Efficient self-assembly of DNA-functionalized fluorophores and gold nanoparticles with DNA functionalized silicon surfaces: The effect of oligomer spacers

Nucleic Acids Research

Volumn 41, Issue 7, 2013, Pages

  Milton, James A ^a   Patole, Samson ^a   Yin, Huabing ^a   Xiao, Qiang ^a   Brown, Tom ^a   Melvin, Tracy ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DNA; ESTER DERIVATIVE; GOLD NANOPARTICLE; HEXAETHYLENE GLYCOL PHOSPHATE DIESTER; NANOPARTICLE; OLIGOMER SPACER; SILICON; SPACER DNA; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DENSITY; DNA DETERMINATION; DNA HYBRIDIZATION; DNA SEQUENCE; ELECTRONICS; FLUORESCENCE; MASS SPECTROMETRY; NANOELECTRONIC DEVICE; NANOSENSOR; NUCLEIC ACID IMMOBILIZATION; PRIORITY JOURNAL;

DNA PROBES; FLUORESCENT DYES; GOLD; IMMOBILIZED NUCLEIC ACIDS; MASS SPECTROMETRY; METAL NANOPARTICLES; OLIGODEOXYRIBONUCLEOTIDES; SILICON;

EID: 84876565359     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt031     Document Type: Article

References (49)

