Nanotechnology applications of nucleic acid programmable protein arrays

Functional Proteomics and Nanotechnology-Based Microarrays

Volumn , Issue , 2010, Pages 1-29

  Nicolini, Claudio ^a   LaBaer, Joshua ^b  

^a UNIVERSITY OF GENOA   (Italy)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77955068579     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.4032/9789814267779     Document Type: Chapter

References (52)

1. Adami, M., Sallam S., Eggenhöffner, R., Sartore, S., Hainsworth, G., LaBaer, J. and Nicolini, C., (2009). Label free NAPPA via nanogravimetry, in Functional Proteomics and Nanotechnology-based Microarrays, Nicolini C. and LaBaer J. Eds, Pan Stanford Series on Nanobiotechnology Volume 2, London, New York and Singapore, pp. 79-93.
2. Anderson, K. S., Ramachandran, N., Wong, J., Raphael, J. V., Hainsworth, E., Demirkan, G., Cramer, D., Aronzon, D., Hodi, F. S., Harris, L., Logvinenko, T. and LaBaer, J. (2008). Application of protein microarrays for multiplexed detection of antibodies to tumor antigens in breast cancer. Journal of Proteome Research, 7, pp. 1490-1499.
3. Berman, H. M., Westbrook, J. D., Gabanyi, M. J., Tao, Y., Shah, R., Kouranov, A., Schwede, T., Arnold, K., Kiefer, F., Bordoli, L., Kopp, J., Podvinec, M., Adams, P. D., Carter, L. G., Minor, W., Nair, R. and LaBaer, J. (2009). The Protein Structure Initiative Structural Genomics Knowledgebase. Nucleic Acid Research, 37, pp. D365-D368.
4. Borrebaeck, C. (2000). Antibodies in diagnostics - from immunoassays to protein chips. Immunology Today, 21, pp. 379-382.
5. Braud, C., Baeten, D., Giral, M., Pallier, A., Ashton-Chess, J., Braudeau, C., Chevalier, C., Lebars, A., Léger, J., Moreau, A., Pechkova, E., Nicolini, C., Soulillou, J. P. and Brouard, S. (2008). Immunosuppressive drug-free operational immune tolerance in human kidney transplants recipients: I. Blood gene expression statistical analysis. Journal of Cellular Biochemistry, 103, pp. 1681-16902.
6. Butcher, R. A., Bhullar, B. S., Perlstein, E. O., Marsischky, G., LaBaer, J. and Schreiber, S. L. (2006). Microarray-based method for monitoring yeast overexpression strains reveals small-molecule targets in TOR pathway. Nature Chemical Biology, 2, 103-109.
7. Cooper, A. A., Gitler, A. D., Cashikar, A., Haynes, C. M., Hill, K. J., Bhullar, B., Liu, K., Xu, K., Strathearn, K. E., Liu, F., Cao, S., Caldwell, K. A., Caldwell, G. A., Marsischky, G., Kolodner, R.D., LaBaer, J., Rochet, J. C., Bonini, N. M. and Lindquist, S. (2006). Alpha-synuclein blocks ER-Golgi traffic and Rab1 rescues neuron loss in Parkinson's models. Science, 313, pp. 324-328.
8. Espejo, A., Cote, J., Bednarek, A., Richard, S. and Bedford, M. T. (2002). A proteindomain microarray identifies novel protein-protein interactions. Biochemical Journal, 367, pp. 697-702.
9. Gavin, A., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J., Michon, A., Cruciat, C., Remor, M., Höfert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier M. A., Copley, R. R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P. Seraphin, B., Kuster, B., Neubauer, G. and Superti-Furga1, G. (2002). Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415, pp. 141-147.
10. Giacomelli, L. and Nicolini, C. (2006). Gene expression of human T lymphocytes cell cycle: Experimental and bioinformatic analysis. Journal of Cellular Biochemistry, 99, pp. 1326-1333.
