DNA microarrays

Angewandte Chemie - International Edition

Volumn 38, Issue 19, 1999, Pages 2865-2869

  Niemeyer, Christof M ^a   Blohm, Dietmar ^a  

^a UNIVERSITY OF BREMEN   (Germany)

Author keywords

Analytical methods; Gene technology; Microarrays; Nucleic acids; Oligonucleotides

Indexed keywords

DNA;

ARTICLE; AUTOMATION; BINDING COMPETITION; COVALENT BOND; DEVICE; DNA STRUCTURE; GENE EXPRESSION; MASS SPECTROMETRY; NUCLEOTIDE SEQUENCE;

EID: 0033523687     PISSN: 14337851     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1521-3773(19991004)38:19<2865::AID-ANIE2865>3.0.CO;2-F     Document Type: Article

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44. Mixed oligomers containing ribo-and deoxyribonucleotides: J. D. Hoheisel, Nucleic Acids Res. 1996, 24, 430; modified uridine and adenosine bases in the brcal analysis: J. G. Hacia, S. A. Woski, J. Fidanza, K. Edgemon, N. Hunt, G. McGall, S. P. Fodor, F. S. Collins, Nucleic Acids Res. 1998, 26, 4975; alkyldeoxycytidine-modified nucleotides (H. K. Nguyen, E. Bonfils, P. Auffray, P. Costaglioli, P. Schmitt, U. Asseline, M. Durand, J. C. Maurizot, D. Dupret, N. T. Thuong, Nucleic Acids Res. 1998, 26, 4249) show uniform duplex stabilities in the presence of chaotropic agents: H. K. Nguyen, O. Fournier, U. Asseline, D. Dupret, N. T. Thuong, Nucleic Acids Res. 1999, 27, 1492; peptide nucleic adids (PNAs) are ideal probe molecules since the duplex stability is only scarcly influenced by the presence of secondary structures: H. F. Arlinghaus, M. N. Kwoka, K. B. Jacobson, Anal. Chem. 1997, 69, 3747; J. Weiler, H. Gausepohl, N. Hauser, O. N. Jensen, J. D. Hoheisel. Nucleic Acids Res. 1997, 25, 2792; see also ref. [3].
45. Mixed oligomers containing ribo-and deoxyribonucleotides: J. D. Hoheisel, Nucleic Acids Res. 1996, 24, 430; modified uridine and adenosine bases in the brcal analysis: J. G. Hacia, S. A. Woski, J. Fidanza, K. Edgemon, N. Hunt, G. McGall, S. P. Fodor, F. S. Collins, Nucleic Acids Res. 1998, 26, 4975; alkyldeoxycytidine-modified nucleotides (H. K. Nguyen, E. Bonfils, P. Auffray, P. Costaglioli, P. Schmitt, U. Asseline, M. Durand, J. C. Maurizot, D. Dupret, N. T. Thuong, Nucleic Acids Res. 1998, 26, 4249) show uniform duplex stabilities in the presence of chaotropic agents: H. K. Nguyen, O. Fournier, U. Asseline, D. Dupret, N. T. Thuong, Nucleic Acids Res. 1999, 27, 1492; peptide nucleic adids (PNAs) are ideal probe molecules since the duplex stability is only scarcly influenced by the presence of secondary structures: H. F. Arlinghaus, M. N. Kwoka, K. B. Jacobson, Anal. Chem. 1997, 69, 3747; J. Weiler, H. Gausepohl, N. Hauser, O. N. Jensen, J. D. Hoheisel. Nucleic Acids Res. 1997, 25, 2792; see also ref. [3].
46. Mixed oligomers containing ribo-and deoxyribonucleotides: J. D. Hoheisel, Nucleic Acids Res. 1996, 24, 430; modified uridine and adenosine bases in the brcal analysis: J. G. Hacia, S. A. Woski, J. Fidanza, K. Edgemon, N. Hunt, G. McGall, S. P. Fodor, F. S. Collins, Nucleic Acids Res. 1998, 26, 4975; alkyldeoxycytidine-modified nucleotides (H. K. Nguyen, E. Bonfils, P. Auffray, P. Costaglioli, P. Schmitt, U. Asseline, M. Durand, J. C. Maurizot, D. Dupret, N. T. Thuong, Nucleic Acids Res. 1998, 26, 4249) show uniform duplex stabilities in the presence of chaotropic agents: H. K. Nguyen, O. Fournier, U. Asseline, D. Dupret, N. T. Thuong, Nucleic Acids Res. 1999, 27, 1492; peptide nucleic adids (PNAs) are ideal probe molecules since the duplex stability is only scarcly influenced by the presence of secondary structures: H. F. Arlinghaus, M. N. Kwoka, K. B. Jacobson, Anal. Chem. 1997, 69, 3747; J. Weiler, H. Gausepohl, N. Hauser, O. N. Jensen, J. D. Hoheisel. Nucleic Acids Res. 1997, 25, 2792; see also ref. [3].
