title: An antibody-based microarray assay for small RNA detection.
abstract: Detection of RNAs on microarrays is rapidly becoming a standard approach for molecular biologists. However, current methods frequently discriminate against structured and/or small RNA species. Here we present an approach that bypasses these problems. Unmodified RNA is hybridized directly to DNA microarrays and detected with the high-affinity, nucleotide sequence-independent, DNA/RNA hybrid-specific mouse monoclonal antibody S9.6. Subsequent reactions with a fluorescently-labeled anti-mouse IgG antibody or biotin-labeled anti-mouse IgG together with fluorescently labeled streptavidin produces a signal that can be measured in a standard microarray scanner. The antibody-based method was able to detect low abundance small RNAs of Escherichia coli much more efficiently than the commonly-used cDNA-based method. A specific small RNA was detected in amounts of 0.25 fmol (i.e. concentration of 10 pM in a 25 microl reaction). The method is an efficient, robust and inexpensive technique that allows quantitative analysis of gene expression and does not discriminate against short or structured RNAs.
authors.affiliation: Bacterial Toxins and Therapeutics Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Zonglin
authors.initials: Z
authors.lastname: Hu
authors.forename: Aixia
authors.initials: A
authors.lastname: Zhang
authors.forename: Gisela
authors.initials: G
authors.lastname: Storz
authors.forename: Susan
authors.initials: S
authors.lastname: Gottesman
authors.forename: Stephen H
authors.initials: SH
authors.lastname: Leppla
mesh_terms: D000911:Antibodies, Monoclonal / Q000276:immunology; D000918:Antibody Specificity; D004247:DNA / Q000737:chemistry; D018076:DNA, Complementary / Q000737:chemistry; D004926:Escherichia coli / Q000235:genetics; D019084:Fluorescent Antibody Technique, Indirect; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000737:chemistry; D012329:RNA, Bacterial / Q000032:analysis; D022661:RNA, Untranslated / Q000032:analysis* / Q000737:chemistry / Q000276:immunology
chemical_list: D000911:Antibodies, Monoclonal; D018076:DNA, Complementary; D015345:Oligonucleotide Probes; D012329:RNA, Bacterial; D022661:RNA, Untranslated; D004247:DNA