Download PDF
Synthesis 2002(6): 0816-0824
DOI: 10.1055/s-2002-25758
SPECIALTOPIC
© Georg Thieme Verlag Stuttgart · New York

Oligonucleotide Arrays from Aldehyde-Bearing Glass with Coated Background

Kendra L. Dombi, Niels Griesang, Clemens Richert*
Department of Chemistry, University of Constance, Fach M 709, 78457 Konstanz, Germany
Fax: +49(7531)884573; e-Mail: Clemens.Richert@uni-konstanz.de;
Further Information

Publication History

Received 28 December 2001
Publication Date:
26 April 2002 (online)

    Permissions and Reprints All articles of this category

Abstract

Presented here is a method for preparing small DNA arra­ys on aldehyde-bearing glass slides. Immobilization involves reductive amination and employs oligonucleotides with 3′-terminal lysine residues, obtained in high yield from solid phase syntheses. Spot patterns are produced by protecting selected areas of the aldehyde slides with wax, coating the free surface with a methyl triethylene glycol derivative, and removing the wax with dichloromethane. The DNA arrays give better signal to noise ratios in hybridization experiments than slides without passified background.

Key words

oligonucleotides - Schiff bases - solid phase synthesis - DNA - molecular recognition

    References

  • Selected references:
  • 1a Fodor SPA. Read JL. Pirrung MC. Stryer L. Lu AT. Solas D. Science  1991,  251:  767 
    Google Scholar
  • 1b Pease AC. Solas D. Sullivan EJ. Cronin MT. Holmes CP. Fodor SPA. Proc. Natl. Acad. Sci. U.S.A.  1994,  91:  5022 
    Google Scholar
  • 1c Schena M. Shalon D. Davis RW. Brown PO. Science  1995,  270:  467 
    Google Scholar
  • 1d DeRisi JL. Iyer VR. Brown PO. Science  1997,  278:  680 
    Google Scholar
  • 1e Singh-Gasson S. Green RD. Yue Y. Nelson C. Blattner F. Cerrina F. Nat. Biotechnol.  1999,  17:  974 
    Google Scholar
  • Selected recent reviews:
  • 2a Ramsay G. Nat. Biotechnol.  1998,  16:  40 
    CrossrefGoogle Scholar
  • 2b Southern EM. Mir K. Shchepinov M. Nat. Genet.  1999,  21:  5 
    CrossrefGoogle Scholar
  • 2c Hacia JG. Nat. Genet.  1999,  21:  42 
    CrossrefGoogle Scholar
  • 2d Bowtell DDL. Nat. Genet.  1999,  21:  25 
    CrossrefGoogle Scholar
  • 2e Lockhardt DJ. Winzeler EA. Nature (London)  2000,  405:  827 
    CrossrefGoogle Scholar
  • 3 Duggan DJ. Bittner M. Chen Y. Meltzer P. Trent JM. Nat. Genet.  1999,  21:  10 
    Google Scholar
  • 4 Debouck C. Goodfellow PN. Nat. Genet.  1999,  21:  48 
    CrossrefGoogle Scholar
  • 5a Chrisey LA. O’Ferrall CE. Spargo BJ. Dulcey CS. Calvert JM. Nucleic Acids Res.  1996,  24:  3040 
    Google Scholar
  • 5b Singh-Gasson S. Green RD. Yue Y. Nelson C. Blattner F. Sussman MR. Cerrina F. Nat. Biotechnol.  1999,  17:  974 
    Google Scholar
  • 6 Lipshutz RJ. Fodor SPA. Gingeras TR. Lockhart DJ. Nat. Genet.  1999,  21:  20 
    Google Scholar
  • 7 Patil N. Berno AJ. Hinds DA. Barrett WA. Doshi JM. Hacker CR. Kautzer CR. Lee DH. Marjoribanks C. McDonough DP. Nguyen BT. Norris MC. Sheehan JB. Shen N. Stern D. Stokowski RP. Thomas DJ. Trulson MO. Vyas KR. Frazer KA. Fodor SP. Cox DR. Science (Washington, D.C.)  2001,  294:  1719 
    CrossrefGoogle Scholar
  • 8 Evertsz EM. Au-Young J. Ruvolo MV. Lim AC. Reynolds MA. BioTechniques  2001,  31:  1182 
    Google Scholar
