journal article·2007-12

Assays Based on Differential Adsorption of Single-stranded and Double-stranded DNA on Unfunctionalized Gold Nanoparticles in a Colloidal Suspension

Huixiang Li, Edward Nelson, Alice Pentland, Joanne Van Buskirk, Lewis Rothberg

Plasmonics· Volume 2· Issue 4
Publisher page

Abstract

Under certain conditions, single-stranded DNA adsorbs to negatively charged gold nanoparticles in a colloid whereas double-stranded DNA does not. We present evidence that this phenomenon can be explained by the difference in their electrostatic properties that in turn reflects conformational differences. The ability to discriminate the hybridization state of DNA on the basis of adsorption behavior can be utilized to design simple colorimetric and fluorimetric assays that take advantage of plasmon resonance in the gold nanoparticles. We present examples where we detect specific target sequences in oligonucleotides and in genomic DNA. Because conformational changes in special DNA sequences can also be induced by analytes such as potassium, we report a potassium ion detection scheme based on the same principle.
Source: openaire · Quality: candidate unverified · Source record ↗

Research context

OpenAlex topics: Advanced biosensing and bioanalysis techniques · Gold and Silver Nanoparticles Synthesis and Applications · Biosensors and Analytical Detection

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

References (28)

Show source-provided references
1. Hood L, Galas D (2003) The digital code of DNA. Nature 421:444–44810.1038/nature01410 ↗
2. Bangs LB (1996) New developments in particle-based immunoassays: introduction. Pure Appl Chem 68:1873–187910.1351/pac199668101873 ↗
3. Elghanian R, Storhoff JJ, Mucic RC, Letsinger RL, Mirkin CA (1997) Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science 277:1078–108110.1126/science.277.5329.1078 ↗
4. Park SJ, Taton MA, Mirkin CA (2002) Array-based electrical detection of DNA with nanoparticle probes. Science 295:1503–150610.1126/science.1067003 ↗
5. Rosi NL, Mirkin CA (2005) Nanostructures in biodiagnostics. Chem Rev 105:1547–156210.1021/cr030067f ↗
6. Storhoff JJ, Elghanian R, Mucic RC, Mirkin CA, Letsinger RL (1998) One-pot colorimetric differentiation of polynucleotides with single base imperfections using gold nanoparticle probes. J Am Chem Soc 120:1959–196410.1021/ja972332i ↗
7. Li HX, Rothberg LJ (2004) Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles. Proc Natl Acad Sci USA 101:14039–14041
8. Li HX, Rothberg LJ (2004) DNA sequence detection using selective fluorescence quenching of tagged oligonucleotide probes by gold nanoparticles. Anal Chem 76:5414–541710.1021/ac049173n ↗
9. Tinland B, Pluen A, Sturm J, Weill G (1997) Persistence length of single-stranded DNA. Macromolecules 30:5763–576510.1021/ma970381+ ↗
10. Hunter RJ (2001) Foundations of colloid science. Oxford University Press, New York
11. Li HX, Rothberg LJ (2004) Label-free colorimetric detection of single nucleotide polymorphisms in amplified genomic DNA. J Am Chem Soc 126:10958–1096110.1021/ja048749n ↗
12. Cai P, Huang QY, Zhang XW (2006) Microcalorimetric studies of the effects of MgCl2 concentrations and pH on the adsorption of DNA on montmorillonite, kaolinite and goethite. Appl Clay Sci 32:147–15210.1016/j.clay.2005.11.004 ↗
13. Gearheart LA, Ploehn HJ, Murphy CJ (2001) Oligonucleotide adsorption to gold nanoparticles: a surface-enhanced Raman spectroscopy study of intrinsically bent DNA. J Phys Chem 105:12609–1261510.1021/jp0106606 ↗
14. Cheng S, Fockler C, Barnes WM, Higuchi R (1994) Effective amplification of long targets from cloned inserts and human genomic DNA. Proc Natl Acad Sci USA 91:5695–569910.1073/pnas.91.12.5695 ↗
15. Brouxhon S, Konger RL, VanBuskirk J, Sheu TJ, Ryan J, Erdle B, Almudevar A, Breyer RM, Scott G, Pentland AP (2007) Deletion of prostaglandin E2 EP2 receptor protects against ultraviolet-induced carcinogenesis, but increases tumor aggressiveness. J Invest Dermatol 127:439–44610.1038/sj.jid.5700547 ↗
16. Ðapić V, Abdomerović R, Marrington R, Peberdy J, Rodger A, Trent JO, Bates PJ (2003) Biophysical and biological properties of quadruplex oligodeoxyribonucleotides. Nucleic Acids Res 31(8):2097–210710.1093/nar/gkg316 ↗
17. Gilbert DE, Feigon J (1999) Multistranded DNA structures. Curr Opin Struct Biol 9(3):305–31410.1016/S0959-440X(99)80041-4 ↗
18. Simonsson T (2001) G-Quadruplex DNA structures—variations on a theme. Biol Chem 382:621–62810.1515/BC.2001.073 ↗
19. Risitano A, Fox KR (2005) Inosine substitutions demonstrate that intramolecular DNA quadruplexes adopt different conformations in the presence of sodium and potassium. Bioorg Med Chem Lett 15:2047–205010.1016/j.bmcl.2005.02.050 ↗
20. Hud NV, Smith FW, Anet FAL, Feigon J (1996) The selectivity for K+ versus Na+ in DNA quadruplexes is dominated by relative free energies of hydration: a thermodynamic analysis by 1H NMR. Biochemistry 35(48):15383–1539010.1021/bi9620565 ↗
21. Lu M, Guo Q, Kallenbach NR (1992) Structure and stability of sodium and potassium complexes of dT4G4 and dT4G4T. Biochemistry 31(9):2455–245910.1021/bi00124a003 ↗
22. Wang LH, Liu XF, Hu XF, Song SP, Fan CH (2006) Unmodified gold nanoparticles as a colorimetric probe for potassium DNA aptamers. Chem Commun 36:3780–378210.1039/b607448k ↗
23. Bock LC, Griffin LC, Latham JA, Vermaas EH, Toole JJ (1992) Selection of single-stranded-DNA molecules that bind and inhibit human thrombin. Nature 355(6360):564–56610.1038/355564a0 ↗
24. Nagatoishi S, Nojima T, Juskowiak B, Takenaka S (2005) A pyrene-labeled G-quadruplex oligonucleotide as a fluorescent probe for potassium ion detection in biological applications. Angew Chem 44:5067–507010.1002/anie.200501506 ↗
25. Ueyama H, Takagi M, Takenaka S (2002) A novel potassium sensing in aqueous media with a synthetic oligonucleotide derivative. Fluorescence resonance energy transfer associated with guanine quartet–potassium ion complex formation. J Am Chem Soc 124:14286–1428710.1021/ja026892f ↗
26. Crossley R, Goolamali Z, Sammes PG (1994) Synthesis and properties of a potential extracellular fluorescent probe for potassium. J Chem Soc Perkin Trans 2:1615–162310.1039/p29940001615 ↗
27. Minta A, Tsien RY (1989) Fluorescent indicators for cytosolic sodium. J Biol Chem 264(32):19449–1945710.1016/S0021-9258(19)47321-3 ↗
28. HX Li, Rothberg LJ (2005) Rapid detection of specific sequences in RNA using differential adsorption of single-stranded oligonucleotides on gold nanoparticles. Anal Chem 77:6229–623310.1021/ac050921y ↗