Direct fluorescence detection of RNA on microarrays by surface-initiated enzymatic polymerization

Analytical Chemistry

Volumn 85, Issue 1, 2013, Pages 426-433

  Tjong, Vinalia ^a   Yu, Hua ^a,b   Hucknall, Angus ^a   Chilkoti, Ashutosh ^a,b  

^a Duke University   (United States)

^b DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYADENOSINE; DIRECT DETECTION; DNA STRANDS; DYNAMIC RANGE; ENZYMATIC POLYMERIZATION; FLUORESCENCE DETECTION; IMMOBILIZED PEPTIDE; LIMIT OF DETECTION; MRNA TARGETS; RNA MOLECULES; RNA-DNA HYBRIDS; SEQUENTIAL ADDITION; SURFACE-INITIATED; TRIPHOSPHATE;

CATALYSIS; DNA; FLUORESCENCE; FLUOROPHORES; MICROARRAYS; POLYMERIZATION; YEAST;

RNA;

CARBOCYANINE; CYANINE DYE 3; EXORIBONUCLEASE; FLUORESCENT DYE; POLY(A)-SPECIFIC RIBONUCLEASE; POLYADENYLATE SPECIFIC RIBONUCLEASE; RNA;

ARTICLE; CHEMISTRY; DNA MICROARRAY; ENZYMOLOGY; METABOLISM; NUCLEIC ACID AMPLIFICATION; NUCLEIC ACID HYBRIDIZATION; POLYMERIZATION; SACCHAROMYCES CEREVISIAE; SURFACE PROPERTY;

CARBOCYANINES; EXORIBONUCLEASES; FLUORESCENT DYES; NUCLEIC ACID AMPLIFICATION TECHNIQUES; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERIZATION; RNA; SACCHAROMYCES CEREVISIAE; SURFACE PROPERTIES;

EID: 84871779578     PISSN: 00032700     EISSN: 15206882     Source Type: Journal    
DOI: 10.1021/ac303132j     Document Type: Article

References (44)

