Ordered self-assembled locked nucleic acid (LNA) structures on gold(111) surface with enhanced single base mismatch recognition capability

Langmuir

Volumn 28, Issue 9, 2012, Pages 4325-4333

  Mishra, Sourav ^a   Ghosh, Srabani ^a   Mukhopadhyay, Rupa ^a  

^a DEPARTMENT OF MATERIALS SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMIC FORCE MICROSCOPIES (AFM); DETECTION CAPABILITY; DISCRIMINATION RATIO; DNA RECOGNITION; DNA TARGETS; HIGH RESOLUTION; IMMERSION METHOD; INCUBATION TIME; LOCKED NUCLEIC ACID; MOLECULAR ORDERING; MOLECULE SURFACE; NUCLEIC ACID-BASED BIOSENSORS; ORDERED ARRANGEMENT; ORIENTATIONAL TRANSITIONS; REFLECTION ABSORPTION; SELF-ASSEMBLED; SINGLE-BASE MISMATCH; SOLID SURFACE; TIME-SCALES;

ATOMIC FORCE MICROSCOPY; BIOSENSORS; GOLD; MOLECULES; MONOLAYERS;

DNA;

GOLD; NUCLEIC ACID;

ARTICLE; ATOMIC FORCE MICROSCOPY; CHEMISTRY;

GOLD; MICROSCOPY, ATOMIC FORCE; NUCLEIC ACIDS;

EID: 84857823743     PISSN: 07437463     EISSN: 15205827     Source Type: Journal    
DOI: 10.1021/la204026j     Document Type: Article

References (56)