  • 9 Wang DG. Fan J.-B. Siao C.-J. Berno A. Young P. Sapolsky R. Ghandour G. Perkins N. Winchester E. Spencer J. Krugylak L. Stein L. Hsie L. Topalogou T. Hubbell E. Robinson E. Mittmann M. Morris MS. Shen N. Kilburn D. Rioux J. Nusbaum C. Rozen S. Hudson TJ. Lipshutz R. Chee M. Lander ES. Science (Washington, D.C.)  1998,  280:  1077 
    CrossrefGoogle Scholar
  • 10 Weiler J. Gausepohl H. Hauser N. Jensen ON. Hoheisel JD. Nucleic Acids Res.  1997,  25:  2792 
    CrossrefGoogle Scholar
  • 11 Sauer M. Brecht A. Charisse K. Maier M. Gerster M. Stemmler I. Gauglitz G. Bayer E. Anal. Chem.  1999,  71:  2850 
    CrossrefGoogle Scholar
  • 12 Fidanza JA. McGall GH. Nucleosides Nucleotides  1999,  18:  1293 
    Google Scholar
  • 13 Bonnet G. Tyagi S. Libchaber A. Kramer FR. Proc. Natl. Acad. Sci. U.S.A.  1999,  96:  6171 
    CrossrefGoogle Scholar
  • 14a Healey BG. Matson RS. Walt DR. Anal. Biochem.  1997,  251:  270 
    Google Scholar
  • 14b Steemers FJ. Ferguson JA. Walt DR. Nat. Biotechnol.  2000,  18:  91 
    Google Scholar
  • 15a Yu CJ. Wan Y. Yowanto H. Li J. Tao C. Janes MD. Tan CL. Blackburn GF. Meade TJ. J. Am. Chem. Soc.  2001,  123:  11155 
    CrossrefGoogle Scholar
  • 15b Livache T. Fouque B. Roget A. Marchand J. Bidan G. Téoule R. Mathis G. Anal. Biochem.  1998,  255:  188 
    CrossrefGoogle Scholar
  • 16 Seela F. Becher G. Nucleic Acids Res.  2001,  29:  2069 
    CrossrefGoogle Scholar
  • 17 Nguyen H.-K. Fournier O. Asseline U. Dupret D. Thuong NT. Nucleic Acids Res.  1999,  27:  1492 
    CrossrefGoogle Scholar
  • 18 Kryatova OP. Connors WH. Bleczinski CF. Mokhir AA. Richert C. Org. Lett.  2001,  3:  987 
    CrossrefGoogle Scholar
  • 19 Bleczinski CF. Richert C. J. Am. Chem. Soc.  1999,  121:  10889 
    CrossrefGoogle Scholar
  • 20 Barnes TW. Turner DH. J. Am. Chem. Soc.  2001,  123:  9186 
    CrossrefGoogle Scholar
  • 21 Cheung VG. Morley M. Aguilar F. Massimi A. Kucherlapati R. Childs G. Nat. Genet.  1999,  21:  15 
    Google Scholar
  • 22a Pirrung MC. Odenbaugh AL. Davis JD. Langmuir  2000,  16:  2185 
    CrossrefGoogle Scholar
  • 22b Pirrung MC. Connors RV. Odenbaugh AL. Montague-Smith MP. Walcott NG. Tollett JJ. J. Am. Chem. Soc.  2000,  122:  1873 
    CrossrefGoogle Scholar
  • 23 Zhao X. Nampalli S. Serino AJ. Kumar S. Nucleic Acids Res.  2001,  29:  955 
    CrossrefGoogle Scholar
  • 24 Lamture JB. Beattie KL. Burke BE. Eggers MD. Ehrlich DJ. Fowler R. Hollis MA. Kosicki BB. Reich RK. Smith SR. Nucleic Acids Res.  1994,  22:  2121 
    Google Scholar
  • 25 Guo Z. Guilfoyle RA. Thiel AJ. Wang R. Smith LM. Nucleic Acids Res.  1994,  22:  5456 
    Google Scholar
  • 26 Podyminogin MA. Lukhtanov EA. Reed MW. Nucleic Acids Res.  2001,  29:  5090 
    CrossrefGoogle Scholar
  • 27 Rogers Y.-H. Jiang-Baucom P. Huang Z.-J. Bogdanov V. Anderson S. Boyce-Jacino MT. Anal. Biochem.  1999,  266:  23 
    CrossrefGoogle Scholar
  • 28a Beier M. Hoheisel JD. Nucleic Acids Res.  1999,  27:  1970 
    CrossrefGoogle Scholar
  • 28b Strother T. Hamers RJ. Smith LM. Nucleic Acids Res.  2000,  28:  3535 
    CrossrefGoogle Scholar
  • 29 Chrisey LA. Lee GU. O" Ferrall CE. Nucleic Acids Res.  1996,  24:  3031 
    CrossrefGoogle Scholar
  • 30a Peterlinz KA. Georgiadis RM. J. Am. Chem. Soc.  1997,  119:  3401 
    CrossrefGoogle Scholar