1. Duggan, D. J.; Bittner, M.; Chen, Y.; Meltzer, P.; Trent, J. M. Nature genetics 1999, 21, 10-14
2. Schulze, A.; Downward, J. Nature cell biology 2001, 3, E190-195
3. Barrett, J. C.; Kawasaki, E. S. Drug discovery today 2003, 8, 134-141
4. Liu, Y. T. Infectious disorders drug targets 2008, 8, 183-188
5. Wang, D.; Coscoy, L.; Zylberberg, M.; Avila, P. C.; Boushey, H. A.; Ganem, D.; DeRisi, J. L. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 15687-15692
6. Nelson, P. T.; Baldwin, D. A.; Scearce, L. M.; Oberholtzer, J. C.; Tobias, J. W.; Mourelatos, Z. Nat Methods 2004, 1, 155-161
7. Thomson, J. M.; Parker, J.; Perou, C. M.; Hammond, S. M. Nat Methods 2004, 1, 47-53
8. Shingara, J.; Keiger, K.; Shelton, J.; Laosinchai-Wolf, W.; Powers, P.; Conrad, R.; Brown, D.; Labourier, E. Rna-a Publication of the Rna Society 2005, 11, 1461-1470
9. Wang, H.; Ach, R. A.; Curry, B. Rna-a Publication of the Rna Society 2007, 13, 151-159
10. Vorwerk, S.; Ganter, K.; Cheng, Y.; Hoheisel, J.; Stahler, P. F.; Beier, M. New Biotechnol 2008, 25, 142-149
11. Zhou, W. J.; Chen, Y.; Corn, R. M. Anal. Chem. 2011, 83, 3897-3902
12. Freeman, W. M.; Walker, S. J.; Vrana, K. E. Biotechniques 1999, 26, 112-125
13. Coller, J. A. In Batch Effects and Noise in Microarray Experiments: Sources and Solutions; Scherer, A., Ed.; John Wiley & Sons, Ltd, 2009, pp 5-17.
14. Wark, A. W.; Lee, H. J.; Corn, R. M. Angew Chem Int Edit 2008, 47, 644-652
15. Naef, F.; Magnasco, M. O. Phys. Rev. E 2003, 68, 0119061-0119064
16. Hucknall, A.; Kim, D.-H.; Rangarajan, S.; Hill, R. T.; Reichert, W. M.; Chilkoti, A. Adv. Mater. 2009, 21, 1968-1971
17. Chow, D. C.; Lee, W. K.; Zauscher, S.; Chilkoti, A. J. Am. Chem. Soc. 2005, 127, 14122-14123
18. Tjong, V.; Yu, H.; Hucknall, A.; Rangarajan, S.; Chilkoti, A. Anal. Chem. 2011, 83, 5153-5159
19. Fang, S. P.; Lee, H. J.; Wark, A. W.; Corn, R. M. J. Am. Chem. Soc. 2006, 128, 14044-14046
20. Hucknall, A.; Rangarajan, S.; Chilkoti, A. Adv. Mater. 2009, 21, 2441-2446
21. Paredes, E.; Evans, M.; Das, S. R. Methods 2011, 54, 251-259
22. Proudnikov, D.; Mirzabekov, A. Nucleic acids research 1996, 24, 4535-4542
23. Garnier, A.; Husken, D.; Weiler, J. Nucleosides, nucleotides & nucleic acids 2001, 20, 1181-1185
24. Qin, P. Z.; Pyle, A. M. Methods 1999, 18, 60-70
25. Paredes, E.; Das, S. R. Chembiochem: a European journal of chemical biology 2011, 12, 125-131
26. Hilario, E. Mol Biotechnol 2004, 28, 77-80
27. Igloi, G. L. Anal. Biochem. 1996, 233, 124-129
28. Cole, K.; Truong, V.; Barone, D.; McGall, G. Nucleic acids research 2004, 32, e86
29. Lingner, J.; Keller, W. Nucleic acids research 1993, 21, 2917-2920
30. Martin, G.; Keller, W. Rna-a Publication of the Rna Society 1998, 4, 226-230
31. Rosemeyer, V.; Laubrock, A.; Seibl, R. Anal. Biochem. 1995, 224, 446-449
32. Jensen, K. K.; Orum, H.; Nielsen, P. E.; Norden, B. Biochemistry-Us 1997, 36, 5072-5077
33. Lee, J. M.; Cho, H.; Jung, Y. Angew Chem Int Edit 2010, 49, 8662-8665
34. Liang, R.-Q.; Li, W.; Li, Y.; Tan, C.-y.; Li, J.-X.; Jin, Y.-X.; Ruan, K.-C. Nucleic acids research 2005, 33, e17
35. Hu, Z. L.; Zhang, A. X.; Storz, G.; Gottesman, S.; Leppla, S. H. Nucleic acids research 2006, 34
36. Liu, W. T.; Guo, H.; Wu, J. H. Appl. Environ. Microbiol. 2007, 73, 73-82
37. Mehlmann, M.; Townsend, M. B.; Stears, R. L.; Kuchta, R. D.; Rowlen, K. L. Anal. Biochem. 2005, 347, 316-323
38. Squires, T. M.; Messinger, R. J.; Manalis, S. R. Nat. Biotechnol. 2008, 26, 417-426
39. Sheehan, P. E.; Whitman, L. J. Nano Lett. 2005, 5, 803-807
40. Werner, A. Nucleic acids research 2010, 39, e17
41. Cui, Z.-Q.; Zhang, Z.-P.; Zhang, X.-E.; Wen, J.-K.; Zhou, Y.-F.; Xie, W.-H. Nucleic acids research 2005, 33, 3245-3252
42. Smith, D. E.; Perkins, T. T.; Chu, S. Macromolecules 1996, 29, 1372-1373
43. Fixe, F.; Branz, H. M.; Louro, N.; Chu, V.; Prazeres, D. M.; Conde, J. P. Biosensors & bioelectronics 2004, 19, 1591-1597
44. Bin, X.; Sargent, E. H.; Kelley, S. O. Anal. Chem. 2010, 82, 5928-5931