A nanoplasmonic molecular ruler for measuring nuclease activity and dna footprinting

Nature Nanotechnology

Volumn 1, Issue 1, 2006, Pages 47-52

  Liu, Gang L ^a   Yin, Yadong ^b,c,f   Kunchakarra, S ^b   Mukherjee, Bipasha ^b   Gerion, Daniele ^b,d   Jett, Stephen D ^e   Bear, David G ^e   Gray, Joe W ^b   Alivisatos, A Paul ^b,c   Lee, Luke P ^a   Chen, Fanqing Frank ^b  

^a University of California at Berkeley   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^e UNIVERSITY OF NEW MEXICO HEALTH SCIENCES CENTER   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; DNA;

CHEMISTRY; DNA FOOTPRINTING; ENZYME ACTIVATION; GENETICS; LETTER; METHODOLOGY; SURFACE PLASMON RESONANCE; ULTRASTRUCTURE;

DEOXYRIBONUCLEASES; DNA; DNA FOOTPRINTING; ENZYME ACTIVATION; SURFACE PLASMON RESONANCE;

EID: 33847628151     PISSN: 17483387     EISSN: 17483395     Source Type: Journal    
DOI: 10.1038/nnano.2006.51     Document Type: Article

References (30)

1. Behrens, S., Fuchs, B.M. & Amann, R. The effect of nucleobase-specific fluorescence quenching on in situ hybridization with rRNA-targeted oligonucleotide probes. Syst. Appl. Microbiol. 27, 565–572 (2004).
2. Smith, J. & Anslyn, E.V. Radioactive end labeling to determine hydrolytic rates of nuclease mimics. Anal. Biochem. 220, 53–57 (1994).
3. Hillier, S.C. et al. An electrochemical study of enzymatic oligonucleotide digestion. Bioelectrochemistry 63, 307–310 (2004).
4. Alivisatos, A.P. et al. Organization of ‘nanocrystal molecules’ using DNA. Nature 382, 609–611 (1996).
5. Zanchet, D., Micheel, C.M., Parak, W.J., Gerion, D. & Alivisatos, A.P. Electrophoretic isolation of discrete Au nanocrystal/DNA conjugates. Nano Lett. 1, 32–35 (2001).
6. Taton, T.A., Mirkin, C.A. & Letsinger, R.L. Scanometric DNA array detection with nanoparticle probes. Science 289, 1757–1760 (2000).
7. Storhoff, J.J., Elghanian, R., Mucic, R. C., Mirkin, C. A. & Letsinger, R. L. One-pot colorimetric differentiation of polynucleotides with single base imperfections using gold nanoparticle probes. J. Am. Chem. Soc. 120, 1959–1964 (1998).
8. Mirkin, C.A., Letsinger, R.L., Mucic, R.C. & Storhoff, J.J. A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 382, 607–609 (1996).
9. Sonnichsen, C., Reinhard, B.M., Liphardt, J. & Alivisatos, A.P. A molecular ruler based on plasmon coupling of single gold and silver nanoparticles. Nature Biotechnol. 23, 741–745 (2005).
10. Homola, J., Yee, S.S. & Gauglitz, G. Surface plasmon resonance sensors: Review. Sensor Actuat. B-Chem. 54, 3–15 (1999).
11. Karlsson, R. SPR for molecular interaction analysis: A review of emerging application areas. J. Mol. Recognit. 17, 151–161 (2004).
12. Mulvaney, P. Surface plasmon spectroscopy of nanosized metal particles. Langmuir 12, 788–800 (1996).
13. Elghanian, R., Storhoff, J.J., Mucic, R.C., Letsinger, R.L. & Mirkin, C.A. Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science 277, 1078–1081 (1997).
14. Eck, D., Helm, C.A., Wagner, N.J. & Vaynberg, K.A. Plasmon resonance measurements of the adsorption and adsorption kinetics of a biopolymer onto gold nanocolloids. Langmuir 17, 957–960 (2001).
15. Englebienne, P., Van Hoonacker, A. & Verhas, M. High-throughput screening using the surface plasmon resonance effect of colloidal gold nanoparticles. Analyst 126, 1645–1651 (2001).
16. Nath, N. & Chilkoti, A.A colorimetric gold nanoparticle sensor to interrogate biomolecular interactions in real time on a surface. Anal. Chem. 74, 504–509 (2002).
17. Sun, Y.G. & Xia, Y.N. Increased sensitivity of surface plasmon resonance of gold nanoshells compared to that of gold solid colloids in response to environmental changes. Anal. Chem. 74, 5297–5305 (2002).
18. McFarland, A.D. & Van Duyne, R.P. Single silver nanoparticles as real-time optical sensors with zeptomole sensitivity. Nano Lett. 3, 1057–1062 (2003).
19. Raschke, G. et al. Biomolecular recognition based on single gold nanoparticle light scattering. Nano Lett. 3, 935–938 (2003).
20. Oldenburg, S.J., Genick, C.C., Clark, K.A. & Schultz, D.A. Base pair mismatch recognition using plasmon resonant particle labels. Anal. Biochem. 309, 109–116 (2002).
21. Parak, W.J. et al. Conformation of oligonucleotides attached to gold nanocrystals probed by gel electrophoresis. Nano Lett. 3, 33–36 (2003).
22. Bohren, C.F. & Huffman, D.R. Absorption and Scattering of Light by Small Particles (Wiley, New York, 1983).
23. Mazur, J. & Jernigan, R.L. Distance-dependent dielectric-constants and their application to double-helical DNA. Biopolymers 31, 1615–1629 (1991).
24. King, K., Benkovic, S.J. & Modrich, P. Glu-111 is required for activation of the DNA cleavage center of EcoRI endonuclease. J. Biol. Chem. 264, 11807–11815 (1989).
25. Pavco, P.A. & Steege, D.A. Elongation by Escherichia coli RNA polymerase is blocked in vitro by a site-specific DNA binding protein. J. Biol. Chem. 265, 9960–9969 (1990).
26. Jett, S.D. & Bear, D.G. Snapshot blotting — Transfer of nucleic-acids and nucleoprotein complexes from electrophoresis gels to grids for electron-microscopy. Proc. Natl Acad. Sci. USA 91, 6870–6874 (1994).
27. Legerski, R.J., Hodnett, J.L. & Gray, H.B. Jr. Extracellular nucleases of pseudomonas BAL 31. III. Use of the double-strand deoxyriboexonuclease activity as the basis of a convenient method for the mapping of fragments of DNA produced by cleavage with restriction enzymes. Nucleic Acids Res. 5, 1445–1464 (1978).
28. Doron-Mor, I. et al. Sensitivity of transmission surface plasmon resonance (T-SPR) spectroscopy: Self-assembled multilayers on evaporated gold island films. Chem. Eur. J. 11, 5555–5562 (2005).
29. Wanunu, M. et al. Branched coordination multilayers on gold. J. Am. Chem. Soc. 127, 17877–17887 (2005).
30. Mizu, M., Koumoto, K., Kimura, T., Sakurai, K. & Shinkai, S. Protection of polynucleotides against nuclease-mediated hydrolysis by complexation with schizophyllan. Biomaterials 25, 3109–3116 (2004).