================================
Psoralen-qPCR supercoiling assay
================================

.. warning:: 
   This protocol is deprecated. It did not work well with our original UV crosslinker, and could not measure plasmids.


.. note:: This protocol was used for the experiments described in Babos and Galloway, Cell Stem Cell, 2019 for measuring DNA supercoiling using psoralen intercalation as a metric of negative supercoiling. Psoralen preferentially incorporates into underwound DNA (negatively supercoiled DNA).

Experiment setup
-----------------
1. Prepare half of a 6-well **plate** per replicate.
   For conditions in triplicate, this means **1.5 6-well plates** per condition!
2. Treat cells according to your experiment.
3. If you want to arrest the cell cycle prior to measurement, treat the cells with
   1 μM aphidicolin for 1.5 to 2 hours prior to cell harvest and DNA extraction.

=========== =============   =============  =========
Chemical    Concentration   Molar mass      mg / mL
Aphidicolin 1 μM            338.48 g/mol
=========== =============   =============  =========