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Molecular Biology Reports

, Volume 43, Issue 7, pp 639–651 | Cite as

The genome-wide DNA sequence specificity of the anti-tumour drug bleomycin in human cells

  • Vincent Murray
  • Jon K. Chen
  • Mark M. Tanaka
Original Article

Abstract

The cancer chemotherapeutic agent, bleomycin, cleaves DNA at specific sites. For the first time, the genome-wide DNA sequence specificity of bleomycin breakage was determined in human cells. Utilising Illumina next-generation DNA sequencing techniques, over 200 million bleomycin cleavage sites were examined to elucidate the bleomycin genome-wide DNA selectivity. The genome-wide bleomycin cleavage data were analysed by four different methods to determine the cellular DNA sequence specificity of bleomycin strand breakage. For the most highly cleaved DNA sequences, the preferred site of bleomycin breakage was at 5′-GT* dinucleotide sequences (where the asterisk indicates the bleomycin cleavage site), with lesser cleavage at 5′-GC* dinucleotides. This investigation also determined longer bleomycin cleavage sequences, with preferred cleavage at 5′-GT*A and 5′- TGT* trinucleotide sequences, and 5′-TGT*A tetranucleotides. For cellular DNA, the hexanucleotide DNA sequence 5′-RTGT*AY (where R is a purine and Y is a pyrimidine) was the most highly cleaved DNA sequence. It was striking that alternating purine–pyrimidine sequences were highly cleaved by bleomycin. The highest intensity cleavage sites in cellular and purified DNA were very similar although there were some minor differences. Statistical nucleotide frequency analysis indicated a G nucleotide was present at the −3 position (relative to the cleavage site) in cellular DNA but was absent in purified DNA.

Keywords

Bleomycin Cleavage sites DNA sequence specificity Genome-wide Illumina DNA sequencing Next-generation sequencing 

Notes

Acknowledgments

Support of this work by the University of New South Wales, Science Faculty Research Grant Scheme is gratefully acknowledged.

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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  1. 1.School of Biotechnology and Biomolecular SciencesUniversity of New South WalesSydneyAustralia

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