DNA-length-dependent quenching of fluorescently labeled iron oxide nanoparticles with gold, graphene oxide and MoS2 nanostructures

ACS Applied Materials and Interfaces

Volumn 6, Issue 15, 2014, Pages 12100-12110

  Balcioglu, Mustafa ^a   Rana, Muhit ^a   Robertson, Neil ^a   Yigit, Mehmet V ^a,b  

^a STATE UNIVERSITY OF NEW YORK   (United States)

^b STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

DNA; gold; graphene oxide; iron oxide; nanoparticle

Indexed keywords

EFFICIENCY; FLUORESCENCE; GOLD; GRAPHENE; IRON OXIDES; METAL NANOPARTICLES; MOLECULES; MOLYBDENUM COMPOUNDS; NANOPARTICLES; NANOSTRUCTURES; OLIGONUCLEOTIDES; QUENCHING;

FLUORESCENCE EMISSION; FLUORESCENT NANOPARTICLES; GRAPHENE OXIDES; IRON OXIDE NANOPARTICLE; NANOPARTICLE SURFACE; QUENCHING EFFICIENCY; SINGLE-STRANDED DNA MOLECULES;

DNA;

CARBOCYANINE; CY5.5 CYANINE DYE; DNA; FERRIC ION; FERRIC OXIDE; GOLD; GRAPHITE; METAL NANOPARTICLE; OLIGONUCLEOTIDE; OXIDE; SINGLE STRANDED DNA;

ADSORPTION; CHEMISTRY; HYDRODYNAMICS; KINETICS; MATERIALS TESTING; NANOTECHNOLOGY; PARTICLE SIZE; SURFACE PROPERTY;

ADSORPTION; CARBOCYANINES; DNA; DNA, SINGLE-STRANDED; FERRIC COMPOUNDS; GOLD; GRAPHITE; HYDRODYNAMICS; KINETICS; MATERIALS TESTING; METAL NANOPARTICLES; NANOTECHNOLOGY; OLIGONUCLEOTIDES; OXIDES; PARTICLE SIZE; SURFACE PROPERTIES;

EID: 84906262912     PISSN: 19448244     EISSN: 19448252     Source Type: Journal    
DOI: 10.1021/am503553h     Document Type: Article

References (70)

