Full-text resources of PSJD and other databases are now available in the new Library of Science.
Visit https://bibliotekanauki.pl


Preferences help
enabled [disable] Abstract
Number of results


2014 | 95 | 1 | 5-16

Article title

Application of epoxy functional silanes in the preparation of DNA microarrays

Title variants

Languages of publication



Nucleic acid microarrays have recently become one of the basic techniques in the study of gene expression. Owing to progress in the field of miniaturization, thousands of oligonucleotides differing in terms of their sequences can be systematically placed on a small area of a solid support (usually glass). These probes are capable of simultaneously interacting with a large number of longer nucleic acids from particular genes. Nucleic acid microarray construction technology consists, primarily, of the appropriate functionalization of a glass surface with the use of organofunctional silanes. Oligonucleotides known as probes are attached to a functionalized surface using, for instance, the lithography technique and, after being linked to the surface, they are subjected to hybridization with complementary and labelled fragments of nucleic acids known as samples of unknown sequences. In this paper, we present a method for constructing DNA microarrays that is based on the use of microscopic slides modified with epoxy functional group-containing silanes. This study was aimed at optimizing the production of DNA microarrays. The study tested the usefulness of four different epoxy functional silanes with one or three alkoxy groups. In addition, slides were silanized with the use of alkylsilane. The glass slides were characterized using a goniometer and an atomic force microscope (AFM). The synthesized amino linker-containing oligonucleotide probes were printed onto the glass slides in order to check the effectiveness of their attachment to the solid surface.










