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Korean Society for Biochemistry and Molecular Biology (생화학분자생물학회)
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Comparison of Hybridization Behavior between Double and Single Strand of Targets and the Application of Asymmetric PCR Targets in cDNA Microarray

  • Wei, Qing (State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University) ;
  • Liu, Sanzhen (Shanghai BioStar Genechip Institute) ;
  • Huang, Jianfeng (Shanghai BioStar Genechip Institute) ;
  • Mao, Xueying (Shanghai BioStar Genechip Institute) ;
  • Chu, Xiaohui (Shanghai BioStar Genechip Institute) ;
  • Wang, Yu (State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University) ;
  • Qiu, Minyan (Shanghai BioStar Genechip Institute) ;
  • Mao, Yumin (State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University) ;
  • Xie, Yi (State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University) ;
  • Li, Yao (State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University)
  • Published : 2004.07.31
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Abstract

Double stranded targets on the cDNA microarray contain representatives of both the coding and noncoding strands, which will introduce hybridization competition with probes. Here, the effect of double and single strands of targets on the signal intensity and the ratios of Cy5/Cy3 within the same slide were compared. The results show that single stranded targets can increase the hybridization efficiency without changing the Cy5/Cy3 ratio. Based on these results, a new strategy was established by generating cDNA targets with asymmetric PCR, instead of conventional PCR, to increase the sensitivity of the cDNA microarray. Furthermore, the feasibility of this approach was validated. The results indicate that the cDNA microarray system based on asymmetric PCR is more sensitive, with no decrease in the reliability and reproducibility as compared with that based on conventional symmetric PCR.

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