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Optimization of single-base-pair mismatch discrimination in oligonucleotide microarraysThe discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.
Document ID
20040087707
Acquisition Source
Legacy CDMS
Document Type
Reprint (Version printed in journal)
Authors
Urakawa, Hidetoshi
(University of Washington Seattle, WA 98195, United States)
El Fantroussi, Said
Smidt, Hauke
Smoot, James C.
Tribou, Erik H.
Kelly, John J.
Noble, Peter A.
Stahl, David A.
Date Acquired
August 21, 2013
Publication Date
May 1, 2003
Publication Information
Publication: Applied and environmental microbiology
Volume: 69
Issue: 5
ISSN: 0099-2240
Subject Category
Life Sciences (General)
Distribution Limits
Public
Copyright
Other
Keywords
NASA Discipline Life Sciences Technologies
Non-NASA Center

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