1. Li, Z. H.; Hayman, R. B.; Walt, D. R. Detection of Single-Molecule DNA Hybridization Using Enzymatic Amplification in an Array of Femtoliter-Sized Reaction Vessels J. Am. Chem. Soc. 2008, 130, 12622
2. Kamahori, M.; Ishige, Y.; Shimoda, M. Detection of DNA hybridization and extension reactions by an extended-gate field-effect transistor: Characterizations of immobilized DNA-probes and role of applying a superimposed high-frequency voltage onto a reference electrode Biosens. Bioelectron. 2008, 23, 1046
3. Briones, C.; Marti, E. M.; Navarro, C. G.; Parro, V.; Roman, E.; Gago, J. A. M. Ordered Self-Assembled Monolayers of Peptide Nucleic Acids with DNA Recognition Capability Phys. Rev. Lett. 2004, 93, 208103
4. Berganza, J.; Olabarria, G.; Garcia, R.; Verdoy, D.; Rebollo, A.; Arana, S. DNA microdevice for electrochemical detection of Escherichia coli 0157:H7 molecular marker Biosens. Bioelectron. 2007, 22, 2132
5. Kwon, Y-W; Lee, C. H.; Choi, D-H; Jin, J. I. Materials science of DNA J Mater. Chem. 2009, 19, 1353
6. Arya, S. K.; Solanki, P. R.; Datta, M.; Malhotra, B. D. Recent advances in self-assembled monolayers based biomolecular electronic device Biosens. Bioelectron. 2009, 24, 2810
7. Sharma, J.; Chhabra, R.; Andersen, C. S.; Gothelf, K. V.; Yan, H.; Liu, Y. Toward Reliable Gold Nanoparticle Patterning On Self-Assembled DNA Nanoscaffold J. Am. Chem. Soc. 2008, 130, 7820
8. Love, J. C.; Estroff, L. A.; Kriebel, J. K.; Nuzzo, R. G.; Whitesides, G. M. Self-Assembled Monolayers of Thiolates on Metals as a Form of Nanotechnology Chem. Rev. 2005, 105, 1103
9. Lang, H. P.; Hegner, M.; Meyer, E.; Gerber, Ch. Nanomechanics from atomic resolution to molecular recognition based on atomic force microscopy technology Nanotechnology 2002, 13, R29-R36
10. Liu, M.; Amro, N. A.; Chow, C. S.; Liu, G. Production of Nanostructures of DNA on Surfaces Nano Lett. 2002, 2, 863
11. Kasemo, B. Biological surface science Surf. Sci. 2002, 500, 656
12. Herne, T. M.; Tarlov, M. J. Characterization of DNA Probes Immobilized on Gold Surfaces J. Am. Chem. Soc. 1997, 119, 8916
13. Levicky, R.; Herne, T. M.; Tarlov, M. J.; Satija, S. K. Using Self-Assembly To Control the Structure of DNA Monolayers on Gold: A Neutron Reflectivity Study J. Am. Chem. Soc. 1998, 120, 9787
14. Steel, A. B.; Herne, T. M.; Tarlov, M. J. Electrochemical Quantitation of DNA Immobilized on Gold Anal. Chem. 1998, 70, 4670
15. Mourougou-Candoni, N.; Naud, C.; Thibaudau, F. Adsorption of Thiolated Oligonucleotides on Gold Surfaces: An Atomic Force Microscopy Study Langmuir 2003, 19, 682
16. Wang, H.; Tang, Z.; Li, Z.; Wang, E. Self-assembled monolayer of ssDNA on Au(111) substrate Surf. Sci. 2001, 480, L389
17. Casero, E.; Darder, M.; Díaz, D. J.; Pariente, F.; Martín-Gago, J. A.; Abruna, H.; Lorenzo, E. XPS and AFM Characterization of Oligonucleotides Immobilized on Gold Substrates Langmuir 2003, 19, 6230
18. Singh, S. K.; Nielsen, P.; Koshkin, A. A.; Wengel, J. LNA (locked nucleic acids): synthesis and high-affinity nucleic acid recognition Chem. Commun. 1998, 455
19. Koshkin, A. A.; Nielsen, P.; Meldgaard, M.; Rajwanshi, V. K.; Singh, S. K.; Wengel, J. LNA (Locked Nucleic Acid): An RNA Mimic Forming Exceedingly Stable LNA:LNA Duplexes J. Am. Chem. Soc. 1998, 120, 13252
20. Vester, B.; Wengel, J. LNA (Locked Nucleic Acid): High-Affinity Targeting of Complementary RNA and DNA Biochemistry 2004, 43, 13233
21. Kurreck, J.; Wyszko, E.; Gillen, C.; Erdmann, V. A. Design of antisense oligonucleotides stabilized by locked nucleic acids Nucleic Acids Res. 2002, 30, 1911
22. Martinez, K.; Estevez, M. -C.; Wu, Y.; Phillips, J. A.; Medley, C. D.; Tan, W. Locked Nucleic Acid Based Beacons for Surface Interaction Studies and Biosensor Development Anal. Chem. 2009, 81, 3448
23. Pande, V.; Nilsson, L. Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations Nucleic Acids Res. 2008, 36, 1508
24. Ugozzoli, L. A.; Latorra, D.; Pucket, R.; Arar, K.; Hamby, K. Real-time genotyping with oligonucleotide probes containing locked nucleic acids Anal. Biochem. 2004, 324, 143
25. Fritz, J.; Baller, M. K.; Lang, H. P.; Rothuizen, H.; Vettiger, P.; Meyer, E.; Güntherodt, H.-J.; Gerber, Ch.; Gimzewski, J. K. Translating Biomolecular Recognition into Nanomechanics Science 2000, 288, 316
26. Mukhopadhyay, R.; Lorentzen, M.; Kjems, J.; Besenbacher, F. Nanomechanical Sensing of DNA Sequences Using Piezoresistive Cantilevers Langmuir 2005, 21, 8400
27. Drummond, T. G.; Hill, M. G.; Barton, J. K. Electrochemical DNA sensors Nat. Biotechnol. 2003, 21, 1192
28. Hansen, J. A.; Mukhopadhyay, R.; Hansen, J. O.; Gothelf, K. V. Femtomolar Electrochemical Detection of DNA Targets Using Metal Sulfide Nanoparticles J. Am. Chem. Soc. 2006, 128, 3860
