Substrate Patterning and Activation Strategies for DNA Chip Fabrication

Chapter
Part of the Topics in Current Chemistry book series (TOPCURRCHEM, volume 260)

Abstract

The immobilization of nucleic acids onto substrates in array fabrication is a complex process involving three major steps: (i) the chemical modification of the arrayed material in such a fashion that it can interact with complementary functionalities present on the substrate to form a stable bond; (ii) the coating of the support surface with adequate functional groups to allow specific binding and prevent nonspecific adsorption of the material to be arrayed; and (iii) the use of a delivery system that brings small quantities of the arrayed material to specific positions on the surface. Different types of nucleic acids or their analogues (cDNA, oligonucleotides or peptide nucleic acids), supports (silica, gold, polymeric membranes and gels), surface activation chemistries (organosilanes, thiols) and patterning tools can be used for these purposes and will be described in this review.

DNA immobilization Surface chemistry Surface activation Patterning DNA arrays 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Hitt E (2004) Scientist 18:38 Google Scholar
  2. 2.
    Holloway AJ, van Laar RK, Tothill RW, Bowtell DDL (2002) Nat Gen 32:481 Google Scholar
  3. 3.
    Stears RL, Martinsky T, Schena M (2003) Nature Medicine 9:140 Google Scholar
  4. 4.
    Wheatley JB, Lyttle MH, Hocker MD, Schmidt DE (1996) J Chromatography A 726:77 CrossRefGoogle Scholar
  5. 5.
    Skrzypczynski Z, Wayland S (2004) Biocon Chem 15:583 Google Scholar
  6. 6.
    Skrzypczynski Z, Wayland S (2003) Biocon Chem 14:642 Google Scholar
  7. 7.
    Rogers YH, Jiang-Baucom P, Huang ZJ, Bogdanov V, Anderson S, Boyce-Jacino MT (1999) Anal Biochem 266:23 CrossRefGoogle Scholar
  8. 8.
    Charles PT, Vora GJ, Andreadis JD, Fortney AJ, Meador CE, Dulcey CS, Stenger DA (2003) Langmuir 19:1586 CrossRefGoogle Scholar
  9. 9.
    Defrancq E, Hoang A, Vinet F, Dumy P (2003) Bioorg Med Chem Lett 13:2683 CrossRefGoogle Scholar
  10. 10.
    Boncheva M, Scheibler L, Lincoln P, Vogel H, Akerman B (1999) Langmuir 15:4317 CrossRefGoogle Scholar
  11. 11.
    Fang SY, Bergstrom DE (2003) Biocon Chem 14:80 Google Scholar
  12. 12.
    Guzaev A, Lonnberg H (1999) Tetrahedron 55:9101 CrossRefGoogle Scholar
  13. 13.
    Brown R, Smith WE, Graham D (2001) Tetrahedron Lett 42:2197 Google Scholar
  14. 14.
    Kumar A, Larsson O, Parodi D, Liang Z (2000) Nucleic Acid Res 28:e71 Google Scholar
  15. 15.
    Kumar A, Liang Z (2001) Nucleic Acid Res 29:e2 Google Scholar
  16. 16.
    Maier MA, Yannopoulos CG, Mohamed N, Roland A, Fritz H, Mohan V, Just G, Manoharan M (2003) Biocon Chem 14:18 Google Scholar
  17. 17.
    Safinya CR (2001) Curr Opin Struc Biol 11:440 Google Scholar
  18. 18.
    Shchepinov MS, CaseGreen SC, Southern EM (1997) Nucleic Acid Res 25:1155 Google Scholar
  19. 19.
    Guo Z, Guilfoyle RA, Thiel AJ, Wang R, Smith LM (1994) Nucleic Acid Res 22:5456 Google Scholar
  20. 20.
    Chou CC, Chen CH, Lee TT, Konan P (2004) Nucleic Acid Res 32:e99 Google Scholar
  21. 21.
    Bruce IJ, Taylor J, Todd M, Davies MJ, Borioni E, Sangregorio C, Sen T (2004) J Magn Magn Mat 284:145–160 CrossRefGoogle Scholar
  22. 22.
    Petrovykh DY, Kimura-Suda H, Tarlov MJ, Whitman LJ (2004) Langmuir 20:429 CrossRefGoogle Scholar
  23. 23.
    Kimura-Suda H, Petrovykh DY, Tarlov MJ, Whitman LJ (2003) J Am Chem Soc 125:9014 CrossRefGoogle Scholar
  24. 24.
    Wolf LK, Gao Y, Georgiadis RM (2004) Langmuir 20:3357 Google Scholar
  25. 25.