1. Wei, Q.; Nagi, R.; Sadeghi, K.; Feng, S.; Yan, E.; Ki, S. J.; Caire, R.; Tseng, D.; Ozcan, A. Detection and Spatial Mapping of Mercury Contamination in Water Samples Using a Smart-Phone ACS Nano 2014, 8, 1121-1129
2. Hamner, K. L.; Maye, M. M. Thermal Aggregation Properties of Nanoparticles Modified with Temperature Sensitive Copolymers Langmuir 2013, 29, 15217-15223
3. Huang, H.; Song, W.; Chen, G.; Reynard, J. M.; Ohulchanskyy, T. Y.; Prasad, P. N.; Bright, F. V.; Lovell, J. F. Pd-Porphyrin-Cross-Linked Implantable Hydrogels with Oxygen-Responsive Phosphorescence Adv. Healthcare Mater. 2014, 3, 891-896
4. Liu, J. Adsorption of DNA onto Gold Nanoparticles and Graphene Oxide: Surface Science and Applications Phys. Chem. Chem. Phys. 2012, 14, 10485-10496
5. Piao, Y.; Liu, F.; Seo, T. S. A Novel Molecular Beacon Bearing a Graphite Nanoparticle as a Nanoquencher for in Situ mRNA Detection in Cancer Cells ACS Appl. Mater. Interfaces 2012, 4, 6785-6789
6. Li, J.-L.; Tang, B.; Yuan, B.; Sun, L.; Wang, X.-G. A Review of Optical Imaging and Therapy Using Nanosized Graphene and Graphene Oxide Biomaterials 2013, 34, 9519-9534
7. Morales-Narvaez, E.; Merkoci, A. Graphene Oxide as an Optical Biosensing Platform Adv. Mater. 2012, 24, 3298-3308
8. Yigit, M. V.; Zhu, L.; Ifediba, M. A.; Zhang, Y.; Carr, K.; Moore, A.; Medarova, Z. Noninvasive MRI-SERS Imaging in Living Mice Using an Innately Bimodal Nanomaterial ACS Nano 2010, 5, 1056-1066
9. Wang, P.; Yigit, M. V.; Medarova, Z.; Wei, L.; Dai, G.; Schuetz, C.; Moore, A. Combined Small Interfering RNA Therapy and in Vivo Magnetic Resonance Imaging in Islet Transplantation Diabetes 2011, 60, 565-571
10. Alexander, C. M.; Maye, M. M.; Dabrowiak, J. C. DNA-Capped Nanoparticles Designed for Doxorubicin Drug Delivery Chem. Commun. (Cambridge, U. K.) 2011, 47, 3418-3420
11. Alexander, C. M.; Dabrowiak, J. C.; Maye, M. M. Investigation of the Drug Binding Properties and Cytotoxicity of DNA-Capped Nanoparticles Designed as Delivery Vehicles for the Anticancer Agents Doxorubicin and Actinomycin D Bioconjugate Chem. 2012, 23, 2061-2070
12. Hamner, K. L.; Alexander, C. M.; Coopersmith, K.; Reishofer, D.; Provenza, C.; Maye, M. M. Using Temperature-Sensitive Smart Polymers to Regulate DNA-Mediated Nanoassembly and Encoded Nanocarrier Drug Release ACS Nano 2013, 7, 7011-7020
13. 3+ Ion Sensors ACS Appl. Mater. Interfaces 2012, 4, 5576-5582
14. Bunz, U. H.; Rotello, V. M. Gold Nanoparticle-Fluorophore Complexes: Sensitive and Discerning "Noses" for Biosystems Sensing Angew. Chem., Int. Ed. 2010, 49, 3268-3279
15. Xia, F.; Zuo, X.; Yang, R.; Xiao, Y.; Kang, D.; Vallee-Belisle, A.; Gong, X.; Yuen, J. D.; Hsu, B. B.; Heeger, A. J.; Plaxco, K. W. Colorimetric Detection of DNA, Small Molecules, Proteins, and Ions Using Unmodified Gold Nanoparticles and Conjugated Polyelectrolytes Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 10837-10841
16. Yang, L.; Liu, C.; Ren, W.; Li, Z. Graphene Surface-Anchored Fluorescence Sensor for Sensitive Detection of Microrna Coupled with Enzyme-Free Signal Amplification of Hybridization Chain Reaction ACS Appl. Mater. Interfaces 2012, 4, 6450-6453
17. Chou, S. S.; De, M.; Luo, J.; Rotello, V. M.; Huang, J.; Dravid, V. P. Nanoscale Graphene Oxide (nGO) as Artificial Receptors: Implications for Biomolecular Interactions and Sensing J. Am. Chem. Soc. 2012, 134, 16725-16733
