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Gold Nanoparticle Based FRET for DNA Detection

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Abstract

The nanoscience revolution that sprouted throughout the 1990s is having great impact in current and future DNA detection technology around the world. In this review, we report our recent progress on gold nanoparticle based fluorescence resonance energy transfer assay to monitor DNA hybridization as well as the cleavage of DNA by nucleases. We tried to discuss a reasonable account of the science and the important fundamental work carried out in this area. We also report the development of a compact, highly specific, inexpensive and user-friendly optical fiber laser-induced fluorescence sensor based on fluorescence quenching by nanoparticles to detect single-strand DNA hybridization at femtomolar level.

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References

  1. Wang J (2000) From DNA biosensors to gene chips. Nucleic Acids Res 28:3011–3016

    Article  CAS  Google Scholar 

  2. Umek RM, Lin SW, Vielmetter J, Terbrueggen RH, Irvine B, Yu CJ, Kayyem JF, Yowanto H, Blackburn GF, Farkas DH, Chen YP (2001) Electronic detection of nucleic acids: a versatile platform for molecular diagnostics. J Mol Diagnostics 3:74–84

    CAS  Google Scholar 

  3. Heller MJ (2002) DNA microarray technology: devices, systems, and applications. Annu Rev Biomed Eng 4:129–153

    Article  CAS  Google Scholar 

  4. Schork NJ, Fallin D, Lanchbury JS (2000) Single nucleotide polymorphisms and the future of genetic epidemiology. Clin Genet 58:250–264

    Article  CAS  Google Scholar 

  5. Balakin KV, Korshun VA, Mikhalev II, Maleev GV, Malakhov AD, Prokhorenko IA, Berlin YA (1998) Conjugates of oligonucleotides with polyaromatic fluorophores as promising DNA probes. Biosens Bioelectron 13:771–778

    Article  CAS  Google Scholar 

  6. Cao YWC, Jin RC, Mirkin CA (2002) Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection. Science 297:1536–1540

    Article  CAS  Google Scholar 

  7. Mirkin CA, Letsinger RL, Mucic RC, Storhoff JJ (1996) A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 382:607–610

    Article  CAS  Google Scholar 

  8. Nie S, Emory SR (1997) Probing single molecules and single nanoparticles by surface-enhanced raman scattering. Science 275:1102–1104

    Article  CAS  Google Scholar 

  9. Sato K, Hosokawa K, Maeda M (2003) Rapid aggregation of gold nanoparticles induced by non-cross-Linking DNA hybridization. J Am Chem Soc 125:8102

    Article  CAS  Google Scholar 

  10. Aslan K, Lakowicz JR, Geddes CD (2005) Plasmon light scattering in biology and medicine: New sensing approaches, visions and perspectives.Curr Opin Chem Biol 9:538–544

    Article  CAS  Google Scholar 

  11. Aslan K, Holley P, Davies L, Lakowicz JR, Geddes CD (2005) Angular-ratiometric plasmon-resonance based light scattering for bioaffinity sensing. J Am Chem Soc 127:12115–12121

    Article  CAS  Google Scholar 

  12. Aslan K, Geddes CD (2005) Metal-enhanced fluorescence: An emerging tool in biotechnology. Curr Opin Biotechnol 16:55–62

    Article  CAS  Google Scholar 

  13. Zhang X, Young MA, Lyandres O, Van Duyne RP (2005) Rapid detection of an anthrax biomarker by surface-enhanced raman spectroscopy. J Am Chem Soc 127:4484

    Article  CAS  Google Scholar 

  14. Ryan BC, Kwong GA, Radu CG, Witte ON, Heath JR (2007) DNA -Encoded antibody libraries: a unified platform for multiplexed cell sorting and detection of genes and proteins. J Am Chem Soc 129:1959–1967

    Article  CAS  Google Scholar 

  15. Francisco GJ, Viana BP, Jose R (2007) Gold nanoparticle based systems in genetics. Current Pharmacogenomics 5:39–47

    Article  Google Scholar 

  16. Rodrigo M, Pedro B, Leandro R, Goncalo D, Leonardo S, RicardoF, Elvira F (2007) Amorphous/nanocrystalline silicon biosensor for the specific identification of unamplified nucleic acid sequences using gold nanoparticle probes. Appl Phys Lett 023903/1-023903/3

