen, I.; Krammer, H.; Braun, D. Hybridization Kinetics is Different inside Cells Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 21649-21654
5. Makovets, S.; Blackburn, E. H. DNA Damage Signaling Prevents Deleterious Telomere Addition at DNA Breaks Nat. Cell Biol. 2009, 11, 1383-1386
6. Mandal, P. K.; Blanpain, C.; Rossi, D. J. DNA Damage Response in Adult Stem Cells: Pathways and Consequences Nat. Rev. Mol. Cell Biol. 2011, 12, 198-202
7. Tullius, T. D. Metals and Molecular Biology. In Metal-DNA Chemistry; Tullius, T. D., Ed.; ACS Symposium Series; American Chemical Society: Washington, DC, 1989; Vol. 402, Chapter 1, pp 1-23.
8. Dubyak, G. R. Ion Homeostasis, Channels, and Transporters: An Update on Cellular Mechanisms Adv. Physiol. Educ. 2007, 28, 143-154
9. Müller, J. Functional Metal Ions in Nucleic Acids Metallomics 2010, 2, 318-327
10. Rönnbäck, L.; Hansson, E. Chronic Encephalopathies Induced by Mercury or Lead: Aspects of Underlying Cellular and Molecular Mechanisms Br. J. Ind. Med. 1992, 49, 233-240
11. Gray, H. B. Biological Inorganic Chemistry at the Beginning of the 21st Century Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 3563-3568
12. Ma, H.; Wan, C.; Zewail, A. H. Dynamics of Ligand Substitution in Labile Cobalt Complexes Resolved by Ultrafast T-Jump Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 12754-12757
13. Lippard, S. J. The Inorganic Side of Chemical Biology Nat. Chem. Biol. 2006, 2, 504-507
14. Hud, N. V. Nucleic Acid-Metal Ion Interactions; Royal Society of Chemistry: Cambridge, UK, 2009; pp 75-112.
15. Predki, P. F.; Sarkars, B. Effect of Replacement of "Zinc Finger" Zinc on Estrogen Receptor DNA Interactions J. Biol. Chem. 1992, 267, 5842-5846
16. Palmiter, R. D. The Elusive Function of Metallothioneins Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 8428-8430
17. Rothemund, P. W. K. Folding DNA to Create Nanoscale Shapes and Patterns Nature 2006, 440, 297-302
18. Kalek, M.; Andreas, S. M.; Wengel, J. Effective Modulation of DNA Duplex Stability by Reversible Transition Metal Complex Formation in the Minor Groove J. Am. Chem. Soc. 2007, 129, 9392-9400
19. Tanaka, K.; Tengeiji, A.; Kato, T.; Toyama, N.; Shionoya, M. A Discrete Self-Assembled Metal Array in Artificial DNA Science 2003, 299, 1212-1213
20. Kwon, Y.; Lee, C. H.; Choi, D.; Jin, J. Materials Science of DNA J. Mater. Chem. 2009, 19, 1353-1380
21. Liu, Z.; Tan, C.; Guo, X.; Kao, Y.-T.; Li, J.; Wang, L.; Sancar, A.; Zhong, D. Dynamics and Mechanism of Cyclobutane Pyrimidine Dimer Repair by DNA Photolyase Proc. Natl. Acad. Sci. U.S.A. 2011, 10.1073/pnas.1110927108
22. Kim, J.; Doose, S.; Neuweiler, H.; Sauer, M. The Initial Step of DNA Hairpin Folding: A Kinetic Analysis Using Fluorescence Correlation Spectroscopy Nucleic Acids Res. 2006, 34, 2516-2527
23. Orden, A. V.; Jung, J. Review Fluorescence Correlation Spectroscopy for Probing the Kinetics and Mechanisms of DNA Hairpin Formation Biopolymers 2007, 89, 1-16
24. Wagenknecht, H. Fluorescent DNA Base Modifications and Substitutes: Multiple Fluorophore Labeling and the DETEQ Concept Ann. N.Y. Acad. Sci. 2008, 1130, 122-130
