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Optimization Of Single-Base-Pair Mismatch Discrimination In Oligonucleotide Microarrays, Hidetoshi Urakawa, Said El Fantroussi, H Smidt, James C. Smoot, Erik H. Tribou, John J. Kelly, Peter A. Noble, David A. Stahl
Optimization Of Single-Base-Pair Mismatch Discrimination In Oligonucleotide Microarrays, Hidetoshi Urakawa, Said El Fantroussi, H Smidt, James C. Smoot, Erik H. Tribou, John J. Kelly, Peter A. Noble, David A. Stahl
Biology: Faculty Publications and Other Works
The 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 …
Direct Profiling Of Environmental Microbial Populations By Thermal Dissociation Analysis Of Native Rrnas Hybridized To Oligonucleotide Microarrays, Said El Fantroussi, Hidetoshi Urakawa, Anne E. Bernhard, John J. Kelly, Peter A. Noble, H Smidt, G M. Yershov, David A. Stahl
Direct Profiling Of Environmental Microbial Populations By Thermal Dissociation Analysis Of Native Rrnas Hybridized To Oligonucleotide Microarrays, Said El Fantroussi, Hidetoshi Urakawa, Anne E. Bernhard, John J. Kelly, Peter A. Noble, H Smidt, G M. Yershov, David A. Stahl
Biology: Faculty Publications and Other Works
Oligonucleotide microarrays were used to profile directly extracted rRNA from environmental microbial populations without PCR amplification. In our initial inspection of two distinct estuarine study sites, the hybridization patterns were reproducible and varied between estuarine sediments of differing salinities. The determination of a thermal dissociation curve (i.e., melting profile) for each probe-target duplex provided information on hybridization specificity, which is essential for confirming adequate discrimination between target and nontarget sequences.