Fabrication of a microarray using a combination of the large circular sense and antisense DNA.
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.
Doh
Kyung-Oh
KO
Department of Physiology, Yeungnam University School of Medicine, Daegu 705-717, Korea. kodoh@ynu.ac.kr
Lee
Yun-Han
YH
Han
Kil-Hwan
KH
Uhm
Seok-Yong
SY
Kim
Jong-Pil
JP
Bae
Yun-Ui
YU
Park
Jeong-Hoh
JH
Moon
Ik-Jae
IJ
Park
Jong-Gu
JG
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
D016373:DNA, Antisense; D018076:DNA, Complementary; D004277:DNA, Single-Stranded