25. Hud, N. V. Nucleic Acid-Metal Ion Interactions; Royal Society of Chemistry: Cambridge, UK, 2009; pp 154-175.
26. Bustamante, C. Direct Observation and Manipulation of Single DNA Molecules Using Fluorescence Microscopy Annu. Rev. Biophys. Biophys. Chem. 1991, 20, 415-446
27. Fan, H. Y.; Shek, Y. L.; Amiri, A.; Dubins, D. N.; Heerklotz, H.; Macgregor, R. B., Jr.; Chalikian, T. V. Volumetric Characterization of Sodium-Induced G-Quadruplex Formation J. Am. Chem. Soc. 2011, 133, 4518-4526
28. Mao, X.; Gmeiner, W. H. NMR Study of the Folding-Unfolding Mechanism for the Thrombin-Binding DNA Aptamer d(GGTTGGTGTGGTTGG) Biophys. Chem. 2005, 113, 155-160
29. Schmeing, T. M.; Ramakrishnan, V. What Recent Ribosome Structures Have Revealed about the Mechanism of Translation Nature 2009, 461, 1234-1242
30. Derrington, I. M.; Butler, T. Z.; Collins, M. D.; Manrao, E.; Pavlenok, M.; Niederweis, M.; Gundlach, J. H. Nanopore DNA Sequencing with MspA Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 16060-16065
31. Venkatesan, B. M.; Bashir, R. Nanopore Sensors for Nucleic Acid Analysis Nat. Nanotechnol. 2012, 7, 615-624
32. Kasianowicz, J. J.; Brandin, E.; Branton, D.; Deamer, D. W. Characterization of Individual Polynucleotide Molecules Using a Membrane Channel Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 13770-13773
33. Sutherland, T. C.; Dinsmore, M. J.; Kraatz, H.-B.; Lee, J. S. An Analysis of Mismatched Duplex DNA Unzipping through a Bacterial Nanopore Biochem. Cell Biol. 2004, 82, 407-412
34. Howorka, S.; Cheley, S.; Bayley, H. Sequence-Specific Detection of Individual DNA Strands Using Engineered Nanopores Nat. Biotechnol. 2001, 19, 636-639
35. Howorka, S.; Siwy, Z. Nanopore Analytics: Sensing of Single Molecules Chem. Soc. Rev. 2009, 38, 2360-84
36. Deamer, D. Nanopore Analysis of Nucleic Acids Bound to Exonucleases and Polymerases Annu. Rev. Biophys. 2010, 39, 79-90
37. Jetha, N. N.; Wiggin, M.; Marziali, A. Forming an α-Hemolysin Nanopore for Single-Molecule Analysis Methods Mol. Biol. 2009, 544, 113-27
38. Healy, K. Nanopore-Based Single-Molecule DNA Analysis Nanomedicine 2007, 2, 459-81
39. Efcavitch, J. W.; Thompson, J. F. Single-Molecule DNA Analysis Annu. Rev. Anal. Chem. 2010, 3, 109-28
40. Song, L. Z.; Hobaugh, M. R.; Shustak, C.; Cheley, S.; Bayley, H.; Gouaux, J. E. Structure of Staphylococcal α-Hemolysin, a Heptameric Transmembrane Pore Science 1996, 274, 1859
41. Cheley, S.; Braha, O.; Lu, X.; Conlan, S.; Bayley, H. A Functional Protein Pore with a "Retro" Transmembrane Domain Protein Sci. 1999, 8, 1257
42. Andrews, P. Estimation of Molecular Size and Molecular Weights of Biological Compounds by Gel Filtration Methods Biochem. Anal. 1970, 18, 1-53
43. Montal, M.; Mueller, P. Formation of Bimolecular Membranes from Lipid Monolayers and a Study of Their Electrical Properties Proc. Natl. Acad. Sci. U.S.A. 1972, 69, 3561-3566
44. Zuker, M. Mfold Web Server for Nucleic Acid Folding and Hybridization Prediction Nucleic Acids Res. 2003, 31, 3406-3415