47. Mixed oligomers containing ribo-and deoxyribonucleotides: J. D. Hoheisel, Nucleic Acids Res. 1996, 24, 430; modified uridine and adenosine bases in the brcal analysis: J. G. Hacia, S. A. Woski, J. Fidanza, K. Edgemon, N. Hunt, G. McGall, S. P. Fodor, F. S. Collins, Nucleic Acids Res. 1998, 26, 4975; alkyldeoxycytidine-modified nucleotides (H. K. Nguyen, E. Bonfils, P. Auffray, P. Costaglioli, P. Schmitt, U. Asseline, M. Durand, J. C. Maurizot, D. Dupret, N. T. Thuong, Nucleic Acids Res. 1998, 26, 4249) show uniform duplex stabilities in the presence of chaotropic agents: H. K. Nguyen, O. Fournier, U. Asseline, D. Dupret, N. T. Thuong, Nucleic Acids Res. 1999, 27, 1492; peptide nucleic adids (PNAs) are ideal probe molecules since the duplex stability is only scarcly influenced by the presence of secondary structures: H. F. Arlinghaus, M. N. Kwoka, K. B. Jacobson, Anal. Chem. 1997, 69, 3747; J. Weiler, H. Gausepohl, N. Hauser, O. N. Jensen, J. D. Hoheisel. Nucleic Acids Res. 1997, 25, 2792; see also ref. [3].
48. Mixed oligomers containing ribo-and deoxyribonucleotides: J. D. Hoheisel, Nucleic Acids Res. 1996, 24, 430; modified uridine and adenosine bases in the brcal analysis: J. G. Hacia, S. A. Woski, J. Fidanza, K. Edgemon, N. Hunt, G. McGall, S. P. Fodor, F. S. Collins, Nucleic Acids Res. 1998, 26, 4975; alkyldeoxycytidine-modified nucleotides (H. K. Nguyen, E. Bonfils, P. Auffray, P. Costaglioli, P. Schmitt, U. Asseline, M. Durand, J. C. Maurizot, D. Dupret, N. T. Thuong, Nucleic Acids Res. 1998, 26, 4249) show uniform duplex stabilities in the presence of chaotropic agents: H. K. Nguyen, O. Fournier, U. Asseline, D. Dupret, N. T. Thuong, Nucleic Acids Res. 1999, 27, 1492; peptide nucleic adids (PNAs) are ideal probe molecules since the duplex stability is only scarcly influenced by the presence of secondary structures: H. F. Arlinghaus, M. N. Kwoka, K. B. Jacobson, Anal. Chem. 1997, 69, 3747; J. Weiler, H. Gausepohl, N. Hauser, O. N. Jensen, J. D. Hoheisel. Nucleic Acids Res. 1997, 25, 2792; see also ref. [3].
49. Mixed oligomers containing ribo-and deoxyribonucleotides: J. D. Hoheisel, Nucleic Acids Res. 1996, 24, 430; modified uridine and adenosine bases in the brcal analysis: J. G. Hacia, S. A. Woski, J. Fidanza, K. Edgemon, N. Hunt, G. McGall, S. P. Fodor, F. S. Collins, Nucleic Acids Res. 1998, 26, 4975; alkyldeoxycytidine-modified nucleotides (H. K. Nguyen, E. Bonfils, P. Auffray, P. Costaglioli, P. Schmitt, U. Asseline, M. Durand, J. C. Maurizot, D. Dupret, N. T. Thuong, Nucleic Acids Res. 1998, 26, 4249) show uniform duplex stabilities in the presence of chaotropic agents: H. K. Nguyen, O. Fournier, U. Asseline, D. Dupret, N. T. Thuong, Nucleic Acids Res. 1999, 27, 1492; peptide nucleic adids (PNAs) are ideal probe molecules since the duplex stability is only scarcly influenced by the presence of secondary structures: H. F. Arlinghaus, M. N. Kwoka, K. B. Jacobson, Anal. Chem. 1997, 69, 3747; J. Weiler, H. Gausepohl, N. Hauser, O. N. Jensen, J. D. Hoheisel. Nucleic Acids Res. 1997, 25, 2792; see also ref. [3].
