Characterizing the Surface Structure of Nucleic Acid Microarrays
EMSL Project ID
1654
Abstract
Designing nucleic acid based microarrays for detection of bacterial pathogens and bacteria, important for bioremediation. Procedure involves coating a glass slide with a self-assembled monolayer (SAM) that binds oligonucleotide capture probes. Capture probes are deposited in 150 mm spots in an array pattern. Target nucleic acids are then hybridized on this microarray and detected via a fluorescent dye. .. Target hybridization may be limited by steric interference from densely packed capture oligos, or poor efficiency of solid-solution phase chemistry. May be able to obviate these factors using linker molecules that allow selective control of oligo density while elevating the capture oligos above the slide surface. 1) Quantify coverage of both surfaces across six dilutions (0.01%, 0.03%, 0.1%, 0.3%, 1%, 3%) using dip coating method...including a vapor-coated slide of each type plus one uncoated slide ( total 15). Broad scanning resolution (150 mm) aimed at the approximate center of each. 2) Use two linkers to elevate our capture oligos above an amino-silane surface (ca. 11 E)... Using different proportions of each, selectively remove cleavable linkers and control density of capture oligos. Quantify relative coverage of each linker on amino-silane surface...Slides with/without cleavage (total 14) plus 2 unlinked control slides....Broad scanning resolution (150 mm) aimed at center of slide. 3) Capture oligos will be deposited in 20 X 20 arrays on unmodified surfaces (epoxy- and amino-silane) and surfaces with cleaved and uncleaved linkers (4 slides). Target areas (150 mm) require careful positioning for a 50 mm scan. May need several readings/slide. Control readings can be taken in arbitrary locations outside of the array. Phosphorous will serve as the signature element for the oligos and we'll also scan for C, N, S, and S-S groups.
Project Details
Project type
Exploratory Research
Start Date
1999-11-15
End Date
2001-04-01
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members