FAQ: Can I use GelRed® with the Low Molecular Weight and 50 bp DNA Ladders from NEB?
While agarose gels can be pre-cast with GelRed, the migration and resolution of DNA ladders might be affected. According to the manufacturer, high affinity nucleic acid binding dyes can alter the DNA migration during electrophoresis. For the Low Molecular Weight and 50 bp DNA Ladders specifically, which are made up of sticky-ended DNA fragments, the ladder bands will likely smear when gels are pre-cast with GelRed. Post-staining with GelRed results in superior sensitivity and eliminates the possibility of dye interference. These ladders, however, will run as expected with pre-cast gels if they first undergo a blunting treatment (through a polymerase fill-in or nuclease blunting reaction).