50. The hybridization efficiencies, determined experimentally for a set of array-bound oligomers, are used to generate heuristic rules by means of bioinformatic procedures employing neuronal networks. The next generation of oligomers is designed by following these rules: D. J. Lockhart, H. Dong, M. C. Byrne, M. T. Follettie, M. V. Gallo, M. S. Chee, M. Mittmann, C. Wang, M. Kobayashi, H. Horton, E. L. Brown, Nat. Biotechnol. 1996, 14, 1675.
51. Surface plasmon resonance: a) S. J. Wood, Microchem. J. 1992, 47, 330;
52. b) analysis of enzymatic DNA manipulations: P. Nilsson, B. Persson, M. Uhlen, P. A. Nygren, Anal. Biochem. 1995, 224, 400;
53. c) elipsometry: D. E. Gray, S. C. Case-Green, T. S. Fell, P. J. Dobson, E. M. Southern, Langmuir 1997, 13, 2833;
54. d) optical grating coupler: F. F. Bier, F. W. Scheller, Biosens. Bioelectron. 1996, 11, 669;
55. e) resonance mirror: H. J. Watts, D. Yeung, H. Parkes, Anal. Chem. 1995, 67, 4283;
56. f) reflectometric interference spectroscopy: J. Piehler, A. Brecht, G. Gauglitz, M. Zerlin, C. Maul, R. Thiericke, S. Grabley, Anal. Biochem. 1997, 249, 94.
57. Nucleic acid hybridization can be detected by means of the piezoelectric quartz crystal microbalance (QCM): Y. Okahata, Y. Matsunobu, K. Ijiro, M. Mukae, A. Murakami, K. Makino, J. Am. Chem. Soc. 1992, 114, 8299;
58. b) S. Yamaguchi, T. Shimomura, Anal. Chem. 1993, 65, 1925;
59. c) K. Ito, K. Hashimoto, Y. Ishimori, Anal. Chim. Acta 1996, 327, 29;
60. d) hybridization using QCM-bound DNA multilayers: F. Caruso, E. Rodda, D. N. Furlong, K. Niikura, Y. Okahata, Anal. Chem. 1997, 69, 2043;
61. e) detection of single mismatches by means of QCM-bound PNA probes: J. Wang, P. E. Nielsen, M. Jiang, X. Cai, J. R. Fernandas, D. H. Grant, M. Ozsoz, A. Beglieter, M. Mowat, Anal. Chem. 1997, 69, 5200;
62. f) hybridization with QCM-bound DNA dendrimers: J. Wang, M. Jiang, T. W. Nilsen, R. C. Getts, J. Am. Chem. Soc. 1998, 120, 8281;
63. g) detection of the enzymatic activity of a DNA polymerase at surfaces of a QCM: K. Niikura, M. Hisao, Y. Okahata, J. Am. Chem. Soc. 1998, 120, 8537; for electrochemical analysis of hybridization, see J. Wang, Chem. Eur. J. 1999, 5, 1681.
64. g) detection of the enzymatic activity of a DNA polymerase at surfaces of a QCM: K. Niikura, M. Hisao, Y. Okahata, J. Am. Chem. Soc. 1998, 120, 8537; for electrochemical analysis of hybridization, see J. Wang, Chem. Eur. J. 1999, 5, 1681.
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66. This principle has been developed by the US company Nanogen: a) C. F. Edman, D. E. Raymond, D. J. Wu, E. Tu, R. G. Sosnowski, W. F. Butler, M. Nerenberg, M. J. Heller, Nucleic Acids Res. 1997, 25, 4907;
67. b) R. G. Sosnowski, E. Tu, W. F. Butler, J. P. O'Connell, M. J. Heller, Proc. Natl. Acad. Sci. USA 1997, 94, 1119;
68. c) J. Cheng, E. L. Sheldon, L. Wu, A. Uribe, L. O. Gerrue, J. Carrino, M. J. Heller, J. P. O'Connell, Nat. Biotechnol. 1998, 16, 541;
69. d) P. N. Gilles, D. J. Wu, C. B. Foster, P. J. Dillon, S. J. Chanock, Nat. Biotechnol. 1999, 17, 365.
70. a) Review: E. Nordhoff, F. Kirpekar, P. Roepstorff, Mass Spectrom. Rev. 1996, 15, 67;
71. b) enzymatic elongation of immobilized oligomers with dideoxy terminators allows the detection of SNPs even in heterozygous probands: G. S. Higgins, D. P. Little, H. Köster, Biotechniques 1997, 23, 710;
72. c) MALDI-MS sequencing of the human p53 gene: D. J. Fu, K. Tang, A. Braun, D. Reuter, B. Darnhofer-Demar, D. P. Little, M. J. O'Donnell, C. R. Cantor, H. Köster, Nat. Biotechnol. 1998, 16, 381;