11. Haab, B., Dunham, M. and Brown, P. (2001). Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biology, 2, pp. 4.1-4.13.
12. Ho, Y., Gruhler, A., Heilbut, A., Bader, G., Moore, L., Adams, S., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L., Wolting, C., Donaldson, I., Schandorff, S., Shewnarane, J., Vo, M., Taggart, J., Goudreault, M., Muskat, B., Alfarano, C., Dewar, D., Lin, Z., Michalickova, K., Willems, A.R., Sassi, H., Nielsen, P.A., Rasmussen, K.J., Andersen, J.R., Johansen, L.E., Hansen, L.H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Sørensen, B.D., Matthiesen, J., Hendrickson, R.C., Gleeson, F., Pawson, T., Moran, M.F., Durocher, D., Mann, M., Hogue, C.W.V., Figeys, D. and Tyers, M. (2002). Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415, pp. 180-183.
13. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. (2001). A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proceedings of the National Academy of Sciences USA, 98, pp. 4569-4574.
14. Jona, G. and Snyder, M. (2003). Recent developments in analytical and functional protein microarrays. Current Opinion in Molecular Therapeutics, 5, pp. 271-277.
15. LaBaer, J. and Ramachandran, N. (2005). Protein microarrays as tools for functional proteomics. Current Opinion in Chemical Biology, 9, pp. 14-19.
16. MacBeath, G. and Schreiber, S. (2000). Printing proteins as microarrays for highthroughput function determination. Science, 289, pp. 1760-1763.
17. Mitchell, P. (2002). A perspective on protein microarrays. Nature Biotechnology, 20, pp. 225-229.
18. Murphy, R. F. and LaBaer, J. (2009). Locations Everyone: Lights, Camera, Action!. Journal of Proteome Research, 8, pp. 1.
19. Newman, J. R. and Keating, A. E. (2003). Comprehensive identification of human bZIP interactions with coiled-coil arrays. Science, 300, pp. 2097-2101.
20. Nicolini, C. (2006). Nanogenomics for medicine. Nanomedicine, 1, pp. 147-151.
21. Nicolini, C. (2009). Nanobiotechnology and Nanobiosciences, Pan Stanford Series on Nanobiotechnology, Volume 1, Ed. C. Nicolini, London, New York and Singapore, pp. 1-376.
22. Nicolini, C., Bruzzese, D., Sivozhelezov, V. and Pechkova, E. (2008). Langmuir-Blodgett based lipase nanofilms of unique structure-function relationship. Biosystems, 94, pp. 228-232.
23. Nicolini, C., Malvezzi, A. M., Tomaselli, A., Sposito, D., Tropiano, G. and Borgogno, E. (2002). DNASER I: Layout and Data Analysis, IEEE Transactions on Nanobioscience, 1, pp. 67-72.
24. Paweletz, C. P., Charboneau, L., Bichsel, V. E., Simone, N. L., Chen, T., Gillespie, J. W., Emmert-Buck, M. R., Roth, M. J., Petricoin, I. E. and Liotta, L. A. (2001). Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 20, pp. 1981-1989.
25. Pechkova, E. and Nicolini, C. (2006). Structure and growth of ultrasmall protein microcrystals by synchrotron radiation: II. μGISAXS and microscopy of lysozyme. Journal of Cellular Biochemistry, 97, pp. 553-560.
26. Pechkova, E., Chong, S., Tripathi, S. and Nicolini, C. (2009a). Cell free expression and APA for NAPPA and protein nanocrystallography. In Functional Proteomics and Nanotechnology-based Microarrays, Nicolini C. and LaBaer J. Eds, Pan Stanford Series on Nanobiotechnology Volume 2, London, New York and Singapore, pp. 121-147.
27. Pechkova, E., Sartore, M., Giacomelli, L. and Nicolini, C. (2007). Atomic force microscopy of protein films and crystals. Review of Scientific Instruments, 78, pp. 093704-1-093704-7.
