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dc.creatorElmose, Jennifer Leader
dc.creatorLane, Samantha
dc.creatorCall, Douglas
dc.description.abstractA number of investigators have proposed using DNA microarrays as part of pathogen detection assays. False negative hybridizations can occur if the target DNA hybridizes to itself and other target DNA, thus inhibiting hybridization to complementary microarray probes. We hypothesized that longer probes can compete with this ‘secondary structure’ better than shorter probes. To test this we constructed a prototype microarray using a series of short and long probes that were specific to the 16S ribosomal DNA gene of Escherichia coli. Three different targets (PCR un-nick translated, PCR nick translated, and nick translated genomic DNA) were hybridized to an array and assessed by a Tyramide Signal Amplification (TM) biotin system. Our results verified that hybridization of short probes to target sequences is greatly affected by secondary structure, while long probes provide enhanced signal intensities. Using long probes can offer three specific advantages to microarray design: 1) mitigation of secondary structure, 2) enhanced analytical sensitivity, and 3) greater tolerance to base pair mismatches.
dc.publisherWashington State University. Graduate School. McNair Program.en
dc.rightsIn copyright
dc.subjectbiological probes
dc.subjectDNA microarrays
dc.subjectbiological probe length
dc.subjectbiological probe secondary structure
dc.subject16S ribosomal DNA
dc.subjectEscherichia coli
dc.subjectPolymerase Chain Reaction
dc.subjectpathogen detection assays
dc.subjectoligonucleotide probes
dc.subjectexperimental methodology
dc.titleEffects of Probe Length and Secondary Structure on DNA Microarray Hybridizations: Implications for Design of Pathogen Detection Assays
dc.description.citationElmose, Jennifer Leader and Samantha Lane and Douglas Call. Effects of Probe Length and Secondary Structure on DNA Microarray Hybridizations: Implications for Design of Pathogen Detection Assays. WSU McNair Journal. (3) Fall 2005. p 68-80.

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  • McNair Journal
    The McNair Journal is a publication created through the Ronald E. McNair Program, which is administered by the Graduate School at Washington State University.

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