29. Sanborn, M. E.; Connolly, B. K.; Gurunathan, K.; Levitus, M. Fluorescence Properties and Photophysics of the Sulfoindocyanine Cy3 Linked Covalently to DNA J. Phys. Chem. B 2007, 111, 11064
30. Jia, K.; Wan, Y.; Xia, A.; Li, S.; Gong, F.; Yang, G. Characterization of Photoinduced Isomerization and Intersystem Crossing of the Cyanine Dye Cy3 J. Phys. Chem. A 2007, 111, 1593
31. Nuzzo, R. G.; Allara, D. L. Adsorption of Bifunctional Organic Disulfides on Gold Surfaces J. Am. Chem. Soc. 1983, 105, 4481
32. Ghosh, S.; Mukhopadhyay, R. An atomic force microscopy investigation on self-assembled peptide nucleic acid structures on gold(111) surface J. Colloid Interface Sci. 2011, 360, 52
33. Young, J. T.; Boerio, F. J.; Zhang, Z.; Beck, T. L. Molecular Structure of Monolayers from Thiol-Terminated Polyimide Model Compounds on Gold. 1. A Spectroscopic Investigation Langmuir 1996, 12, 1219
34. Trenary, M. Reflection Absorption Infrared Spectroscopy and the Structure of Molecular Adsorbates on Metal Surfaces Annu. Rev. Phys. Chem. 2000, 51, 381
35. Silverstein, R.; Webster, F. Spectroscopic Identification of Organic Compounds, 6 th ed.; John Wiley & Sons Inc: New York, 2006; Chapter 3.
36. Banyay, M.; Sarkar, M.; Gräslund, A. A library of IR bands of nucleic acids in solution Biophys. Chem. 2003, 104, 477
37. Ihs, A.; Liedberg, B. Chemisorption of L-Cysteine and 3-Mercaptopropionic Acid on Gold and Copper Surfaces: An Infrared Reflection-Absorption Study J. Colloid Interface Sci. 1991, 144, 282
38. Manna, A.; Imae, T.; Yogo, T.; Aoi, K.; Okazaki, M. Synthesis of Gold Nanoparticles in a Winsor II Type Microemulsion and Their Characterization J. Colloid Interface Sci. 2002, 256, 297
39. Wang, Z.; Liu, D.; Dong, S. In-situ FTIR study on adsorption and oxidation of native and thermally denatured calf thymus DNA at glassy carbon electrodes Biophys. Chem. 2001, 89, 87
40. Yamada, T.; Shirasaka, K.; Takano, A.; Kawai, M. Adsorption of cytosine, thymine, guanine and adenine on Cu(1 1 0) studied by infrared reflection absorption spectroscopy Surf. Sci. 2004, 561, 233
41. Mateo-Martí, E.; Briones, C.; Pradier, C. M.; Martín-Gago, J. A. A DNA biosensor based on peptide nucleic acids on gold surfaces Biosens. Bioelectron. 2007, 22, 1926
42. Petrovykh, D. Y.; Kimura-Suda, H.; Whitman, L. J.; Tarlov, M. J. Quantitative Analysis and Characterization of DNA Immobilized on Gold J. Am. Chem. Soc. 2003, 125, 5219
43. 8 Spectrochim. Acta 1991, 47A, 177
44. Shimanouchi, T.; Tsuboi, M.; Kyogoku, Y. In The Structure and Properties of Biomolecules and Biological Systems, Advances in Chemical Physics; Duchesne, J., Eds.; Interscience: London, 1964; p 435.
45. Tsuboi, M. In Applied Spectroscopy Reviews; Brame, E. G. J., Eds.; Dekker: New York, 1969; p 45.
46. Taillandier, E.; Liquier, J. Infrared spectroscopy of DNA Methods Enzymol. 1992, 211, 307
47. Liquier, J.; Taillandier, E. In Infrared Spectroscopy of Biomolecules; Mantsch, H. H.; Chapman, D., Eds.; Wiley-Liss, Inc: New York, 1996; p 131.
48. 2 double helix studied by FT-i.r. spectroscopy Spectrochim. Acta 1990, 46A, 107
49. Pohle, W.; Fritzsche, H. A new conformation-specific infrared band of A-DNA in films Nucleic Acids Res. 1980, 8, 2527
50. Okahata, Y.; Kawase, M.; Niikura, K.; Ohtake, F.; Furusawa, H.; Ebara, Y. Kinetic Measurements of DNA Hybridization on an Oligonucleotide-Immobilized 27-MHz Quartz Crystal Microbalance Anal. Chem. 1998, 70, 1288
51. Demers, L. M.; Mirkin, C. A.; Mucic, R. C.; Reynolds, R. A.; Letsinger, R. L.; Elghanian, R.; Viswanadham, G. A Fluorescence-Based Method for Determining the Surface Coverage and Hybridization Efficiency of Thiol-Capped Oligonucleotides Bound to Gold Thin Films and Nanoparticles Anal. Chem. 2000, 72, 5535
52. Braasch, D. A.; Corey, D. R. Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA Chem. Biol. 2001, 8, 1
53. Schwartz, D. K. Mechanisms and Kinetics of Self-Assembled Monolayer Formation Annu. Rev. Phys. Chem. 2001, 52, 107
54. You, Y.; Moreira, B. G.; Behlke, M. A.; Owczarzy, R. Design of LNA probes that improve mismatch Discrimination Nucleic Acids Res. 2006, 34, e60
55. Lee, C. Y.; Gong, P.; Harbers, G. M.; Grainger, D. W.; Castner, D. G.; Gamble, L. J. Surface Coverage and Structure of Mixed DNA/Alkylthiol Monolayers on Gold: Characterization by XPS, NEXAFS, and Fluorescence Intensity Measurements Anal. Chem. 2006, 78, 3316
56. Wackerbarth, H.; Grubb, M.; Wengel, J.; Chorkendorff, Ib.; Ulstrup, J. Adsorption and surface dynamics of short DNA and LNA oligonucleotides on single-crystal Au(111) electrode surfaces Surf. Sci. 2006, 600, L122