28. Pechkova, E., Tripathi, S. and Nicolini, C. (2009b). μGISAXS of LB protein films: effect of temperature on long range order. Journal of Synchrotron Radiation, 16, pp. 330-335.
29. Pechkova, E., Tripathi, S., Spera, R. and Nicolini, C. (2008b). Groel crystal growth and characterization. Biosystems, 94, pp. 223-227.
30. Pechkova, E., Vasile, F., Spera, R. and Nicolini, C. (2008a). Crystallization of alpha and beta subunits of IF2 translation initiation factor from Archabacteria Sulfolobus Solfataricus. Journal of Crystal Growth, 310, pp. 3767-3770.
31. Ramachandran, N., Anderson, K. S., Raphael, J. V., Hainsworth, E., Sibani, S., Montor, W. R., Pacek, M., Wong, J., Elianne, M., Sanda, M. G., Hu, Y., Lovinenko, T. and LaBaer, J. (2008c). Tracking humoral responses using self assembling protein microarrays. Proteomics Clinical Application, 2, pp. 1518-1527.
32. Ramachandran, N., Hainsworth, E., Bhullar, B., Eisenstein, S., Rosen, B., Lau, A. Y., Walter, J. C. and LaBaer, J. (2004). Self-assembling protein microarrays. Science, 305, pp. 86-90.
33. Ramachandran, N., Raphael, J.V., Hainsworth, E., Demirkan, G., Fuentes, M.G., Rolfs, A., Hu, Y.H., LaBaer, J. (2008a). Next-generation high-density self-assembling functional protein arrays. Nature Methods, 5, pp. 535-538.
34. Ramachandran, N., Srivastava, S. and LaBaer, J. (2008b). Applications of protein microarrays for biomarker discovery. Proteomics Clinical Application, 2, 1444-1459.
35. Rolfs, A., Montor, W. R., Yoon, S. S., Hu, Y., Bhullar, B., Kelley, F., McCarron, S., Jepson, D. A., Shen, B., Taycher, E., Mohr, S. E., Zuo, D. M., Williamson, J., Mekalanos, J. and LaBaer, J. (2008). Production and sequence validation of a complete full length ORF collection for the pathogenic bacterium Vibrio cholerae. Proceedings of the National Academy of Sciences USA, 105, pp. 4364-4369.
36. Sartore, M., Bezerra Correia Terencio, T., Eggenhöffner, R., Stura, E., Hainsworth, G., LaBaer, J. and Nicolini, C. (2009). Label free detection of NAPPA: atomic force microscopy. In Functional Proteomics and Nanotechnology-based Microarrays, Nicolini C. and LaBaer J. Eds, Pan Stanford Series on Nanobiotechnology Volume 2, London, New York and Singapore, pp. 109-120.
37. Sartore, M., Pace, R., Faraci, P., Nardelli, D., Adami, M., Ram, M. K. and Nicolini, C. (2000). Controlled-atmosphere chamber for atomic force microscopy investigations. Review of Scientific Instruments, 71, pp. 1-5.
38. Sivozhelezov, V., Braud, C., Giacomelli, L., Pechkova, E., Giral, M., Soulillou, J. P., Brouard, S. and Nicolini C. (2008). Immunosuppressive drug-free operational immune tolerance in human kidney transplants recipients: II. Nonstatistical gene microarray analysis. Journal of Cellular Biochemistry, 103, pp. 1693-1706.
39. Sivozhelezov, V., Giacomelli, L., Tripathi, S. and Nicolini, C. (2006). Gene expression in the cell cycle of human T lymphocytes: I. Predicted gene and protein networks. Journal of Cellular Biochemistry, 97, pp. 1137-1150.
