Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics.

ABSTRACT: Application of high-density microarrays to the diagnostic analysis of microbial communities is challenged by the optimization of oligonucleotide probe sensitivity and specificity, as it is generally unfeasible to experimentally test thousands of probes. This study investigated the adjustment of hybridization stringency using formamide with the idea that sensitivity and specificity can be optimized during probe design if the hybridization efficiency of oligonucleotides with target and non-target molecules can be predicted as a function of formamide concentration. Sigmoidal denaturation profiles were obtained using fluorescently labeled and fragmented 16S rRNA gene amplicon of Escherichia coli as the target with increasing concentrations of formamide in the hybridization buffer. A linear fre

SUBMITTER: Yilmaz LS 

PROVIDER: S-EPMC3428302 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature