In this proposal a new sequencing method called abasic site sequencing: AbS-Seq will be developed and applied to the sequencing of abasic sites in context of DNA post-synthetic modifications and the position of abasic site DNA lesions on the genome.
Abasic sites are places on the genome where the nucleobase has been removed. This “gap” can be a result of DNA damage due to exo- (smoke, tar) or endogenous sources (reactive oxygen species, alkylation) or can occur spontaneous in processes called de-purination/de-pyrimidination. Additionally, a set of specialized enzymes can remove a variety of modified/damaged nucleobases as part of a specialized cellular repair mechanism known as the Base Excission Repair (BER) pathway.
In this proposal the sequencing of the naturally abundant abasic site DNA lesions will be investigated. The aim is to elucidate the sequence context of these DNA damages and their relation to the event of transcription. By the conversion of the small molecular probes into entities that can be used for pulldown and thus for the enrichment of abasic site containing DNA fragments, those part of the genome containing abasic sites can be sequenced. Such a strategy can be used to provide insights in the correlation between active gene expression and DNA damage in health and disease. Additionally, it is proposed to use the enzymes from the BER for the sequencing of post-synthetic DNA modifications by creating abasic sites in vitro. The same enrichment method can then be applied to map the modifications of interest on a genome scale. In addition, base resolution may be acquired by the comparison of sequencing data from native samples and the converted abasic sites.
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