  17. Bao-An D, Zheng-Ping L, Cheng-Hui L (2006) One-step homogeneous detection of DNA hybridization with gold nanoparticle probes by using a linear light-scattering technique. Angew Chem Int Ed 45:8022–8025

    Article  Google Scholar 

  18. Das J, Aziz MA, Yang H (2006) A nanocatalyst-based assay for proteins: DNA -free ultrasensitive electrochemical detection using catalytic reduction of p-nitrophenol by gold- nanoparticle labels. J Am Chem Soc 128:16022–16023

    Article  CAS  Google Scholar 

  19. Yeung SW, Lee T, Ming-Hung C, Hong C, Ming I (2006) A DNA biochip for on-the-spot multiplexed pathogen identification. Nucl Acids Res 34:e118/1–e118/7

    Article  CAS  Google Scholar 

  20. Hong OE, Lee M-Y, Nam D, Yoon S-H, Kim HC (2005) Inhibition assay of biomolecules based on Fluorescence Resonance Energy Transfer (FRET) between quantum dots and gold nanoparticles. J Am Chem Soc 127:3270–3271

    Article  CAS  Google Scholar 

  21. Reinhard BM, Siu M, Agarwal H, Alivisatos AP, Liphardt J (2005) Calibration of dynamic molecular rulers based on plasmon coupling between gold nanoparticles. Nano Lett 5:2246–2252

    Article  CAS  Google Scholar 

  22. Yun CS, Javier A, Jennings T, Fisher M, Hira S, Peterson S, Hopkins B, Reich NO, Strouse GF (2005) Nanometal surface energy transfer in optical rulers, breaking the FRET barrier. J Am Chem Soc 127:3115–3119

    Article  CAS  Google Scholar 

  23. Gaylord BS, Heeger AJ, Bazan GC (2002) DNA detection using water-soluble conjugated polymers and peptide nucleic acid probes. Proc Natl Acad Sci U S A 99:10954–10957

    Article  CAS  Google Scholar 

  24. Benoit D. (2005). Quantum dots: DNA detectives. Nature Mat 4:797–798

    Article  CAS  Google Scholar 

  25. Zhang C-Y, Yeh H-C, Kuroki MT, Wang T-H (2005) Single-quantum-dot-based DNA nanosensor. Nature Mat 4:826–831

    Article  Google Scholar 

  26. Peterson AW, Wolf lK, Georgiadis RM (2002) Hybridization of mismatched or partially matched DNA at surfaces. J Am Chem Soc 124:14601–14607

    Article  CAS  Google Scholar 

  27. Cooper MA, Dultsev FN, Minson T, Ostanin VP, Abell C, Klenerman D (2001) Direct and sensitive detection of a human virus by rupture event scanning. Nat Biotechnol 19:833–837

    Article  CAS  Google Scholar 

  28. Fan C, Plaxco KW, Heeger AJ (2003) Electrochemical interrogation of conformational changes as a reagentless method for the sequence-specific detection of DNA. Proc Natl Acad Sci USA 100:9134–9137

    Article  CAS  Google Scholar 

  29. Boon EM, Ceres DM, Drummond TG, Hill MG, Barton JK (2000) Mutation detection by electrocatalysis at DNA-modified electrodes. Nat Biotechnol 18:1096–1100

    Article  CAS  Google Scholar 

  30. Fritz J, Cooper EB, Gaudet S, Sorger PK, Manalis SR (2002) Electronic detection of DNA by its intrinsic molecular charge. Proc Natl Acad Sci U S A 99:14141–14142

    Google Scholar 

  31. Patolsky F, Lichtenstein A, Willner I (2001) Detection of single-base DNA mutations by enzyme-amplified electronic transduction. Nat Biotechnol 19:253–257

    Article  CAS  Google Scholar 

  32. Yu CJ, Wan YJ, Yowanto H, Li J, Tao CL, James MD, Tan CL, Blackburn GF, Meade TJ (2001) Electronic detection of single-base mismatches in DNA with ferrocene-modified probes. J Am Chem Soc 123:11155–11161

