Integrated in silico and biological validation of the blocking effect of Cot-1 DNA on Microarray-CGH

  • Authors:
    • Seung-Hui Kang
    • Chan Hee Park
    • Hei Cheul Jeung
    • Ki-Yeol Kim
    • Sun Young Rha
    • Hyun Cheol Chung
  • View Affiliations

  • Published online on: June 1, 2007     https://doi.org/10.3892/ijmm.19.6.901
  • Pages: 901-908
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Abstract

In array-CGH, various factors may act as variables influencing the result of experiments. Among them, Cot-1 DNA, which has been used as a repetitive sequence-blocking agent, may become an artifact-inducing factor in BAC array-CGH. To identify the effect of Cot-1 DNA on Microarray-CGH experiments, Cot-1 DNA was labeled directly and Microarray-CGH experiments were performed. The results confirmed that probes which hybridized more completely with Cot-1 DNA had a higher sequence similarity to the Alu element. Further, in the sex-mismatched Microarray-CGH experiments, the variation and intensity in the fluorescent signal were reduced in the high intensity probe group in which probes were better hybridized with Cot-1 DNA. Otherwise, those of the low intensity probe group showed no alterations regardless of Cot-1 DNA. These results confirmed by in silico methods that Cot-1 DNA could block repetitive sequences in gDNA and probes. In addition, it was confirmed biologically that the blocking effect of Cot-1 DNA could be presented via its repetitive sequences, especially Alu elements. Thus, in contrast to BAC-array CGH, the use of Cot-1 DNA is advantageous in controlling experimental variation in Microarray-CGH.

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June 2007
Volume 19 Issue 6

Print ISSN: 1107-3756
Online ISSN:1791-244X

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Spandidos Publications style
Kang S, Park CH, Jeung HC, Kim K, Rha SY and Chung HC: Integrated in silico and biological validation of the blocking effect of Cot-1 DNA on Microarray-CGH. Int J Mol Med 19: 901-908, 2007
APA
Kang, S., Park, C.H., Jeung, H.C., Kim, K., Rha, S.Y., & Chung, H.C. (2007). Integrated in silico and biological validation of the blocking effect of Cot-1 DNA on Microarray-CGH. International Journal of Molecular Medicine, 19, 901-908. https://doi.org/10.3892/ijmm.19.6.901
MLA
Kang, S., Park, C. H., Jeung, H. C., Kim, K., Rha, S. Y., Chung, H. C."Integrated in silico and biological validation of the blocking effect of Cot-1 DNA on Microarray-CGH". International Journal of Molecular Medicine 19.6 (2007): 901-908.
Chicago
Kang, S., Park, C. H., Jeung, H. C., Kim, K., Rha, S. Y., Chung, H. C."Integrated in silico and biological validation of the blocking effect of Cot-1 DNA on Microarray-CGH". International Journal of Molecular Medicine 19, no. 6 (2007): 901-908. https://doi.org/10.3892/ijmm.19.6.901