Ficoll based loading solution

All looped constructs were run in 0.7% agarose gels, cast from LE agarose (Seakem) or Ultrapure Agarose (Life Technologies) dissolved in 0.5x Tris-borate EDTA (TBE) (Biorad). Before loading, samples were mixed with a Ficoll-based loading solution (Promega), which we found to give sharper bands than glycerol-based loading dyes, simplifying quantification. Gels were run for 90-100 minutes at 4 V/cm, unless otherwise noted, and subsequently stained in 1x SYBRGold stain (Invitrogen) for a minimum of 30 minutes before being imaged with a gel imager (Biorad) or laser gel-scanner (GE Typhoon). It is important to note that the standard output file of this imager is often set to a .gel file which has a non-linear intensity scaling. .gel images can be linearized using the imageJ Linearize gel Data plugin (http://rsb.info.nih.gov/ij/plugins/linearize-gel-data.html). Alternatively the gel image can be saved as a linear .tiff file off of the imager. We would like to point out that these expensive imagers are not required for quantification, and we obtained similar results using a blue transilluminator (Invitrogen) and a point and shoot camera (Canon S95).