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Making the Bend: DNA Tertiary Structure and Protein-DNA Interactions
Int. J. Mol. Sci. 2014, 15(7), 13111-13122; doi:10.3390/ijms150713111

DNA Break Mapping Reveals Topoisomerase II Activity Genome-Wide

1,* , 2
1 Laboratory of Pathology, NCI/NIH, Bldg 10 Rm 2N106, 10 Center Drive, Bethesda, MD 20892, USA 2 Computational Biology Branch, NCBI/NLM/NIH, Bldg 38a, 8600 Rockville Pike, Bethesda, MD 20894, USA 3 Systems Biology Center, NHLBI/NIH, Bldg 10 Rm 7B06A, 10 Center Drive, Bethesda, MD 20892, USA
* Author to whom correspondence should be addressed.
Received: 31 May 2014 / Revised: 9 July 2014 / Accepted: 14 July 2014 / Published: 23 July 2014
(This article belongs to the Special Issue Identification and Roles of the Structure of DNA)
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Genomic DNA is under constant assault by endogenous and exogenous DNA damaging agents. DNA breakage can represent a major threat to genome integrity but can also be necessary for genome function. Here we present approaches to map DNA double-strand breaks (DSBs) and single-strand breaks (SSBs) at the genome-wide scale by two methods called DSB- and SSB-Seq, respectively. We tested these methods in human colon cancer cells and validated the results using the Topoisomerase II (Top2)-poisoning agent etoposide (ETO). Our results show that the combination of ETO treatment with break-mapping techniques is a powerful method to elaborate the pattern of Top2 enzymatic activity across the genome.
Keywords: topoisomerases; DNA damage; transcription topoisomerases; DNA damage; transcription
This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Baranello, L.; Kouzine, F.; Wojtowicz, D.; Cui, K.; Przytycka, T.M.; Zhao, K.; Levens, D. DNA Break Mapping Reveals Topoisomerase II Activity Genome-Wide. Int. J. Mol. Sci. 2014, 15, 13111-13122.

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