40. Sivozhelezov, V., Spera, R., Giacomelli, L., Hainsworth, G., LaBaer, J., Bragazzi N. and Nicolini, C. (2009). Bioinformatics and fluorescence DNASER for NAPPA studies on cell transformation and cell cycle. In Functional Proteomics and Nanotechnology-based Microarrays, Nicolini C. and LaBaer J. Eds, Pan Stanford Series on Nanobiotechnology Volume 2, London, New York and Singapore, pp. 31-59.
41. Spera, R. and Nicolini, C. (2007). cAMP induced alterations of chinese hamster ovary cells monitored by mass spectrometry. Journal of Cellular Biochemistry, 102, pp. 473-482.
42. Spera, R. and Nicolini, C. (2008). Nappa microarrays and mass spectrometry: new trends and challenges, Essential in Nanoscience Booklet Series (Taylor & Francis Group/CRC Press).
43. Spera, R., Badino, F., Hainsworth, G., Fuentes, M., Srivastava, S., LaBaer, J. and Nicolini, C. (2009). Label free detection of NAPPA via mass spectrometry. In Functional Proteomics and Nanotechnology-based Microarrays, Nicolini C. and LaBaer J. Eds, Pan Stanford Series on Nanobiotechnology Volume 2, London, New York and Singapore, pp.61-78.
44. Starr, C. and Hanover, J. (1990). Glycosylation of nuclear pore protein p62. Reticulocyte lysate catalyzes O-linked N-acetylglucosamine addition in vitro. Journal of Biological Chemistry, 265, pp. 6868-6873.
45. Stura, E., Bruzzese, D., Grasso, V., Valerio, V., Perlo, P. and Nicolini, C. (2007), Anodic porous alumina as mechanical stability enhancer for Ldl-cholesterol sensitive electrodes. Biosensors & Bioelectronics, 23, pp. 655-660.
46. Stura, E., Larosa, C., Bezerra Correia Terencio, T., Hainsworth, E., Ramachandran, N., LaBaer, J. and Nicolini, C. (2009). Label-free NAPPA: anodic porous alumina. In Functional Proteomics and Nanotechnology-based Microarrays, Nicolini C. and LaBaer J. Eds, Pan Stanford Series on Nanobiotechnology Volume 2, London, New York and Singapore, pp. 95-108.
47. Uetz, P., Giot, L., Cagney, G., Mansfield, T., Judson, R., Knight, J., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., Qureshi-Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M. J., Johnston, M., Fields, S. and Rothberg, J. M. (2000). A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, pp. 623-627.
48. Walhout, A., Sordella, R., Lu, X., Hartley, J., Temple, G., Brasch, M., Thierry-Mieg, N. and Vidal, M. (2000). Protein interaction mapping in C. elegans using proteins involved in vulval development. Science, 287, pp. 116-122.
49. Walter, P. and Blobel, G. (1983). Preparation of microsomal membranes for cotranslational protein translocation. Methods Enzymology, 96, pp. 84-93. Nanotechnology Applications of Nucleic Acid Programmable Protein Arrays 29.
50. Witt, A. E., Hines, L. M., Collins, N. L., Hu, Y., Gunawardane, R. N., Moreira, D., Raphael, J., Jepson, D., Koundinya, M., Rolfs, A., Taron, B., Isakoff, S. J., Brugge, J. S. and LaBaer J. (2006). Functional proteomics approach to investigate the biological activities of cDNAs implicated in breast cancer. Journal of Proteome Research, 5, pp. 599-610.
51. Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S., Houfek, T., Mitchell, T., Miller, P., Dean, R. A., Gerstein, M. and Snyder, M. (2001). Global analysis of protein activities using proteome chips. Science, 293, pp. 2101-2105.
52. Zuo, D. M., Mohr, S. E., Hu, Y. H., Taycher, E., Rolfs, A., Kramer, J., Williamson, J. and LaBaer, J. (2007). PlasmID: a centralized repository for plasmid clone information and distribution. Nucleic Acids Research, 35, pp. D680-D684.