A gold nanoparticle-based strategy for label-free and colorimetric screening of DNA triplex binders

Biochimie

Volumn 92, Issue 10, 2010, Pages 1416-1421

  Chen, Cuie ^a,b   Song, Guangtao ^a,b   Yang, Xinjian ^a,b   Ren, Jinsong ^a,b   Qu, Xiaogang ^a,b  

^a CHANGCHUN INSTITUTE OF APPLIED CHEMISTRY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Aggregation; DNA binders; Gold nanoparticles; High throughput screening; Triplex

Indexed keywords

DNA; GOLD NANOPARTICLE; OLIGONUCLEOTIDE;

ARTICLE; BINDING AFFINITY; CHEMICAL LABELING; CHEMICAL MODIFICATION; COLORIMETRY; HIGH THROUGHPUT SCREENING;

BINDING SITES; COLORIMETRY; DNA; GOLD; HIGH-THROUGHPUT SCREENING ASSAYS; METAL NANOPARTICLES; NUCLEIC ACID CONFORMATION; STAINING AND LABELING;

EID: 77957122526     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2010.07.004     Document Type: Article

References (40)

1. Duca M., Vekhoff P., Oussedik K., Halby L., Arimondo P.B. The triple helix: 50 years later, the outcome. Nucleic Acids Res. 2008, 36:5123-5138.
2. Igoucheva O., Alexeev V., Yoon K. Oligonucleotide-directed mutagenesis and targeted gene correction: a mechanistic point of view. Curr. Mol. Med. 2004, 4:445-463.
3. Buchini S., Leumann C.J. Recent improvements in antigene technology. Curr. Opin. Chem. Biol. 2003, 7:717-726.
4. Vasquez K.M., Wang G., Havre P.A., Glazer P.M. Chromosomal mutations induced by triplex-forming oligonucleotides in mammalian cells. Nucleic Acids Res. 1999, 27:1176-1181.
5. Vasquez K.M., Narayanan L., Glazer P.M. Specific mutations induced by triplex-forming oligonucleotides in mice. Science 2000, 290:530-533.
6. Jain A., Wang G., Vasquez K.M. DNA triple helices: biological consequences and therapeutic potential. Biochimie 2008, 90(8):1117-1130.
7. Fox K.R. Targeting DNA with triplexes. Curr. Med. Chem. 2000, 7:17-37.
8. Cassidy S.A., Strekowski L., Wilson W.D., Fox K.R. Effect of a Tripler-binding ligand on parallel and antiparallel DNA triple helices using short unmodified and acridine-linked oligonucleotides. Biochemistry 1994, 33:15338-15347.
9. Wilson W.D., Tanious F.A., Mizan S., Yao S.J., Kiselyov A.S., Zon G., Strekowski L. DNA triple-helix specific intercalators as antigene enhancers - unfused aromatic cations. Biochemistry 1993, 32:10614-10621.
10. Mergny J.L., Duvalvalentin G., Nguyen C.H., Perrouault L., Faucon B., Rougee M., Montenaygarestier T., Bisagni E., Helene C. Triple helix specific ligands. Science 1992, 256:1681-1684.
11. Lee J.S., Latimer L.J.P., Hampel K.J. Coralyne binds tightly to both T.a.T-containing and C.G.C+-containing DNA triplexes. Biochemistry 1993, 32:5591-5597.
12. Arya D.P., Coffee R.L. DNA triple helix stabilization by aminoglycoside antibiotics. Bioorg. Med. Chem. Lett. 2000, 10:1897-1899.
13. Arya D.P., Coffee R.L., Charles I. Neomycin-induced hybrid triplex formation. J. Am. Chem. Soc. 2001, 123:11093-11094.
14. Xi H.J., Kumar S., Dosen-Micovic L., Arya D.P. Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices. Biochimie 2010, 92:514-529.
15. Song G.T., Xing F.F., Qu X.G., Chaires J.B., Ren J.S. Oxazine 170 induces DNA: RNA: DNA triplex formation. J. Med. Chem. 2005, 48:3471-3473.
16. Scaria P.V., Shafer R.H. Binding of ethidium-bromide to a DNA triple helix - evidence for intercalation. J. Biol. Chem. 1991, 266:5417-5423.
17. Marchand C., Bailly C., Nguyen C.H., Bisagni E., Garestier T., Helene C., Waring M.J. Stabilization of triple helical DNA by a benzopynidoquinoxaline intercalator. Biochemistry 1996, 35:5022-5032.
18. Silver G.C., Sun J.S., Nguyen C.H., Boutorine A.S., Bisagni E., Helene C. Stable triple-helical DNA complexes formed by benzopyridoindole- and benzopyridoquinoxaline-oligonucleotide conjugates. J. Am. Chem. Soc. 1997, 119:263-268.
19. Chaires J.B., Ren J., Hamelberg D., Kumar A., Pandya V., Boykin D.W., Wilson W.D. Structural selectivity of aromatic diamidines. J. Med. Chem. 2004, 47:5729-5742.