73. d) nucleic acids of more than 500 kDa can be detected by means of an infrared laser: S. Berkenkamp, F. Kirpekar, F. Hillenkamp, Science 1998, 281, 260;
74. e) MALDI-MS analysis of length polymorphisms: A. Braun, D. P. Little, D. Reuter, B. Müller-Mysok, H. Köster, Genomics 1997, 46, 18; P. L. Ross, P. Belgrader, Anal. Chem. 1997, 69, 3966.
75. e) MALDI-MS analysis of length polymorphisms: A. Braun, D. P. Little, D. Reuter, B. Müller-Mysok, H. Köster, Genomics 1997, 46, 18; P. L. Ross, P. Belgrader, Anal. Chem. 1997, 69, 3966.
76. a) Single-molecule detection using fluorescence spectroscopy (review: S. Weiss, Science 1999, 283, 1676) has recently been applied to the analysis of DNA hybridization (W. Trabesinger, G. J. Schutz, H. J. Gruber, H. Schindler, T. Schmidt, Anal. Chem. 1999, 71, 279) and RNA transcription (A. M. Femino, F. S. Fay, K. Fogarty, R. H. Singer, Science 1998, 280, 585);
77. a) Single-molecule detection using fluorescence spectroscopy (review: S. Weiss, Science 1999, 283, 1676) has recently been applied to the analysis of DNA hybridization (W. Trabesinger, G. J. Schutz, H. J. Gruber, H. Schindler, T. Schmidt, Anal. Chem. 1999, 71, 279) and RNA transcription (A. M. Femino, F. S. Fay, K. Fogarty, R. H. Singer, Science 1998, 280, 585);
78. a) Single-molecule detection using fluorescence spectroscopy (review: S. Weiss, Science 1999, 283, 1676) has recently been applied to the analysis of DNA hybridization (W. Trabesinger, G. J. Schutz, H. J. Gruber, H. Schindler, T. Schmidt, Anal. Chem. 1999, 71, 279) and RNA transcription (A. M. Femino, F. S. Fay, K. Fogarty, R. H. Singer, Science 1998, 280, 585);
79. b) surface-immobilized DNA can be amplified by isothermal "rolling circle amplification": P. M. Lizardi, X. Huang, Z. Zhu, P. Bray-Ward, D. C. Thomas, D. C. Ward, Nat. Genet. 1998, 19, 225.
80. Peptide arrays (R. Frank, Tetrahedron 1992, 48, 9217) are used, for instance, for the screening of antibodies: A. Kramer, J. Schneider-Mergener, Methods. Mol. Biol. 1998, 87, 25; photolithographical immobilization of immunglobulins: L. F. Rozsnyai, D. R. Benson, S. P. A. Fodor, P. G. Schultz, Angew. Chem. 1992, 104, 801; Angew. Chem. Int. Ed. Engl. 1992, 31, 759; "DNA-direcled immobilization" (DDI) uses DNA arrays as immobilization matrices for antibodies and enzymes, and thus, allows the fabrication of mixed arrays containing both nucleic acids and proteins: C. M. Niemeyer, L. Boldt, B. Ceyhan, D. Blohm, Anal. Biochem. 1999, 268, 54; protein microarrays for the screening of gene expression: A. Lueking, M. Horn, H. Eickhoff, K. Bussow, H. Lehrach, G. Walter, Anal. Biochem. 1999, 270, 103.
81. Peptide arrays (R. Frank, Tetrahedron 1992, 48, 9217) are used, for instance, for the screening of antibodies: A. Kramer, J. Schneider-Mergener, Methods. Mol. Biol. 1998, 87, 25; photolithographical immobilization of immunglobulins: L. F. Rozsnyai, D. R. Benson, S. P. A. Fodor, P. G. Schultz, Angew. Chem. 1992, 104, 801; Angew. Chem. Int. Ed. Engl. 1992, 31, 759; "DNA-direcled immobilization" (DDI) uses DNA arrays as immobilization matrices for antibodies and enzymes, and thus, allows the fabrication of mixed arrays containing both nucleic acids and proteins: C. M. Niemeyer, L. Boldt, B. Ceyhan, D. Blohm, Anal. Biochem. 1999, 268, 54; protein microarrays for the screening of gene expression: A. Lueking, M. Horn, H. Eickhoff, K. Bussow, H. Lehrach, G. Walter, Anal. Biochem. 1999, 270, 103.