18. Stobiecka, M.; Hepel, M. Multimodal Coupling of Optical Transitions and Plasmonic Oscillations in Rhodamine B Modified Gold Nanoparticles Phys. Chem. Chem. Phys. 2011, 13, 1131-1139
19. Li, H.; Rothberg, L. Colorimetric Detection of DNA Sequences Based on Electrostatic Interactions with Unmodified Gold Nanoparticles Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 14036-14039
20. Parak, W. J.; Pellegrino, T.; Micheel, C. M.; Gerion, D.; Williams, S. C.; Alivisatos, A. P. Conformation of Oligonucleotides Attached to Gold Nanocrystals Probed by Gel Electrophoresis Nano Lett. 2002, 3, 33-36
21. Dulkeith, E.; Ringler, M.; Klar, T. A.; Feldmann, J.; Munoz Javier, A.; Parak, W. J. Gold Nanoparticles Quench Fluorescence by Phase Induced Radiative Rate Suppression Nano Lett. 2005, 5, 585-589
22. Chhabra, R.; Sharma, J.; Wang, H.; Zou, S.; Lin, S.; Yan, H.; Lindsay, S.; Liu, Y. Distance-Dependent Interactions between Gold Nanoparticles and Fluorescent Molecules with DNA as Tunable Spacers Nanotechnology 2009, 20, 485201
23. Huang, P.-J. J.; Liu, J. DNA-Length-Dependent Fluorescence Signaling on Graphene Oxide Surface Small 2012, 8, 977-983
24. Mao, H. Y.; Laurent, S.; Chen, W.; Akhavan, O.; Imani, M.; Ashkarran, A. A.; Mahmoudi, M. Graphene: Promises, Facts, Opportunities, and Challenges in Nanomedicine Chem. Rev. 2013, 113, 3407-3424
25. Geim, A. K. Graphene: Status and Prospects Science 2009, 324, 1530-1534
26. Novoselov, K. S.; Geim, A. K.; Morozov, S. V.; Jiang, D.; Zhang, Y.; Dubonos, S. V.; Grigorieva, I. V.; Firsov, A. A. Electric Field Effect in Atomically Thin Carbon Films Science 2004, 306, 666-669
27. Geim, A. K.; Novoselov, K. S. The Rise of Graphene Nat. Mater. 2007, 6, 183-191
28. Chung, C.; Kim, Y. K.; Shin, D.; Ryoo, S. R.; Hong, B. H.; Min, D. H. Biomedical Applications of Graphene and Graphene Oxide Acc. Chem. Res. 2013, 46, 2211-2224
29. Rana, M.; Balcioglu, M.; Robertson, N.; Yigit, M. V. Nano-Graphene Oxide as a Novel Platform for Monitoring the Effect of LNA Modification on Nucleic Acid Interactions Analyst 2014, 139, 714-720
30. Li, S.; Aphale, A. N.; Macwan, I. G.; Patra, P. K.; Gonzalez, W. G.; Miksovska, J.; Leblanc, R. M. Graphene Oxide as a Quencher for Fluorescent Assay of Amino Acids, Peptides, and Proteins ACS Appl. Mater. Interfaces 2012, 4, 7069-7075
31. Balcioglu, M.; Rana, M.; Yigit, M. V. Doxorubicin Loading on Graphene Oxide, Iron Oxide and Gold Nanoparticle Hybrid J. Mater. Chem. B 2013, 1, 6187-6193
32. Li, F.; Pei, H.; Wang, L. H.; Lu, J. X.; Gao, J. M.; Jiang, B. W.; Zhao, X. C.; Fan, C. H. Nanomaterial-Based Fluorescent DNA Analysis: A Comparative Study of the Quenching Effects of Graphene Oxide, Carbon Nanotubes, and Gold Nanoparticles Adv. Funct. Mater. 2013, 23, 4140-4148
33. Wang, Y.; Li, Z.; Wang, J.; Li, J.; Lin, Y. Graphene and Graphene Oxide: Biofunctionalization and Applications in Biotechnology Trends Biotechnol. 2011, 29, 205-212
34. Fu, X.; Lou, T.; Chen, Z.; Lin, M.; Feng, W.; Chen, L. "Turn-on" Fluorescence Detection of Lead Ions Based on Accelerated Leaching of Gold Nanoparticles on the Surface of Graphene ACS Appl. Mater. Interfaces 2012, 4, 1080-1086
35. Liu, Y. M.; Punckt, C.; Pope, M. A.; Gelperin, A.; Aksay, I. A. Electrochemical Sensing of Nitric Oxide with Functionalized Graphene Electrodes ACS Appl. Mater. Interfaces 2013, 5, 12624-12630
