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

Paper DN-MoM8
Quantitative XPS Imaging of DNA Microarray Surfaces

Monday, November 13, 2006, 10:20 am, Room 2014

Session: Nucleic Acids at Surfaces I
Presenter: L.J. Gamble, University of Washington
Authors: L.J. Gamble, University of Washington
C.-Y. Lee, University of Washington
G.M. Harbers, Colorado State University
D.W. Grainger, Colorado State University
D.G. Castner, University of Washington
Correspondent: Click to Email
Successful development and optimization of DNA-functionalized surfaces for microarray and biosensor applications requires the accurate and quantitative characterization of immobilized DNA chemistry and structure on various substrates. Previous studies showed that X-ray photoelectron spectroscopy (XPS) is well-suited for sensitive characterization of unpatterned DNA surfaces prepared from bulk solution coupling reactions. However, applying techniques such as XPS to microscopic microarray features (ranging from tens to hundreds of micrometers in diameter) remains a challenge. Recent improvements in imaging photoelectron spectroscopy have allowed more detailed studies of micro-patterned surfaces. In this work, XPS imaging and time-of-flight secondary ion mass spectrometry is applied to the study of patterned DNA surfaces relevant to real world microarray applications. Immobilized DNA probe and target surface compositions on two different commercially available microarray polymer slides are compared using microarray and macro-spot format as well as bulk modification. Distribution of DNA molecules on the microarray slides was determined by chemical mapping of unique nucleotides signals (nitrogen and phosphorus). In addition, the relative amount of probe and target DNA molecules on individual micorarray spots was quantified using region of interest scans. Results indicate that microarray printing on commercial microarray slides produces distinct differences in immobilized DNA density in comparison to bulk solution coupling reaction. Differences in spot size and immobilized probe and target DNA densities on the two commercial microarray slides will be discussed.