  • 30b Brockman JM. Nelson BP. Corn RM. Annu. Rev. Phys. Chem.  2000,  51:  41 
    CrossrefGoogle Scholar
  • 31 Shchepinov MS. Case-Green SC. Southern EM. Nucleic Acids Res.  1997,  25:  1155 
    CrossrefGoogle Scholar
  • 32 Shchepinov MS. Mir KU. Elder JK. Frank-Kamenetskii MD. Southern EM. Nucleic Acids Res.  1999,  27:  3035 
    CrossrefGoogle Scholar
  • 33 Zammatteo N. Jeanmart L. Hamels S. Courtois S. Louette P. Hevesi L. Remacle J. Anal. Biochem.  2000,  280:  143 
    CrossrefGoogle Scholar
  • 34 Lindroos K. Lijedahl U. Raitio M. Syvänen A.-C. Nucleic Acids Res.  2001,  29:  e69 
    CrossrefGoogle Scholar
  • 35 Adessi C. Matton G. Ayala G. Turcatti G. Mermod J.-J. Mayer P. Kawashima E. Nucleic Acids Res.  2000,  28:  e87 
    CrossrefGoogle Scholar
  • 36a Mokhir AA. Tetzlaff CN. Herzberger S. Mosbacher A. Richert C. J. Comb. Chem.  2001,  3:  374 
    CrossrefGoogle Scholar
  • 36b Mokhir AA. Richert C. Nucleic Acids Res.  2000,  28:  4254 
    CrossrefGoogle Scholar
  • 36c Altman RK. Schwope I. Sarracino DA. Tetzlaff CN. Bleczinski CF. Richert C. J. Comb. Chem.  1999,  1:  493 
    CrossrefGoogle Scholar
  • 37 Schwope I. Bleczinski CF. Richert C. J. Org. Chem.  1999,  64:  4749 
    CrossrefGoogle Scholar
  • 38 Diehl F. Grahlmann S. Beier M. Hoheisel JD. Nucleic Acids Res.  2001,  29:  e38 
    CrossrefGoogle Scholar
  • Selected references:
  • 39a Siegel RR. Harder P. Dahint R. Grunze M. Josse F. Mrksich M. Whitesides GM. Anal. Chem.  1997,  69:  3321 
    Google Scholar
  • 39b Beyer D. Knoll W. Ringsdorf H. Wang JH. Timmons RB. Sluka P. J. Biomed. Mat. Res.  1997,  36:  181 
    Google Scholar
  • 39c Yousaf MN. Mrksich M. J. Am. Chem. Soc.  1999,  121:  4286 
    Google Scholar
  • 39d Piehler J. Brecht A. Valiokas R. Liedberg B. Gauglitz G. Biosens. Bioelectron.  2000,  15:  473 
    Google Scholar
  • 39e Hayward RE. Cameron G. Kozlowski RZ. Drug Disc. Today  2001,  6:  1263 
    Google Scholar
  • 40 Maskos U. Southern EM. Nucleic Acids Res.  1992,  20:  1679 
    Google Scholar
  • 41 Butler JH. Cronin M. Anderson KM. Biddison GM. Chatelain F. Cummer M. Davi DJ. Fisher L. Frauendorf AW. Frueh FW. Gjerstad C. Harper TF. Kernahan SD. Long DQ. Pho M. Walker JA. Brennan TW. J. Am. Chem. Soc.  2001,  123:  8887 
    CrossrefGoogle Scholar
  • 42 Heimann U. Herzhoff M. Vögtle F. Chem. Ber.  1979,  112:  1392 
    Google Scholar
  • 43 Schmidt M. Amstutz R. Crass G. Seebach D. Chem. Ber.  1980,  113:  1691 
    Google Scholar
  • 44 Peterson AW. Heaton RJ. Georgiadis R. J. Am. Chem. Soc.  2000,  122:  7837 
    CrossrefGoogle Scholar
  • 45 Crick FHC. J. Mol. Biol.  1966,  19:  548 
    CrossrefPubMedGoogle Scholar
  • 46 Sambrook J. Fritsch EF. Maniatis T. Molecular Cloning - A Laboratory Manual   2nd ed., Vol. 3:  Cold Spring Harbor Laboratory Press; New York: 1989.  p.B.12 
    Google Scholar
  • 47a Tetzlaff CN. Schwope I. Bleczinski CF. Steinberg JA. Richert C. Tetrahedron Lett.  1998,  39:  4215 
    CrossrefGoogle Scholar
  • 47b Bannwarth W. Helv. Chim. Acta  1988,  71:  1517 
    CrossrefGoogle Scholar
  • 47c Mag M. Engels JW. Nucleic Acids Res.  1989,  17:  5973 
    CrossrefGoogle Scholar
48

Developed at the U.S. National Institutes of Health and available on the internet via http://rsb.info.nih.gov/nih-image/.