20. 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 1997, 277:1078-1081.
21. Wang Z.X., Levy R., Fernig D.G., Brust M. Kinase-catalyzed modification of gold nanoparticles: a new approach to colorimetric kinase activity screening. J. Am. Chem. Soc. 2006, 128:2214-2215.
22. Stoeva S.I., Lee J.S., Smith J.E., Rosen S.T., Mirkin C.A. Multiplexed detection of protein cancer markers with biobarcoded nanoparticle probes. J. Am. Chem. Soc. 2006, 128:8378-8379.
23. Liu J.W., Lu Y. Fast colorimetric sensing of adenosine and cocaine based on a general sensor design involving aptamers and nanoparticles. Angew. Chem. Int. Ed. 2006, 45:90-94.
24. Song G.T., Chen C., Qu X.G., Miyoshi D., Ren J.S., Sugimoto N. Small-molecule-directed assembly: a gold nanoparticle-based strategy for screening of homo-adenine DNA duplex binders. Adv. Mater. 2008, 20:706-710.
25. Song G.T., Chen C., Qu X.G., Miyoshi D., Ren J.S., Sugimoto N. A simple, universal colorimetric assay for endonuclease methyltransferase activity and inhibition based on an enzyme-responsive nanoparticle system. ACS Nano 2009, 3:1183-1189.
26. Han M.S., Lytton-Jean A.K.R., Oh B.K., Heo J., Mirkin C.A. Colorimetric screening of DNA-binding molecules with gold nanoparticle probes. Angew. Chem. Int. Ed. 2006, 45:1807-1810.
27. Han M.S., Lytton-Jean A.K.R., Mirkin C.A. A gold nanoparticle based approach for screening triplex DNA binders. J. Am. Chem. Soc. 2006, 128:4954-4955.
28. Li H.X., Rothberg L. Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles. Proc. Natl. Acda. Sci. U.S.A. 2004, 101:14036-14039.
29. Li H.X., Rothberg L. Detection of specific sequences in RNA using differential adsorption of single-stranded oligonucleotides on gold nanoparticles. Anal. Chem. 2005, 77:6229-6233.
30. Zhao W.A., Chiuman W., Lam J.C.F., Brook M.A., Li Y.F. Simple and rapid colorimetric enzyme sensing assays using non-crosslinking gold nanoparticle aggregation. Chem. Commun. 2007, 3729-3731.
31. Wang L.H., Liu X.F., Hu X.F., Song S.P., Fan C.H. Unmodified gold nanoparticles as a colorimetric probe for potassium DNA aptamers. Chem. Commun. 2006, 3780-3782.
32. 2+ ions by oligonucleotide-gold-nanoparticle hybrids and DNA-based machines. Angew. Chem. Int. Ed. 2008, 47:3927-3931.
33. Wang J., Wang L.H., Liu X.F., Liang Z.Q., Song S.P., Li W.X., Li G.X., Fan C.H. A gold nanoparticle-based aptamer target binding readout for ATP assay. Adv. Mater. 2007, 19:3943-3947.
34. Coller H.A., Grandori C., Tamayo P., Colbert T., Lander E.S., Eisenman R.N., Golub T.R. Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion. Proc. Natl. Acda. Sci. U.S.A 2000, 97:3260-3265.
35. Postel E.H., Flint S.J., Kessler D.J., Hogan M.E. Evidence that a triplex-forming oligodeoxyribonucleotide binds to the C-Myc promoter in Hela-cells, thereby reducing C-Myc messenger-RNA levels. Proc. Natl. Acda. Sci. U.S.A 1991, 88:8227-8231.
36. McGuffie E.M., Catapano C.V. Design of a novel triple helix-forming oligodeoxyribonucleotide directed to the major promoter of the c-myc gene. Nucleic Acids Res. 2002, 30:2701-2709.
37. Catapano C.V., McGuffie E.M., Pacheco D., Carbone G.M.R. Inhibition of gene expression and cell proliferation by triple helix-forming oligonucleotides directed to the c-myc gene. Biochemistry 2000, 39:5126-5138.
38. McGuffie E.M., Pacheco D., Carbone G.M.R., Catapano C.V. Antigene and antiproliferative effects of a c-myc-targeting phosphorothioate triple helix-forming oligonucleotide in human leukemia cells. Cancer Res. 2000, 60:3790-3799.
39. Ren J.S., Chaires J.B. Sequence and structural selectivity of nucleic acid binding ligands. Biochemistry 1999, 38:16067-16075.
40. Reha D., Kabelac M., Ryjacek F., Sponer J., Sponer J.E., Elstner M., Suhai S., Hobza P. Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4',6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study. J. Am. Chem. Soc. 2002, 124:3366-3376.