    Brandt O, Feldner J, Stephan A, Schroder M, Schnolzer M, Arlinghaus HF, Hoheisel JD, Jacob A (2003) Nucleic Acid Res 31 Google Scholar
  26. 26.
    Matysiak S, Hauser NC, Wurtz S, Hoheisel JD (1999) Nucleosid Nucleotid 18:1289 Google Scholar
  27. 27.
    Strother T, Cai W, Zhao XS, Hamers RJ, Smith LM (2000) J Am Chem Soc 122:1205 CrossRefGoogle Scholar
  28. 28.
    Southern E, Mir K, Shchepinov M (1999) Nat Gen 21:5 Google Scholar
  29. 29.
    Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G (1999) Nat Gen 21:15 Google Scholar
  30. 30.
    Frey BL, Corn RM (1996) Anal Chem 68:3187 Google Scholar
  31. 31.
    Beaucage SL (2001) Curr Med Chem 8:1213 Google Scholar
  32. 32.
    Consolandi C, Castiglioni B, Bordoni R, Busti E, Battaglia C, Bernardi LR, De Bellis G (2002) Nucleosid Nucleotid Nucleic Acids 21:561 Google Scholar
  33. 33.
    Chu SK, Hsu M, Ku WC, Tu CY, Tseng YT, Lau WK, Yan RY, Ma JT, Tzeng CM (2003) Biochem J 374:625 Google Scholar
  34. 34.
    Sen T, Bruce IJ (2005) Langmuir 21:7029–7035 Google Scholar
  35. 35.
    Pirrung MC (2002) Angew Chem-Int Edn 41:1277 Google Scholar
  36. 36.
    Oh SJ, Cho SJ, Kim CO, Park JW (2002) Langmuir 18:1764 Google Scholar
  37. 37.
    Halliwell CM, Cass AEG (2001) Anal Chem 73:2476 CrossRefGoogle Scholar
  38. 38.
    Beier M, Hoheisel JD (1999) Nucleic Acid Res 27:1970 Google Scholar
  39. 39.
    Dolan PL, Wu Y, Ista LK, Metzenberg RL, Nelson MA, Lopez GA (2001) Nucleic Acid Res 29:e107 Google Scholar
  40. 40.
    Benters R, Niemeyer CM, Wohrle D (2001) Chembiochem 2:686 CrossRefGoogle Scholar
  41. 41.
    Trevisiol E, Le Berre-Anton V, Leclaire J, Pratviel G, Caminade AM, Majoral JP, Francois JM, Meunier B (2003) New J Chem 27:1713 Google Scholar
  42. 42.
    Le Berre V, Trevisiol E, Dagkessamanskaia A, Sokol S, Caminade AM, Majoral JP, Meunier B, Francois J (2003) Nucleic Acid Res 31:e88 Google Scholar
  43. 43.
    Glazer M, Fidanza J, McGall G, Frank C (2001) Chem Mater 13:4773 CrossRefGoogle Scholar
  44. 44.
    Lin Z, Strother T, Cai W, Cao XP, Smith LM, Hamers RJ (2002) Langmuir 18:788 Google Scholar
  45. 45.
    Strother T, Hamers RJ, Smith LM (2000) Nucleic Acid Res 28:3535 Google Scholar
  46. 46.
    Schouten S, Stroeve P, Longo ML (1999) Langmuir 15:8133 CrossRefGoogle Scholar
  47. 47.
    Peterson AW, Heaton RJ, Georgiadis RM (2001) Nucleic Acid Res 29:5163 Google Scholar
  48. 48.
    Aqua T, Naaman R, Daube SS (2003) Langmuir 19:10 573 CrossRefGoogle Scholar
  49. 49.
    Bamdad C (1998) Biophys J 75:1997 Google Scholar
  50. 50.
    Wang Y, Vaidya B, Farquar HD, Stryjewski W, Hammer RP, McCarley RL, Soper SA, Cheng YW, Barany F (2003) Anal Chem 75:1130 Google Scholar
  51. 51.
    Shamansky LM, Davis CB, Stuart JK, Kuhr WG (2001) Talanta 55:909 CrossRefGoogle Scholar
  52. 52.
    Liu DJ, Perdue RK, Sun L, Crooks RM (2004) Langmuir 20:5905 Google Scholar
  53. 53.
    Livache T, Bazin H, Mathis G (1998) Clin Chim Act 278:171 CrossRefGoogle Scholar
  54. 54.
    Livache T, Guedon P, Brakha C, Roget A, Levy Y, Bidan G (2001) Synt Met 121:1443 Google Scholar
  55. 55.
    Livache T, Maillart E, Lassalle N, Mailley P, Corso B, Guedon P, Roget A, Levy Y (2003) J Pharm Biomed Anal 32:687 CrossRefGoogle Scholar
  56. 56.
    Matson RS, Rampal J, Pentoney SL, Anderson PD, Coassin P (1995) Anal Biochem 224:110 CrossRefGoogle Scholar
  57. 57.
    Matson RS, Rampal JB, Coassin PJ (1994) Anal Biochem 217:306 CrossRefGoogle Scholar
  58. 58.
    Matson RS, Rampal JB, Coassin PJ (1994) Anal Biochem 220:225 CrossRefGoogle Scholar
  59. 59.
    Timofeev EN, Kochetkova SV, Mirzabekov AD, Florentiev VL (1996) Nucleic Acid Res 24:3142 Google Scholar
  60. 60.