36. He, Y.; Huang, G.; Cui, H. Quenching the Chemiluminescence of Acridinium Ester by Graphene Oxide for Label-Free and Homogeneous DNA Detection ACS Appl. Mater. Interfaces 2013, 5, 11336-11340
37. Shi, Y.; Yi, C.; Zhang, Z.; Zhang, H.; Li, M.; Yang, M.; Jiang, Q. Peptide-Bridged Assembly of Hybrid Nanomaterial and Its Application for Caspase-3 Detection ACS Appl. Mater. Interfaces 2013, 5, 6494-6501
38. Dey, R. S.; Raj, C. R. Redox-Functionalized Graphene Oxide Architecture for the Development of Amperometric Biosensing Platform ACS Appl. Mater. Interfaces 2013, 5, 4791-4798
39. Ryoo, S.-R.; Lee, J.; Yeo, J.; Na, H.-K.; Kim, Y.-K.; Jang, H.; Lee, J. H.; Han, S. W.; Lee, Y.; Kim, V. N.; Min, D.-H. Quantitative and Multiplexed Microrna Sensing in Living Cells Based on Peptide Nucleic Acid and Nano Graphene Oxide (Pango) ACS Nano 2013, 7, 5882-5891
40. Dong, H.; Ding, L.; Yan, F.; Ji, H.; Ju, H. The Use of Polyethylenimine-Grafted Graphene Nanoribbon for Cellular Delivery of Locked Nucleic Acid Modified Molecular Beacon for Recognition of Microrna Biomaterials 2011, 32, 3875-3882
41. Reed, J. C.; Zhu, H.; Zhu, A. Y.; Li, C.; Cubukcu, E. Graphene-Enabled Silver Nanoantenna Sensors Nano Lett. 2012, 12, 4090-4094
42. Tang, L.; Wang, Y.; Liu, Y.; Li, J. DNA-Directed Self-Assembly of Graphene Oxide with Applications to Ultrasensitive Oligonucleotide Assay ACS Nano 2011, 5, 3817-3822
43. Ryoo, S. R.; Lee, J.; Yeo, J.; Na, H. K.; Kim, Y. K.; Jang, H.; Lee, J. H.; Han, S. W.; Lee, Y.; Kim, V. N.; Min, D. H. Quantitative and Multiplexed Microrna Sensing in Living Cells Based on Peptide Nucleic Acid and Nano Graphene Oxide (Pango) ACS Nano 2013, 7, 5882-5891
44. Kim, H.; Namgung, R.; Singha, K.; Oh, I. K.; Kim, W. J. Graphene Oxide-Polyethylenimine Nanoconstruct as a Gene Delivery Vector and Bioimaging Tool Bioconjugate Chem. 2011, 22, 2558-2567
45. Xu, C.; Yang, D.; Mei, L.; Lu, B.; Chen, L.; Li, Q.; Zhu, H.; Wang, T. Encapsulating Gold Nanoparticles or Nanorods in Graphene Oxide Shells as a Novel Gene Vector ACS Appl. Mater. Interfaces 2013, 5, 2715-2724
46. Shen, H.; Liu, M.; He, H.; Zhang, L.; Huang, J.; Chong, Y.; Dai, J.; Zhang, Z. PEGylated Graphene Oxide-Mediated Protein Delivery for Cell Function Regulation ACS Appl. Mater. Interfaces 2012, 4, 6317-6323
47. Liu, H.; Si, M.; Deng, Y.; Neal, A. T.; Du, Y.; Najmaei, S.; Ajayan, P. M.; Lou, J.; Ye, P. D. Switching Mechanism in Single-Layer Molybdenum Disulfide Transistors: An Insight into Current Flow across Schottky Barriers ACS Nano 2014, 8, 1031-1038
48. 2-Based Nanoprobes for Homogeneous Detection of Biomolecules J. Am. Chem. Soc. 2013, 135, 5998-6001
49. Liu, T.; Wang, C.; Gu, X.; Gong, H.; Cheng, L.; Shi, X.; Feng, L.; Sun, B.; Liu, Z. Drug Delivery with PEGylated MoS Nano-Sheets for Combined Photothermal and Chemotherapy of Cancer Adv. Mater. 2014, 26, 3433-3440
50. Wei, Q.; Qi, H.; Luo, W.; Tseng, D.; Ki, S. J.; Wan, Z.; Gorocs, Z.; Bentolila, L. A.; Wu, T. T.; Ozcan, A. Fluorescent Imaging of Single Nanoparticles and Viruses on a Smart Phone ACS Nano 2013, 7, 9147-9155
51. Hennequin, Y.; Allier, C. P.; McLeod, E.; Mudanyali, O.; Migliozzi, D.; Ozcan, A.; Dinten, J. M. Optical Detection and Sizing of Single Nanoparticles Using Continuous Wetting Films ACS Nano 2013, 7, 7601-7609
52. Rana, M.; Balcioglu, M.; Yigit, M. V. Locked Nucleic Acid-Modified Antisense Mir-10b Oligonucleotides Form Stable Duplexes on Gold Nanoparticles Bionanoscience 2014, 4, 195-200