45. Movileanu, L.; Schmittschmitt, J. P.; Scholtz, J. M.; Bayley, H. Interactions of Peptides with a Protein Pore Biophys. J. 2005, 89, 1030-1045
46. Stalling, R. L.; Torney, D. C.; Hildebrand, C. E.; Longmire, J. L.; Deaven, L. L.; Jett, J. H.; Doggett, N. A.; Moyzis, R. K. Physical Mapping of Human Chromosomes by Repetitive Sequence Fingerprinting Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 6128-6222
47. Lin, C. T.; Lin, W. H.; Lyu, Y. L.; Whang-Peng, J. Inverted Repeats as Genetic Elements for Promoting DNA Inverted Duplication: Implications in Gene Amplification Nucleic Acids Res. 2001, 29, 3529-3538
48. Liu, G.; Chen, X.; Bissler, J. J.; RSinden, R.; Leffak, M. Replication-Dependent Instability at (CTG)·(CAG) Repeat Hairpins in Human Cells Nat. Chem. Biol. 2010, 6, 652-659
49. Voineagu, I.; Narayanan, V.; Lobachev, K. S.; Mirkin, S. M. Replication Stalling at Unstable Inverted Repeats: Interplay between DNA Hairpins and Fork Stabilizing Proteins Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 9936-9941
50. Pendergrass, J. C.; Haley, B. E.; Vimy, M. J.; Winfield, S. A.; Lorscheider, F. L. Mercury Vapor Inhalation Inhibits Binding of GTP to Tubulin in Rat Brain: Similarity to a Molecular Lesion in Alzheimer Diseased Brain Neurotoxicology 1997, 18, 315-324
51. Crespo-López, M. E.; Maceîdo, G. L.; Pereira, S. I.; Arrifano, G. P.; Picanço-Diniz, D. L.; do Nascimento, J. L.; Herculano, A. M. Mercury and Human Genotoxicity: Critical Considerations and Possible Molecular Mechanisms Pharmacol. Res. 2009, 60, 212-220
52. Kingman, A.; Albertini, T.; Brown, L. J. Mercury Concentrations in Urine and Whole Blood Associated with Amalgam Exposure in a US Military Population J. Dent. Res. 1998, 77, 461-71
53. Davison, A.; Leach, D. R. F. Two-Base DNA Hairpin-Loop Structures in Vivo Nucleic Acids Res. 1994, 22, 4361-4363
54. Vercoutere, W.; Winters-Hilt, S.; Olsen, H.; Deamer, D.; Haussler, D.; Akeson, M. Rapid Discrimination among Individual DNA Hairpin Molecules at Single-Nucleotide Resolution Using an Ion Channel Nat. Biotechnol. 2001, 19, 248-52
55. Liu, A.; Zhao, Q.; Krishantha, D. M.; Guan, X. Unzipping of Double-Stranded DNA in Engineered α-Hemolysin Pores J. Phys. Chem. Lett. 2011, 12, 1372-1376
56. Kuklenyik, Z.; Marzilli, L. G. Mercury(II) Site-Selective Binding to a DNA Hairpin. Relationship of Sequence-Dependent Intra- and Interstrand Cross-Linking to the Hairpin-Duplex Conformational Transition Inorg. Chem. 1996, 35, 5654-5662
57. 2+-Modulated G-Quadruplex-Based DNAzymes Anal. Chem. 2009, 81, 2144-2149
58. 2+ Ions by Oligonucleotide-Gold-Nanoparticle Hybrids and DNA-Based Machines Angew. Chem., Int. Ed. Engl. 2008, 47, 3927-3931
59. Wen, S.; Zeng, T.; Liu, L.; Zhao, K.; Zhao, Y.; Liu, X.; Wu, H. C. Highly Sensitive and Selective DNA-Based Detection of Mercury(II) with α-Hemolysin Nanopore J. Am. Chem. Soc. 2011, 133, 18312-18317
60. de Zoysa, R. S.; Krishantha, D. M.; Zhao, Q.; Gupta, J.; Guan, X. Translocation of Single-Stranded DNA through the α-Hemolysin Protein Nanopore in Acidic Solutions Electrophoresis 2011, 32, 3034-3041