    Proudnikov D, Timofeev E, Mirzabekov A (1998) Anal Biochem 259:34 CrossRefGoogle Scholar
  61. 61.
    Yi HM, Wu LQ, Sumner JJ, Gillespie JB, Payne GF, Bentley WE (2003) Biotech Bioeng 83:646 CrossRefGoogle Scholar
  62. 62.
    Fuentes M, Mateo C, Garcia L, Tercero JC, Guisan JM, Fernandez-Lafuente R (2004) Biomacromol 5:883 Google Scholar
  63. 63.
    Epstein JR, Leung APK, Lee KH, Walt DR (2003) Biosens Bioelectr 18:541 Google Scholar
  64. 64.
    Battersby BJ, Trau M (2002) Trends Biotech 20:167 Google Scholar
  65. 65.
    Lam KS, Renil M (2002) Curr Opin Chem Biol 6:353 CrossRefGoogle Scholar
  66. 66.
    McGall G, Labadie J, Brock P, Wallraff G, Nguyen T, Hinsberg W (1996) Proc Nat Acad Sci USA 93:13 555 CrossRefGoogle Scholar
  67. 67.
    Pirrung MC, Fallon L, McGall G (1998) J Org Chem 63:241 CrossRefGoogle Scholar
  68. 68.
    Lipshutz RJ, Fodor SPA, Gingeras TR, Lockhart DJ (1999) Nat Gen 21:20 Google Scholar
  69. 69.
    Saluz HP, Iqbal J, Limmon GV, Ruryk A, Wu ZH (2002) Curr Sci 83:829 Google Scholar
  70. 70.
    Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, Cerrina F (1999) Nat Biotech 17:974 CrossRefGoogle Scholar
  71. 71.
    Matysiak S, Reuthner F, Hoheisel JD (2001) Biotechniques 31:896 Google Scholar
  72. 72.
    Frank R (1992) Tetrahedron 48:9217 CrossRefGoogle Scholar
  73. 73.
    Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai HY, He YDD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS (2001) Nat Biotech 19:342 CrossRefGoogle Scholar
  74. 74.
    Blanchard AP, Kaiser RJ, Hood LE (1996) Biosens Bioelectr 11:687 Google Scholar
  75. 75.
    Maskos U, Southern EM (1993) Nucleic Acid Res 21:2267 Google Scholar
  76. 76.
    Maskos U, Southern EM (1993) Nucleic Acid Res 21:4663 Google Scholar
  77. 77.
    Southern EM, Maskos U, Elder JK (1992) Genomics 13:1008 CrossRefGoogle Scholar
  78. 78.
    de Gans BJ, Schubert US (2003) Macromol Rapid Commun 24:659 Google Scholar
  79. 79.
    Lange SA, Benes V, Kern DP, Horber JKH, Bernard A (2004) Anal Chem 76:1641 CrossRefGoogle Scholar
  80. 80.
    Demers LM, Ginger DS, Park SJ, Li Z, Chung SW, Mirkin CA (2002) Science 296:1836 CrossRefGoogle Scholar
  81. 81.
    Xu S, Liu GY (1997) Langmuir 13:127 Google Scholar
  82. 82.
    Wadu-Mesthrige K, Xu S, Amro NA, Liu GY (1999) Langmuir 15:8580 CrossRefGoogle Scholar
  83. 83.
    Amro NA, Xu S, Liu GY (2000) Langmuir 16:3006 Google Scholar
  84. 84.
    Delamarche E, Hoole ACF, Michel B, Wilkes S, Despont M, Welland ME, Biebuyck H (1997) J Phys Chem B 101:9263 CrossRefGoogle Scholar
  85. 85.
    Schwartz PV (2001) Langmuir 17:5971 CrossRefGoogle Scholar
  86. 86.
    Chrisey LA, Oferrall CE, Spargo BJ, Dulcey CS, Calvert JM (1996) Nucleic Acid Res 24:3040 Google Scholar
  87. 87.
    Blanchard AP, Kaiser RJ, Hood LE (1996) Biosens Bioelectr 11:687 Google Scholar
  88. 88.
    Gillmor SD, Thiel AJ, Strother TC, Smith LM, Lagally MG (2000) Langmuir 16:7223 CrossRefGoogle Scholar
  89. 89.
    Zammatteo N, Jeanmart L, Hamels S, Courtois S, Louette P, Hevesi L, Remacle J (2000) Anal Biochem 280:143 CrossRefGoogle Scholar
  90. 90.
    Lindroos K, Liljedahl U, Raitio M, Syvanen AC (2001) Nucleic Acid Res 29:e69 Google Scholar
  91. 91.
    Walsh MK, Wang XW, Weimer BC (2001) J Biochem Biophys Met 47:221 Google Scholar
  92. 92.
    Taylor S, Smith S, Windle B, Guiseppi-Elie A (2003) Nucleic Acid Res 31 Google Scholar
  93. 93.
    Manning M, Harvey S, Galvin P, Redmond G (2003) Mater Sci Eng C-Bio S 23:347 Google Scholar

Authors and Affiliations

  1. 1.Max-Planck Institut für MetallforschungStuttgartGermany
  2. 2.Department of BiosciencesUniversity of KentKentUK

Personalised recommendations