53. Swierczewska, M.; Lee, S.; Chen, X. The Design and Application of Fluorophore-Gold Nanoparticle Activatable Probes Phys. Chem. Chem. Phys. 2011, 13, 9929-9941
54. Ling, J.; Huang, C. Z. Energy Transfer with Gold Nanoparticles for Analytical Applications in the Fields of Biochemical and Pharmaceutical Sciences Anal. Methods 2010, 2, 1439-1447
55. Fan, C.; Wang, S.; Hong, J. W.; Bazan, G. C.; Plaxco, K. W.; Heeger, A. J. Beyond Superquenching: Hyper-Efficient Energy Transfer from Conjugated Polymers to Gold Nanoparticles Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 6297-6301
56. Tu, Y.; Wu, P.; Zhang, H.; Cai, C. Fluorescence Quenching of Gold Nanoparticles Integrating with a Conformation-Switched Hairpin Oligonucleotide Probe for Microrna Detection Chem. Commun. (Cambridge, U. K.) 2012, 48, 10718-10720
57. Acar, H.; Genc, R.; Urel, M.; Erkal, T. S.; Dana, A.; Guler, M. O. Self-Assembled Peptide Nanofiber Templated One-Dimensional Gold Nanostructures Exhibiting Resistive Switching Langmuir 2012, 28, 16347-16354
58. Han, H.; Valle, V.; Maye, M. M. Probing Resonance Energy Transfer and Inner Filter Effects in Quantum Dot-Large Metal Nanoparticle Clusters Using a DNA-Mediated Quench and Release Mechanism J. Phys. Chem. C 2012, 116, 22996-23003
59. Han, H.; Valle, V.; Maye, M. M. Probing the Quenching of CdSe/ZnS Qdots by Au, Au/Ag, and Au/Pd Nanoparticles Nanotechnology 2012, 23, 435401
60. Herne, T. M.; Tarlov, M. J. Characterization of DNA Probes Immobilized on Gold Surfaces J. Am. Chem. Soc. 1997, 119, 8916-8920
61. Tassa, C.; Shaw, S. Y.; Weissleder, R. Dextran-Coated Iron Oxide Nanoparticles: A Versatile Platform for Targeted Molecular Imaging, Molecular Diagnostics, and Therapy Acc. Chem. Res. 2011, 44, 842-852
62. Yigit, M. V.; Mazumdar, D.; Lu, Y. MRI Detection of Thrombin with Aptamer Functionalized Superparamagnetic Iron Oxide Nanoparticles Bioconjugate Chem. 2008, 19, 412-417
63. Yigit, M. V.; Mazumdar, D.; Kim, H. K.; Lee, J. H.; Odintsov, B.; Lu, Y. Smart "Turn-on" Magnetic Resonance Contrast Agents Based on Aptamer-Functionalized Superparamagnetic Iron Oxide Nanoparticles ChemBioChem 2007, 8, 1675-1678
64. Sulek, S.; Mammadov, B.; Mahcicek, D. I.; Sozeri, H.; Atalar, E.; Tekinay, A. B.; Guler, M. O. Peptide Functionalized Superparamagnetic Iron Oxide Nanoparticles as MRI Contrast Agents J. Mater. Chem. 2011, 21, 15157-15162
65. Yigit, M. V.; Moore, A.; Medarova, Z. Magnetic Nanoparticles for Cancer Diagnosis and Therapy Pharm. Res. 2012, 29, 1180-1188
66. Medarova, Z.; Pham, W.; Farrar, C.; Petkova, V.; Moore, A. In Vivo Imaging of siRNA Delivery and Silencing in Tumors Nat. Med. 2007, 13, 372-377
67. Pittet, M. J.; Swirski, F. K.; Reynolds, F.; Josephson, L.; Weissleder, R. Labeling of Immune Cells for in Vivo Imaging Using Magnetofluorescent Nanoparticles Nat. Protoc. 2006, 1, 73-79
68. Yigit, M. V.; Ghosh, S. K.; Kumar, M.; Petkova, V.; Kavishwar, A.; Moore, A.; Medarova, Z. Context-Dependent Differences in miR-10b Breast Oncogenesis Can Be Targeted for the Prevention and Arrest of Lymph Node Metastasis Oncogene 2013, 32, 1530-1538
69. Kumar, M.; Yigit, M.; Dai, G.; Moore, A.; Medarova, Z. Image-Guided Breast Tumor Therapy Using a Small Interfering RNA Nanodrug Cancer Res. 2010, 70, 7553-7561
70. Liu, J.; Lu, Y. Preparation of Aptamer-Linked Gold Nanoparticle Purple Aggregates for Colorimetric Sensing of Analytes Nat. Protoc. 2006, 1, 246-252