    Article  CAS  Google Scholar 

  33. Dubertret B, Calame M, Libchaber AJ (2001) Single-mismatch detection using gold-quenched fluorescent oligonucleotides. Nat Biotechnol 19:365–370

    Article  CAS  Google Scholar 

  34. Han M, Gao X, Su JZ, Nie S (2001) Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules. Nat Biotechnol 19:631–635

    Article  CAS  Google Scholar 

  35. Nam JM, Thaxton CS, Mirkin CA (2003) Nanoparticle-based bio-bar codes for the ultrasensitive detection of proteins. Science 301:1884–1886

    Article  CAS  Google Scholar 

  36. Alivisatos P (2004) The use of nanocrystals in biological detection. Nat Biotechnol 22:47–52

    Article  CAS  Google Scholar 

  37. Park SJ, Taton TA, Mirkin CA (2002) Array-based electrical detection of DNA with nanoparticle probes. Science 295:1503–1506

    Article  CAS  Google Scholar 

  38. Gaylord BS, Bazan GC, Heeger A J (2003) DNA hybridization detection with water-soluble conjugated polymers and chromophore-labeled single-stranded DNA. J Am Chem Soc 125:896–900

    Article  CAS  Google Scholar 

  39. Fan C, Plaxco KW, Heeger AJ (2002) High-efficiency fluorescence quenching of conjugated polymers by proteins. J Am Chem Soc 124:5642–5643

    Article  CAS  Google Scholar 

  40. Ray PC, Fortner A, Darbha GK (2006) Gold nanoparticle based FRET asssay for the detection of DNA cleavage. J Phys Chem B 110:20745

    Article  CAS  Google Scholar 

  41. Ray PC (2006) Label -free diagnostics of single base-mismatch DNA hybridization on gold nano-particles using hyper-Rayleigh Scattering technique. Angew Chem Int Ed 45:1151

    Article  CAS  Google Scholar 

  42. Ray PC, Fortner A, Griffith J, Kim CK, Singh JP, Yu H (2005) Laser induced fluorescence quenching of tagged oligonucleotides probes by gold nanoparticles. Chem Phys Lett 414:259

    Article  CAS  Google Scholar 

  43. Kim C, Singh JP, Fortner A, Griffin J, Darbha GK, & Ray PC (2006) Gold nanoparticle based laser induced fluorescence probe for specific DNA hybridization detection. Nanotechnology 17:3083

    Google Scholar 

  44. Maxwell DJ, Taylor JR, Nie S (2002) Self-assembled nanoparticle probes for recognition and detection of biomolecules. J Am Chem Soc 124:9606

    Article  CAS  Google Scholar 

  45. Li H, Rothberg LJ (2004) DNA sequence detection using selective fluorescence quenching of tagged oligonucleotide probes by gold nanoparticles. Anal Chem 76:5414

    Article  CAS  Google Scholar 

  46. Rosi NL, Mirkin CA (2005) Nanostructures in biodiagnostics. Chem Rev 105:1547

    Article  CAS  Google Scholar 

  47. Orita MS, Sekiya T, Hayashi K (1989) Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain. Genomics 5:874–879

    Article  CAS  Google Scholar 

  48. Whitcombe D, Theaker J, Guy SP, Brown T, Little S (1999) Detection of PCR products using self-probing amplicons and fluorescence. Nat Biotechnol 17:804–807

    Article  CAS  Google Scholar 

  49. Schweitzer B, Wiltshire S, Lambert J, O’Malley S, Kukanskis K, Zhu Z, Kingsmore SF, Lizardi PM, Ward DC (2000) Immunoassays with rolling circle DNA amplification: a versatile platform for ultrasensitive antigen detection. Proc Natl Acad Sci USA 97:10113–10119

    Article  CAS  Google Scholar 

  50. Lakowicz JR (1999) Principles of fluorescence spectroscopy. Kluwer Academic/Plenum, New York

    Google Scholar 

  51. Winzeler EA, Schena M, Davis RW (1999) Fluorescence-based expression monitoring using microarrays. Methods Enzymol 306:3–18

