title: Fabrication of a microarray using a combination of the large circular sense and antisense DNA.
abstract: In the present study, single-stranded large circular (LC)-sense molecules were utilized as probes for DNA microarrays and showed stronger binding signals than those of PCR-amplified cDNA probes. A microarray experiment using 284 LC-sense DNA probes found 6 upregulated and 7 downregulated genes in A549 cells as compared to WI38VA13 cells. Repeated experiments showed largely consistent results, and microarray data strongly correlated with data acquired from quantitative real-time RT-PCR. A large array comprising 5,079 LC-sense DNA was prepared, and analysis of the mean differential expression from dye-swap experiments revealed 332 upregulated and 509 downregulated genes in A549 cells compared to WI38VA13 cells. Subsequent functional analysis using an LC-antisense library of overexpressed genes identified 28 genes involved in A549 cell growth. These experiments demonstrated the proper features of LC-sense molecules as probe DNA for microarray and the potential utility of the combination of LC-sense and -antisense libraries for an effective functional validation of genes.
authors: Department of Physiology, Yeungnam University School of Medicine, Daegu 705-717, Korea. kodoh@ynu.ac.kr
authors: Kyung-Oh
authors: KO
authors: Doh
authors: Yun-Han
authors: YH
authors: Lee
authors: Kil-Hwan
authors: KH
authors: Han
authors: Seok-Yong
authors: SY
authors: Uhm
authors: Jong-Pil
authors: JP
authors: Kim
authors: Yun-Ui
authors: YU
authors: Bae
authors: Jeong-Hoh
authors: JH
authors: Park
authors: Ik-Jae
authors: IJ
authors: Moon
authors: Jong-Gu
authors: JG
authors: Park
mesh_terms: D002461:Cell Line, Transformed; D045744:Cell Line, Tumor; D049109:Cell Proliferation; D016373:DNA, Antisense / Q000235:genetics*; D018076:DNA, Complementary / Q000235:genetics; D004277:DNA, Single-Stranded / Q000235:genetics*; D020869:Gene Expression Profiling / Q000191:economics / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000191:economics / Q000379:methods*; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D016373:DNA, Antisense; D018076:DNA, Complementary; D004277:DNA, Single-Stranded