82. Peptide arrays (R. Frank, Tetrahedron 1992, 48, 9217) are used, for instance, for the screening of antibodies: A. Kramer, J. Schneider-Mergener, Methods. Mol. Biol. 1998, 87, 25; photolithographical immobilization of immunglobulins: L. F. Rozsnyai, D. R. Benson, S. P. A. Fodor, P. G. Schultz, Angew. Chem. 1992, 104, 801; Angew. Chem. Int. Ed. Engl. 1992, 31, 759; "DNA-direcled immobilization" (DDI) uses DNA arrays as immobilization matrices for antibodies and enzymes, and thus, allows the fabrication of mixed arrays containing both nucleic acids and proteins: C. M. Niemeyer, L. Boldt, B. Ceyhan, D. Blohm, Anal. Biochem. 1999, 268, 54; protein microarrays for the screening of gene expression: A. Lueking, M. Horn, H. Eickhoff, K. Bussow, H. Lehrach, G. Walter, Anal. Biochem. 1999, 270, 103.
83. Peptide arrays (R. Frank, Tetrahedron 1992, 48, 9217) are used, for instance, for the screening of antibodies: A. Kramer, J. Schneider-Mergener, Methods. Mol. Biol. 1998, 87, 25; photolithographical immobilization of immunglobulins: L. F. Rozsnyai, D. R. Benson, S. P. A. Fodor, P. G. Schultz, Angew. Chem. 1992, 104, 801; Angew. Chem. Int. Ed. Engl. 1992, 31, 759; "DNA-direcled immobilization" (DDI) uses DNA arrays as immobilization matrices for antibodies and enzymes, and thus, allows the fabrication of mixed arrays containing both nucleic acids and proteins: C. M. Niemeyer, L. Boldt, B. Ceyhan, D. Blohm, Anal. Biochem. 1999, 268, 54; protein microarrays for the screening of gene expression: A. Lueking, M. Horn, H. Eickhoff, K. Bussow, H. Lehrach, G. Walter, Anal. Biochem. 1999, 270, 103.
84. Peptide arrays (R. Frank, Tetrahedron 1992, 48, 9217) are used, for instance, for the screening of antibodies: A. Kramer, J. Schneider-Mergener, Methods. Mol. Biol. 1998, 87, 25; photolithographical immobilization of immunglobulins: L. F. Rozsnyai, D. R. Benson, S. P. A. Fodor, P. G. Schultz, Angew. Chem. 1992, 104, 801; Angew. Chem. Int. Ed. Engl. 1992, 31, 759; "DNA-direcled immobilization" (DDI) uses DNA arrays as immobilization matrices for antibodies and enzymes, and thus, allows the fabrication of mixed arrays containing both nucleic acids and proteins: C. M. Niemeyer, L. Boldt, B. Ceyhan, D. Blohm, Anal. Biochem. 1999, 268, 54; protein microarrays for the screening of gene expression: A. Lueking, M. Horn, H. Eickhoff, K. Bussow, H. Lehrach, G. Walter, Anal. Biochem. 1999, 270, 103.
85. Peptide arrays (R. Frank, Tetrahedron 1992, 48, 9217) are used, for instance, for the screening of antibodies: A. Kramer, J. Schneider-Mergener, Methods. Mol. Biol. 1998, 87, 25; photolithographical immobilization of immunglobulins: L. F. Rozsnyai, D. R. Benson, S. P. A. Fodor, P. G. Schultz, Angew. Chem. 1992, 104, 801; Angew. Chem. Int. Ed. Engl. 1992, 31, 759; "DNA-direcled immobilization" (DDI) uses DNA arrays as immobilization matrices for antibodies and enzymes, and thus, allows the fabrication of mixed arrays containing both nucleic acids and proteins: C. M. Niemeyer, L. Boldt, B. Ceyhan, D. Blohm, Anal. Biochem. 1999, 268, 54; protein microarrays for the screening of gene expression: A. Lueking, M. Horn, H. Eickhoff, K. Bussow, H. Lehrach, G. Walter, Anal. Biochem. 1999, 270, 103.
86. [1], to 2D-protein arrays containing more than 10000 spots.
87. [1], to 2D-protein arrays containing more than 10000 spots.
88. [1], to 2D-protein arrays containing more than 10000 spots.
89. [1], to 2D-protein arrays containing more than 10000 spots.
90. [1], to 2D-protein arrays containing more than 10000 spots.
91. [1], to 2D-protein arrays containing more than 10000 spots.