Sequencing abasic sites in DNA at single-nucleotide resolution.
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Liu, Z. J., Martínez Cuesta, S., van Delft, P., & Balasubramanian, S. (2019). Sequencing abasic sites in DNA at single-nucleotide resolution.. Nature chemistry, 11 (7), 629-637. https://doi.org/10.1038/s41557-019-0279-9
In DNA, the loss of a nucleobase by hydrolysis generates an abasic site. Formed as a result of DNA damage, as well as a key intermediate during the base excision repair pathway, abasic sites are frequent DNA lesions which can lead to mutations and strand breaks. Here we present snAP-seq, a chemical approach that selectively exploits the reactive aldehyde moiety at abasic sites to reveal their location within DNA at single-nucleotide resolution. Importantly, the approach resolves abasic sites from other aldehyde functionalities known to exist in genomic DNA. snAP-seq was validated on synthetic DNA, then applied to two separate genomes. We studied the distribution of thymine modifications in the Leishmania major genome by enzymatically converting these modifications into abasic sites followed by abasic site mapping. We also apply snAP-seq directly to HeLa DNA to provide a map of endogenous abasic sites in human genomic DNA.
Hela Cells, Humans, Leishmania major, DNA Damage, Aldehydes, Thymine, DNA-(Apurinic or Apyrimidinic Site) Lyase, DNA, Molecular Probes, Sequence Analysis, DNA, Base Sequence, Genome, Uracil-DNA Glycosidase, Gene Knockdown Techniques
Wellcome Trust (grant no. 209441/Z/17/Z) Pembroke College, Cambridge and the Herchel Smith Fund Marie Curie Fellow of the European Union (grant no. FP7-PEOPLE-2013-IEF/624885)
Wellcome Trust (099232/Z/12/Z)
Wellcome Trust (209441/Z/17/Z)
External DOI: https://doi.org/10.1038/s41557-019-0279-9
This record's URL: https://www.repository.cam.ac.uk/handle/1810/292408
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