Characteristics of DNA microarrays fabricated on various aminosilane layers

Four kinds of aminosilane layers on glass slides or silicon wafers were prepared. The amine densities of the layers prepared with aminopropylmonoethoxydimethylsilane (APDES), aminopropylmonoethoxydimethylsilane (APMES), a mixture of (aminopropyl)triethoxysilane (APTES) and n-butyltrimethoxysilane (n-BTMS) (v/v = 1:10) are 4.0(+/-0.8), 1.0(+/-0.2), and 0.30(+/-0.6) amine/nm(2), respectively. A substrate with much higher amine density, that is, 40(+/-8) amines/nm(2) was also prepared by allowing aziridine to polymerize on the APDES-treated substrate. AFM revealed that APDES-, APMES-, and APTES/n-BTMS-treated surfaces were relatively flat; on the other hand, an aziridine-treated surface showed embossed morphology. The amine substrates were allowed to react with a heterobifunctional linker succinimidyl 4-maleimido butyrate (SMB), and subsequently pentadecadeoxynucleotides were microarrayed on the SMB-treated substrates. Characteristics of the DNA microarrays including the dynamic range, the mismatch discrimination efficiency, and so forth were examined. Noteworthily, DNA microarrays on the aziridine-polymerized substrate showed much higher fluorescence intensity. At the same time, DNA microarrays from these four substrates were able to discriminate internal- and terminal-mismatched pairs, but the fluorescence ratio was far from the one that thermodynamics implies.