1. Patole, S.N., Pike, A.R., Connolly, B.A., Horrocks, B.R. and Houlton, A. (2003) STM study of DNA films synthesized on Si(111) surfaces. Langmuir, 19, 5457-5463.
2. Strother, T., Hamers, R.J. and Smith, L.M. (2000) Covalent attachment of oligodeoxyribonucleotides to amine-modified Si (001) surfaces. Nucleic Acids Res., 28, 3535-3541.
3. Yin, H.B., Brown, T., Greef, R., Mailis, S., Eason, R.W., Wilkinson, J.S. and Melvin, T. (2004) In: Faupel, M.D.M.P. (ed.), Proc. SPIE Biophotonics New Frontier: From Genome to Proteome, Vol. 5461, pp. 1-8.
4. Yin, H.B., Brown, T., Greef, R., Wilkinson, J.S. and Melvin, T. (2004) Chemical modification and micropatterning of Si(100) with oligonucleotides. Microelectron. Eng., 73-74, 830-836.
5. Yin, H.B., Brown, T., Wilkinson, J.S., Eason, R.W. and Melvin, T. (2004) Submicron patterning of DNA oligonucleotides on silicon. Nucleic Acids Res., 32, e118.
6. Fritzsche, W. and Taton, T.A. (2003) Metal nanoparticles as labels for heterogeneous, chip-based DNA detection. Nanotechnology, 14, R63-R73.
7. Kohler, J.M., Csaki, A., Reichert, J., Moller, R., Straube, W. and Fritzsche, W. (2001) Selective labeling of oligonucleotide monolayers by metallic nanobeads for fast optical readout of DNA-chips. Sens. Actuators B Chem., 76, 166-172. (Pubitemid 32513875)
8. Niemeyer, C.M. and Ceyhan, B. (2001) DNA-directed functionalization of colloidal gold with proteins. Angew. Chem. Int. Ed. Engl., 40, 3685-3688. (Pubitemid 32953038)
9. Storhoff, J.J. and Mirkin, C.A. (1999) Programmed materials synthesis with DNA. Chem. Rev., 99, 1849-1862. (Pubitemid 129585163)
10. Peterson, A.W., Heaton, R.J. and Georgiadis, R. (2000) Kinetic control of hybridization in surface immobilized DNA monolayer films. J. Am. Chem. Soc., 122, 7837-7838.
11. Peterson, A.W., Heaton, R.J. and Georgiadis, R.M. (2001) The effect of surface probe density on DNA hybridization. Nucleic Acids Res., 29, 5163-5168. (Pubitemid 34065435)
12. Watterson, J.H., Piunno, P.A.E., Wust, C.C. and Krull, U.J. (2000) Effects of oligonucleotide immobilization density on selectivity of quantitative transduction of hybridization of immobilized DNA. Langmuir, 16, 4984-4992.
13. Demers, L.M., Mirkin, C.A., Mucic, R.C., Reynolds, R.A., Letsinger, R.L., Elghanian, R. and Viswanadham, G. (2000) 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., 72, 5535-5541.
14. Guo, Z., Guilfoyle, R.A., Thiel, A.J., Wang, R.F. and Smith, L.M. (1994) Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. Nucleic Acids Res., 22, 5456-5465.
15. Parak, W.J., Pellegrino, T., Micheel, C.M., Gerion, D., Williams, S.C. and Alivisatos, A.P. (2003) Conformation of oligonucleotides attached to gold nanocrystals probed by gel electrophoresis. Nano Lett., 3, 33-36. (Pubitemid 37161847)
16. Xu, J. and Craig, S.L. (2005) Thermodynamics of DNA hybridization on gold nanoparticles. J. Am. Chem. Soc., 127, 13227-13231. (Pubitemid 41377614)
17. Shchepinov, M.S., CaseGreen, S.C. and Southern, E.M. (1997) Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res., 25, 1155-1161. (Pubitemid 27303206)
18. Vainrub, A. and Pettitt, B.M. (2003) Sensitive quantitative nucleic acid detection using oligonucleotide microarrays. J. Am. Chem. Soc., 125, 7798-7799. (Pubitemid 36782146)
19. Vainrub, A. and Pettitt, B.M. (2003) Surface electrostatic effects in oligonucleotide microarrays: control and optimization of binding thermodynamics. Biopolymers, 68, 265-270. (Pubitemid 36222404)
20. Gong, P. and Levicky, R. (2008) DNA surface hybridization regimes. Proc. Natl Acad. Sci. USA, 105, 5301-5306. (Pubitemid 351753857)
21. Halperin, A., Buhot, A. and Zhulina, E.B. (2006) Hybridization at a surface: the role of spacers in DNA microarrays. Langmuir, 22, 11290-11304. (Pubitemid 46131348)
22. Halperin, A., Buhot, A. and Zhulina, E.B. (2005) Brush effects on DNA chips: thermodynamics, kinetics, and design guidelines. Biophys. J., 89, 796-811. (Pubitemid 41098967)
23. Cha, T.W., Boiadjiev, V., Lozano, J., Yang, H. and Zhu, X.Y. (2002) Immobilization of oligonucleotides on poly(ethylene glycol) brush-coated Si surfaces. Anal. Biochem., 311, 27-32. (Pubitemid 35463485)
24. Lasseter, T.L., Clare, B.H., Abbott, N.L. and Hamers, R.J. (2004) Covalently modified silicon and diamond surfaces: resistance to nonspecific protein adsorption and optimization for biosensing. J. Am. Chem. Soc., 126, 10220-10221. (Pubitemid 39100756)
25. Peeters, S., Stakenborg, T., Reekmans, G., Laureyn, W., Lagae, L., Van Aerschot, A. and Van Ranst, M. (2008) Impact of spacers on the hybridization efficiency of mixed self-assembled DNA/alkanethiol films. Biosens. Bioelectron., 24, 72-77.
26. Li, S., Li, X., Zhang, J., Zhang, Y., Han, J. and Jiang, L. (2010) Quantitative investigation of the influence of gold nanoparticles on the dynamics of DNA hybridization using a programmed multi-channel quartz crystal microbalance system. Colloids Surfaces Physicochem. Eng. Aspects, 364, 158-162.
