mRNA Fragmentation Protocol (E6116)


Starting Material: 100–200 ng purified mRNA, 200 ng recommended.


  1. mRNA Fragmentation
    1. Mix the following components in a sterile PCR tube:
      Purified mRNA 1–18 μl
      10X RNA Fragmentation Reaction Buffer: 2 μl
      Nuclease-Free Water: variable
      Total volume: 20 μl
    2. Incubate in a preheated thermal cycler for 1–5 minutes at 94°C. Fragmentation time should be adjusted depending on type of RNA and desired sizes of fragments (see Figure 1 on the product page ).
    3. Transfer tube to ice.
    4. Add 2 μl 10X RNA Fragmentation Stop Solution.
  2. Clean Up Fragmented RNA Using RNeasy MinElute Spin Columns
    1. Add 78 μl of the Nuclease-Free Water to the 22 μl fragmented RNA from step 4. Purify sample using RNeasy MinElute Cleanup Kit (Qiagen #74204) following manufacture instructions. Elute in 15.5 μl Nuclease-Free Water. The recovered volume should be ~14.5 μl. 

      Note: column purification removes short RNA Fragments and enriches
      the sample for RNA fragments longer than 200 nucleotides.
  3. Alternatively, Clean Up Fragmented RNA Using Ethanol Precipitation
    1. Mix the following components in a sterile 1.5 ml microcentrifuge tube:
      Fragmented RNA from step4: 22 μl
      3 M Sodium Acetate, pH 5.5: 2 μl
      Linear Acrylamide, 10 mg/ml: 1–2 μl
      100% Ethanol: 60 μl
      Total volume: 85–86 μl
    2. Incubate at -80°C for 30 minutes.
    3. Centrifuge at 14,000 rpm for 25 minutes at 4°C in a microcentrifuge.
    4. Carefully remove ethanol.
    5. Wash pellet with 300 μl of 70% ethanol.
    6. Centrifuge and carefully remove 70% ethanol.
    7. Air dry pellet for up to 10 minutes at room temperature to remove residual ethanol.
    8. Resuspend in 14.5 μl Nuclease-Free Water.