Patent ID: 6986988

Claim:
A method for detection of differential expression of natural antisense messenger RNA (mRNA), comprising: (a) separately obtaining polyA-mRNA-A molecules from cell population A and polyA-mRNA-B molecules from cell population B; (b) separately generating by a reverse transcription enzyme a population of single-stranded cDNA-A molecules from polyA-mRNA-A and a population of single-stranded cDNA-B molecules from polyA-mRNA-B, wherein the polydeoxythymidine containing oligonucleotide primer used to produce the cDNA-B molecules comprises a specific bacteriophage RNA polymerase promoter region close to its 5′ terminus; (c) incubating the combined populations of single-stranded cDNA-A molecules and single-stranded cDNA-B molecules, under conditions allowing hybridization of sense cDNA molecules with antisense cDNA molecules, wherein each single-stranded antisense cDNA molecule that hybridizes has a segment complementary to the sense cDNA molecule and hybridizes thereto to form a hybrid molecule with a double-stranded segment; (d) treating the hybrid molecules with a DNA polymerase having a 5′ to 3′ polymerase activity and a 3′ to 5′ exonuclease activity to remove single-stranded non-hybridized segments of the hybrid molecule from 3′ to 5′ and to extend the double-stranded segment of the hybrid molecule 5′ to 3′ over an adjacent single-stranded segment as template, thereby forming a double-stranded molecule having the RNA polymerase promoter region close to one terminus; (e) using the double-stranded molecule as a template for the specific RNA polymerase to a population of RNA molecules; (f) labeling with a first label the RNA molecules produced in step (e); (g) labeling with a second label as control the polyA-mRNA-A molecules and/or the polyA-mRNA-B molecules of step (a); (h) mixing labeled RNA molecules from steps (f) and (g) and hybridizing them to a DNA microarray, and (i) identifying the genes on the microarray which are preferentially labeled with the labeled RNA molecules of step (f), wherein the genes so identified on the microarray are detected as differentially expressed natural antisense mRNA.