27. Chen, C., Wang, W., Ge, J. and Zhao, X.S. (2009) Kinetics and thermodynamics of DNA hybridization on gold nanoparticles. Nucleic Acids Res., 37, 3756-3765.
28. Storhoff, J.J., Elghanian, R., Mucic, R.C., Mirkin, C.A. and Letsinger, R.L. (1998) One-pot colorimetric differentiation of polynucleotides with single base imperfections using gold nanoparticle probes. J. Am. Chem. Soc., 120, 1959-1964. (Pubitemid 28179167)
29. Fong, K.E. and Yung, L.-Y.L. (2012) Analysis of metallic nanoparticle-DNA assembly formation in bulk solution via localized surface plasmon resonance shift. RSC Adv., 2, 5154-5163.
30. Barchanski, A., Hashimoto, N., Petersen, S., Sajti, C.L. and Barcikowski, S. (2012) Impact of spacer and strand length on oligonucleotide conjugation to the surface of ligand-free laser-generated gold nanoparticles. Bioconjugate Chem., 23, 908-915.
31. Han, M.S., Lytton-Jean, A.K.R., Oh, B.K., Heo, J. and Mirkin, C.A. (2006) Colorimetric screening of DNA-binding molecules with gold nanoparticle probes. Angew. Chem. Int. Ed., 45, 1807-1810. (Pubitemid 44105261)
32. Liu, J.W. and Lu, Y. (2003) A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles. J. Am. Chem. Soc., 125, 6642-6643. (Pubitemid 36667443)
33. Dreyfus, R., Leunissen, M.E., Sha, R., Tkachenko, A., Seeman, N.C., Pine, D.J. and Chaikin, P.M. (2010) Aggregation-disaggregation transition of DNA-coated colloids: experiments and theory. Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 81(4 Pt 1), 041404.
34. Leunissen, M.E., Dreyfus, R., Sha, R., Seeman, N.C. and Chaikin, P.M. (2010) Quantitative study of the association thermodynamics and kinetics of DNA-coated particles for different functionalization schemes. J. Am. Chem. Soc., 132, 1903-1913.
35. Oh, J.-H. and Lee, J.-S. (2011) Designed hybridization properties of DNA-gold nanoparticle conjugates for the ultraselective detection of a single-base mutation in the breast cancer gene BRCA1. Anal. Chem., 83, 7364-7370.
36. Dyadyusha, L., Yin, H., Jaiswal, S., Brown, T., Baumberg, J.J., Booy, F.P. and Melvin, T. (2005) Quenching of CdSe quantum dot emission, a new approach for biosensing. Chem. Commun., 2005, 3201-3203. (Pubitemid 41002394)
37. Bai, X.P., Li, Z.M., Jockusch, S., Turro, N.J. and Ju, J.Y. (2003) Photocleavage of a 2-nitrobenzyl linker bridging a fluorophore to the 50 end of DNA. Proc. Natl Acad. Sci. USA, 100, 409-413. (Pubitemid 36126065)
38. Pitcairn, I.K., Warwick, P.E., Milton, J.A. and Teagle, D.A.H. (2006) Method for ultra-low-level analysis of gold in rocks. Anal. Chem., 78, 1290-1295. (Pubitemid 43271863)
39. Chrisey, L.A., Oferrall, C.E., Spargo, B.J., Dulcey, C.S. and Calvert, J.M. (1996) Fabrication of patterned DNA surfaces. Nucleic Acids Res., 24, 3040-3047. (Pubitemid 26289597)
40. Moiseev, L., Unlu, M.S., Swan, A.K., Goldberg, B.B. and Cantor, C.R. (2006) DNA conformation on surfaces measured by fluorescence self-interference. Proc. Natl Acad. Sci. USA, 103, 2623-2628.
41. Pal, S., Kim, M.J. and Song, J.M. (2008) Quantitation of surface coverage of oligonucleotides bound to chip surfaces: a fluorescence-based approach using alkaline phosphatase digestion. Lab. Chip., 8, 1332-1341.
42. Fahie-Wilson, M. and Halsall, D. (2008) Polyethylene glycol precipitation: proceed with care. Ann. Clin. Biochem., 45, 233-235. (Pubitemid 351724556)
43. McMinn, D.L. and Greenberg, M.M. (1996) Novel solid phase synthesis supports for the preparation of oligonucleotides containing S30-alkyl amines. Tetrahedron, 52, 3827-3840.
44. Stillman, B.A. and Tonkinson, J.L. (2001) Expression microarray hybridization kinetics depend on length of the immobilized DNA but are independent of immobilization substrate. Anal. Biochem., 295, 149-157. (Pubitemid 32756968)
45. Yang, I., Han, M.S., Yim, Y.H., Hwang, E. and Park, S.R. (2004) A strategy for establishing accurate quantitation standards of oligonucleotides: quantitation of phosphorus of DNA phosphodiester bonds using inductively coupled plasma-optical emission spectroscopy. Anal. Biochem., 335, 150-161. (Pubitemid 39446241)
46. Eimer, W. and Pecora, R. (1991) Rotational and translational diffusion of short rodlike molecules in soluton-oligonucleotides. J. Chem. Phys., 94, 2324-2329.
47. Fick, J., Steitz, R., Leiner, V., Tokumitsu, S., Himmelhaus, M. and Grunze, M. (2004) Swelling behavior of self-assembled monolayers of alkanethiol-terminated poly(ethylene glycol): a neutron reflectometry study. Langmuir, 20, 3848-3853.
48. Tokumitsu, S., Liebich, A., Herrwerth, S., Eck, W., Himmelhaus, M. and Grunze, M. (2002) Grafting of alkanethiol-terminated poly(ethylene glycol) on gold. Langmuir, 18, 8862-8870. (Pubitemid 35361314)
49. Harder, P., Grunze, M., Dahint, R., Whitesides, G.M. and Laibinis, P.E. (1998) Molecular conformation in oligo(ethylene glycol)-terminated self-assembled monolayers on gold and silver surfaces determines their ability to resist protein adsorption. J. Phys. Chem. B, 102, 426-436. (Pubitemid 128581104)