    Article  CAS  Google Scholar 

  52. Tyagi S, Kramer FR (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 14:303–308

    Article  CAS  Google Scholar 

  53. Fan C, Wang S, Hong JW, Bazan GC, Plaxco KW, Heeger AJ (2003) Beyond superquenching: hyper-efficient energy transfer from conjugated polymers to gold nanoparticles. Proc Natl Acad Sci USA 100:6297–6301

    Article  CAS  Google Scholar 

  54. Kumaraswamy S, Bergstedt T, Shi X, Rininsland F, Kushon S, Xia W, Ley K, Achyuthan KE, McBranch D, Whitten D (2004) Fluorescent-conjugated polymer superquenching facilitates highly sensitive detection of proteases. Proc Natl Acad Sci USA 101:7511–7515

    Article  CAS  Google Scholar 

  55. Peng X, Wilson TE, Loweth CJ, Bruchez MP, Schultz PG, Alivisatos AP (1996) Organization of ‘nanocrystal molecules’ using DNA. Nature 382:609–611

    Article  Google Scholar 

  56. Bruchez M, Moronne M, Gin P, Weiss S, Alivisatos AP (1998) Semiconductor nanocrystals as fluorescent biological labels. Science 281:2013–2016

    Article  CAS  Google Scholar 

  57. Gersten J, Nitzan A (1981) Spectroscopic properties of molecules interacting with small dielectric particles. J Chem Phys 75:1139–1152

    Article  CAS  Google Scholar 

  58. Forster T (1948) Intermolecular energy transference and fluorescence. Ann Physik 2:55–57

    Article  CAS  Google Scholar 

  59. Mie G (1908) Contributions to the optics of turbid media, especially colloidal metal solutions. Phys Inst Greifswald Annalen der Physik 25:377–445

    Article  CAS  Google Scholar 

  60. Xu Y-I, Wang RT (1998) Electromagnetic scattering by an aggregate of spheres: Theoretical and experimental study of the amplitude scattering matrix. Phys Rev E 58:3931–3948

    Article  CAS  Google Scholar 

  61. Su KH, Wei QH, Zhang X, Mock JJ, Smith DR, Schultz S (2003) Interparticle coupling effects on plasmon resonances of nanogold particles. Nano Lett 3:1087–1090

    Article  CAS  Google Scholar 

  62. Gersten JI, Nitzan A (1985) Photophysics and photochemistry near surfaces and small particles. Surf Sci 158:165–189

    Article  CAS  Google Scholar 

  63. Stoff-Khalili MA, Dall P, Curiel DT (2006) Gene therapy for carcinoma of the breast. Cancer Gene Ther 13:633–647

    Article  CAS  Google Scholar 

  64. Petra S (2006) Fundamental processes in radiation damage of DNA. Angew Chem Int Ed 45:4056–4059

    Article  CAS  Google Scholar 

  65. Li JJ, Geyer R, Tan W (2000) Using molecular beacons as a sensitive fluorescence assay for enzymatic cleavage for single-stranded DNA. Nucleic Acids Res 28:e52

    Article  CAS  Google Scholar 

  66. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory mannual. 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

    Google Scholar 

  67. Orita M, Iwahana H, Kanazawa H, Hayashi K, Sekiya T (1989) Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci USA 86:2766

    Article  CAS  Google Scholar 

  68. Waters TR, Connolly BA (1992) Continuous spectrophotometric assay for restriction endonucleases using synthetic oligodeoxynucleotides and based on the hyperchromic effect. Anal Biochem 204:204

    Article  CAS  Google Scholar 

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Acknowledgement

Dr. Ray thanks NSF-CRIFMU grant # 0443547, NSF-PREM grant # DMR-0611539, ARO grant # W911NF-06-1-0512 and NIH-SCORE grant # S06GM 008047 for their generous funding. William Hardy thanks NSF/LSMAMP grant # HRD-0115807 for his scholarship during matriculation. We also thank reviewers whose valuable suggestion improved the quality of the manuscript.

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Correspondence to Paresh Chandra Ray.

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Ray, P.C., Darbha, G.K., Ray, A. et al. Gold Nanoparticle Based FRET for DNA Detection. Plasmonics 2, 173–183 (2007). https://doi.org/10.1007/s11468-007-9036-9

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  • DOI: https://doi.org/10.1007/s11468-007-9036-9

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