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Integrated in silico and biological validation of the blocking effect of C(o)t-1 DNA on microarray-CGH

 Seung-Hui Kang  ;  Chan Hee Park  ;  Hyun Cheol Chung  ;  Sun Young Rha  ;  Ki-Yeol Kim  ;  Hei Cheul Jeung 
 International Journal of Molecular Medicine, Vol.19 : 901-908, 2007 
Journal Title
 International Journal of Molecular Medicine 
Issue Date
Algorithms ; Alu Elements ; Base Sequence ; DNA/pharmacology* ; DNA Probes/chemistry ; Female ; Humans ; Male ; Molecular Sequence Data ; Nucleic Acid Hybridization/drug effects* ; Nucleic Acid Hybridization/methods* ; Oligonucleotide Array Sequence Analysis/methods* ; Repetitive Sequences, Nucleic Acid ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Signal Processing, Computer-Assisted
Cot-1 DNA ; Microarray-CGH ; sequence similarity ; Alu repetitive elements
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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5. Research Institutes (연구소) > Oral Cancer Research Institute (구강종양연구소) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Internal Medicine (내과학교실) > 1. Journal Papers
Yonsei Authors
Kim, Ki Yeol(김기열) ORCID logo https://orcid.org/0000-0001-5357-1067
Rha, Sun Young(라선영) ORCID logo https://orcid.org/0000-0002-2512-4531
Chung, Hyun Cheol(정현철) ORCID logo https://orcid.org/0000-0002-0920-9471
Jeung, Hei Cheul(정희철) ORCID logo https://orcid.org/0000-0003-0952-3679
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