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Principle of DNA immunoprecipitation (DnaIP) method to analyze damaged genomic regions.
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Figure 1: Principle of DNA immunoprecipitation (DnaIP) method to analyze damaged genomic regions.

Mentions: A powerful experimental method to deal with this problem is based on immunoprecipitation technique. The basic idea of the method is that, after fragmentation of genomic DNA extracted from a specimen, we can isolate only the fragments bearing a marker of specific DNA damage by applying the principle of immunoprecipitation. There are two variations of immunoprecipitation for this purpose that differ in the sort of antigen to which the adopted antibody binds. The first one, DNA immunoprecipitation (DnaIP), uses antibodies that recognize DNA damage itself (Fig. 1). We recently analyzed the distributions of 8-oxoguanine and acrolein-modified adenine residues (acrolein-dA) on the whole genome by cloning and mapping the fragments obtained through DnaIP [3]. In another application, the genomic fragments adducted with benzo(a)pyrene diol epoxides collected in the same way were cloned [4]. The other immunoprecipitation-based method is the example of chromatin immunoprecipitation, which uses antibodies against the proteins associated with DNA damage and repair. Armed with these immunopreciptation-based methods, one can obtain the sample for mapping the sites at which particular genomic damage is generated or processed.

Genome-Scale Approaches to Investigate Oxidative DNA Damage

Akatsuka S, Toyokuni S - J Clin Biochem Nutr (2010)

Bottom Line: In the trend of biological science after the completion of the human genome project, appreciation of an organism as a system rather than the sum of many molecular functions is necessary.The immunoprecipitation-based technique combined with high-density microarrays is one of the promising methods to provide access to such novel research strategies.We propose this sort of research area as oxygenomics.

Affiliation: Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan.

ABSTRACT
In the trend of biological science after the completion of the human genome project, appreciation of an organism as a system rather than the sum of many molecular functions is necessary. On the investigation of DNA damage and repair, therefore, the orientation toward systematic and comprehensive genome-scale approaches is rapidly growing. The immunoprecipitation-based technique combined with high-density microarrays is one of the promising methods to provide access to such novel research strategies. We propose this sort of research area as oxygenomics.

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