The Use of Psoralen Photobinding to Study Transcription-Induced Supercoiling

  • Fedor KouzineEmail author
  • Laura Baranello
  • David Levens
Part of the Methods in Molecular Biology book series (MIMB, volume 1703)


Proteins manipulating intracellular DNA necessarily impart torsional stress, which redistributes across the DNA. Overtwisting and undertwisting of the double helix result in the manifestation of positive and negative DNA supercoiling. A growing body of evidence indicates that DNA topology is an important player in the key regulatory steps of genome function, highlighting the need for biochemical techniques to detect dynamic changes in the DNA structure. Psoralen binding to DNA in vivo is proportional to the level of supercoiling, providing an excellent probe for the topological state of nuclear DNA. Here we describe a psoralen-based methodology to detect transcription-induced DNA supercoiling genome-wide. The DNA samples generated with this approach can be hybridized to microarray platforms or high-throughput sequenced to provide a topological snapshot of the whole genome.

Key words

DNA topology DNA supercoiling Psoralen Transcription Topoisomerases Chromatin High-throughput genomics 


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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  1. 1.Laboratory of PathologyNCI/NIHBethesdaUSA
  2. 2.Laboratory of PathologyNCI/NIHBethesdaUSA

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