The condensation of DNA by cationic polymers can be measured by a reduction of the mobility of DNA on agarose that leads to the retention of DNA in the wells.
- Place calf thymus or plasmid DNA (20 µg/ml) in a microcentrifuge tubes containing 1 ml of water.
- Add cationic polymer to the microcentrifuge tubes to form complexes at different charge ratios.
- Incubated at room temperature for 30 minutes to allow the complexes to form properly.
- After this time place 20 µl aliquots of the complexes in fresh microcentrifuge tubes containing 2 µl of gel loading buffer.
- Load the complexes onto a 0.8 % agarose gel in TBE buffer containing ethidium bromide.
- Electrophorese the gel in TBE buffer at 90V for 60 minutes.
- Visualise and photograph the gel on a UV transilluminator.
This assay can be performed using radiolabelled DNA and analysed on the PhoshorImager to quantify how much DNA is retained in the wells at different charge ratios.