Spectroscopic quantification of covalently immobilized oligonucleotides

Quantitative determination of surface coverage, film thickness and molecular orientation of DNA oligomers covalently attached to aminosilane self-assembled monolayers has been obtained using complementary infrared and photoelectron studies. Spectral variations between surface immobilized oligomers of the different nucleic acids are reported for the first time. Carbodiimide condensation was used for covalent attachment of phosphorylated oligonucleotides to silanized aluminum substrates. Fourier transform infrared (FTIR) spectroscopy and x-ray photoelectron spectroscopy (XPS) were used to characterize the surfaces after each modification step. Infrared reflection-absorption spectroscopy of covalently bound DNA provides orientational information. Surface density and layer thickness are extracted from XPS data. The surface density of immobilized DNA, 2-3 (x10(13)) molecules cm(-2), was found to depend on base composition. Comparison of antisymmetric to symmetric phosphate stretching band intensities in reflection-absorption spectra of immobilized DNA and transmission FTIR spectra of DNA in KBr pellet indicates that the sugar-phosphate backbone is predominantly oriented with the sugar-phosphate backbone lying parallel to the surface, in agreement with the 10-20 Angstrom DNA film thickness derived from XPS intensities. Copyright (C) 2004 John Wiley Sons, Ltd.