Physical description




  • Baldi P., Hatfield G.W. (2002) DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling, Cambridge University Press.
  • Beaucage S.L., CaruthersM.H. (1981) Deoxynucleoside phosphoramidite - a new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Lett. 22: 1859-1862.
  • Beaucage S.L., Iyer R.P. (1992) Advances in the synthesis of oligonucleotides by the phosphoramidite approach. Tetrahedron48: 2223-2311.
  • Blalock E.M. (2003) A Beginner's Guide to Microarrays, Kluwer Academic Publishers.
  • Chiu S.K., HsuM., KuW.C., TuC.Y., TsengY.T., LauW.K., YanR.Y., MaJ.T., TzengC.M. (2003) Synergistic effects of epoxy- and amine-silanes on microarray DNA immobilization and hybridization. Biochem. J. 374(3): 625-632.
  • Chmielewski M.K., Frydrych E., Uszczyńska B., Ratajczak T., MaciejewskiH., FiglerowiczM., MarkiewiczW.T. (2011) Sposób wytwarzania mikromacierzy, Patent application P-395147.
  • Cloarec J.P., DeligianisN., MartinJ.R., LaurenceI., SouteyrandE., PolychronakosC., LawrenceM.F. (2002) Immobilization of homooligonucleotide probe layers onto Si/SiO2 substrates: characterization by electrochemical impedancje measurements and radiolabelling. Biosens. Bioelectron. 17(5): 405-412.
  • Fiedorow R., MarciniecB., Guliński J., MaciejewskiH. (2008) Sposób otrzymywania glicydoksypropylotrialkoksysilanów. Polish Patent. 198548.
  • Fodor S.P.A., RavaR.P., HuangX.C., PeaseA.C., HolmesC.P., AdamsC.L. (1993) Multiplexed biochemical assays with biological chips. Nature364: 555-556.
  • Fodor S.P.A., ReadL., PirrungM.C., StryerL., LuA., SolasD. (1991) Light-directed, spatially addressable parallel chemical synthesis. Science251: 767-773.
  • Froehler B.C., NgaP.G., MatteucciM.D. (1986) Synthesis of DNA viadeoxynucleoside H-phosphonate intermediates;Nucleic Acids Res. 14: 5399.
  • Garegg P.J., RegbergT., StawinskiJ., StrömbergR. (1985) Formation of internucleotidic bond via phosphonate intermediates. Chem. Scr. 25: 280-282.
  • Gershon D.2005. DNA microarrays: more than gene expression. Nature437: 1195-1198.
  • Guo Z., GuilfoyleR.A., ThielA.J., WangR., SmithL.M. (1994) Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. Nucl. Acids Res. 22(24): 5456-5465.
  • Hardiman G. (2003) Microarrays methods and applications: Nuts & Bolts (The Nuts and Bolts Series), Independent Publishers Group.
  • Henke L., KrullU.J. (1999) Immobilization technologies used for nucleic acid biosensors: a review. Can. J. Anal. Sci. Spectrosc. 44(2): 62-70.
  • Horcas I., FernandezR., Gomez-RodriguezJ.M., ColcheroJ., Gomez-HerreroJ., BaroA.M. (2007) WSXM: A software for scanning probe microscopy and a tool for nanotechnology. Rev. Sci. Instrum. 78: 013705-1-013705-8.
  • Khandazhinskaya A.L., KukhanovaM.K., JaskoM.V. (2005) New Nonnucleoside Substrates for Terminal Deoxynucleotidyl Transferase: Synthesis and Dependence of Substrate Properties on Structure. Russ. J. Bioorg. Chem. 31(4): 352-356.
  • Kierzek E., FratczakA. (2008) Mikromacierze izoenergetyczne, nowa metoda badania struktury i oddziaływań RNA. Biotechnologia 4: 144-153.
  • Kordek R., BednarekA.K. (2005)Mikromacierze DNA w badaniach raka piersi. Onkol. Prakt. Klin. 1(1): 10-17.
  • Lin P., Kong Thoo, Kuksa V.A., MaguireN.M. (1998) The Synthesis of Oxa-Analogues and Homologues of Naturally Occurring Polyamines. Synthesis 6: 859-866.
  • Luderer F., Walschus U. (2005)Immobilization of oligonucleotides for biochemical sensing by self-assembled monolayers: Thiol-organic bonding on gold and silanization on silica surfaces. Top. Curr. Chem. 260: 37-56.
  • Luzinov I. et al. (2000) Epoxy-terminated self-assembled monolayers: molecular glues for polymer layers. Langmuir16: 504-516.
  • Maciejewski H., DąbekI., MarciniecB. (2004) Silanowe środki wiążące. Epoksyfunkcyjne karbosilany. Polimery10: 677- 687.
  • Marciniec B., Maciejewski H., PietraszukC., PawlućP., Guliń- skiJ. (2011) Encyclopedia of Catalysis. Ed. Horvath I., J. Wiley & Sons, New York,.
  • Marciniec B. (2002) Catalysis of hydrosilylation of carboncarbon multiple bonds: Recent Progress. Silicon Chem. 1(3): 155-174.
  • Metwallib E., HainesD., BeckerO., ConzoneS., PantanoC.G. (2006) Surface characterizations of mono-, di-, and triaminosilane treated glass substrates. J. Colloid Interf. Sci. 298: 825-831.
  • Piehler J., BrechtA., ValiokasR., LiedbergB., Gauglitz G. (2000)A high-density poly(ethylene glycol) polymer brush for immobilization on glass-type surfaces. Biosens. Bioelectron. 15: 473-481.
  • Pohl E.R., OsterholtzF.D. (1986) Silanes, surfaces and interfaces. Ed. Leyden D. E., Gordon and Breach: New York: 481-500.
  • Simon R.M. (2004) Design and analysis of DNA microarray investigations (Korn EL and McShane LM. eds), SpringerVerlag.
  • Trevino V., Falciani F., Barrera-Saldana H.A. (2007) DNA microarrays: a powerful genomic tool for biomedical and clinical research. Mol. Med. 13: 527-541.
  • Uszczyńska B., Ratajczak T., FrydrychE., MaciejewskiH., FiglerowiczM., MarkiewiczW.T., ChmielewskiM.K. (2012) The application of click chemistry to the production of DNA microarrays. Lab Chip12(6): 1151-1156.
  • Venkatasubbarao S. (2004) Microarrays - status and prospects. Trends Biotechnol. 22: 630-637.
  • Wong A.K.Y., KrullU.J. (2005) Surface characterization of 3- glycidoxypropyltrimethoxysilane films on silicon-based substrates. Anal. Bioanal. Chem. 383: 187-200.
  • Zhang W., ShmulevichI., AstolaJ. (2004) Microarray Quality Control, Wiley-Liss.
  • Zmieńko A., Guzowska-NowowiejskaM., UrbaniakR., PladerW., FormanowiczP., FiglerowiczM. (2011)A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants. Plant Methods. 7(1), art. no. 29.
  • Zuker M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406- 3415.

Document Type


Publication order reference


YADDA identifier

JavaScript is turned off in your web browser. Turn it on to take full advantage of this site, then refresh the page.