AVS 53rd International Symposium
    Nucleic Acids at Surfaces Topical Conference Monday Sessions
       Session DN-MoM

Paper DN-MoM5
Thymine Homo-oligonucleotides as Model Systems for DNA Surface Science

Monday, November 13, 2006, 9:20 am, Room 2014

Session: Nucleic Acids at Surfaces I
Presenter: D.Y. Petrovykh, University of Maryland, College Park
Authors: D.Y. Petrovykh, University of Maryland, College Park
A. Opdahl, National Institute of Standards and Technology
H. Kimura-Suda, National Institute of Standards and Technology
M.J. Tarlov, National Institute of Standards and Technology
L.J. Whitman, Naval Research Laboratory
Correspondent: Click to Email
Monolayers of thymine homo-oligonucleotides [oligo(dT)] on gold offer two characteristics that make them uniquely appropriate model systems for studying the surface science of DNA. First, strong and distinct spectral signatures simplify characterization by the traditional surface science methods, such as X-ray photoelectron spectroscopy (XPS), Fourier-transform infrared (FTIR) spectroscopy, and near-edge X-ray absorption fine structure spectroscopy (NEXAFS). Second, the interactions between thymine nucleotides (dT) and gold surfaces are rather weak. The immobilization of oligo(dT) then strongly depends on the choice of specific or non-specific linker chemistries, e.g., unmodified, thiolated, or block-oligonucleotides. For all linker chemistries, the structure of the deposited oligo(dT) monolayers is controlled by a wide range of experimental parameters: DNA length and concentration, buffer salt concentration and composition, deposition time, temperature, and post-deposition treatments. The beneficial combination of properties that we found for the oligo(dT) model system enabled us to quantify the effects of immobilization conditions on the surface density and conformation of the deposited DNA monolayers. For example, systematic variation of the salt used in deposition buffers produced significant effects in our experiments. The immobilization efficiency for thiolated oligo(dT) was dramatically and nonlinearly modulated by both the identity and the concentration of the buffer salt cations. These and other observed properties of the oligo(dT) model systems are not strongly nucleobase-specific, therefore the model results can be generalized for controlling the immobilization of DNA oligos with arbitrary sequences.