Loading dyes

Loading dyes are mixed this samples to pull them down into a well in a gel and to visually track migration during electrophoresis.

When using fluorescently-labelled (Cy3, Cy5) samples, make sure the tracking dyes do not co-migrate with your sample, otherwise you may be unable to tell if a resulting band originates from your sample or the dye.

For native PAGE, do not use dyes that contain SDS as they may separate double-stranded nucleic acids.

TriTrack

Source

• Contents:
  • 10 mM Tris-HCl (pH 7.6)
  • 0.03 % bromophenol blue
  • 0.03 % xylene cyanol FF
  • 0.15 % orange G
  • 60 % glycerol
  • 60 mM EDTA.
• Uses:
  • Agarose gel
  • Native PAGE

Gel Loading Buffer II

Source

• 1-2X solution
• Contents:
  • 95% Formamide
  • 18 mM EDTA
  • 0.025% each of SDS, Xylene Cyanol, and Bromophenol Blue
• Uses:
  • Polyacrylamide urea gel (denaturing)
  • Non-denaturing agarose gel
• Appearance: Dark blue

Protocol: 1. Mix sample with an equal volume of Gel Loading Buffer II. Vortex briefly. 2. Centrifuge briefly to bring contents of tubes to the bottom. 3. For denaturing PAGE: Heat to 95°C for 5 min to denature any secondary structure. 4. Load directly (while still hot) on the gel.

RNA Loading Dye

Source

• 2X
• Contents:
  • 47.5% Formamide
  • 0.01% SDS
  • 0.01% bromophenol blue
  • 0.005% xylene cyanol
  • 0.5 mM EDTA
• Uses:
  • Polyacrylamide urea gel (denaturing)

Protocol: 1. Add sample to an equal volume of RNA Loading Dye, (2X). Mix well. 2. Heat at 65–70°C for 5–10 minutes to denature RNA. 3. While heating the samples, setup the gel box and flush urea out of the wells with running buffer using a large tip. 4. Load samples.