Ligation of 3´ and 5´ Adaptors (E6160)

Overview

Starting Material:
1–10 μg total RNA. Alternatively, previously isolated small RNA from 1–10 μg total RNA can be used as starting material.

Protocol

  1. For total RNA input of < 5 μg, dilute the 3´ SR Adaptor 3 1:2 in Nuclease-free Water.

    Mix the following components in a sterile PCR tube:
    Input RNA: 1–6 μl
    NEBNext 3´ SR Adaptor 3: 1 μl
    Nuclease-free Water: variable
    ------------------------------------------------------------
    Total volume: 7 μl

  2. Incubate in a preheated thermal cycler for 2 minutes at 70°C.

  3. Transfer tube to ice.

  4. Add the following components:
    3´ Ligation Reaction Buffer (2X): 10 μl
    3´ Ligation Enzyme Mix: 3 μl 
    ------------------------------------------------------------
    Total volume: 20 μl

  5. Incubate for 1 hour at 25°C in a thermal cycler.

  6. Add the following components to the ligation mixture from step 5 and mix well (For total RNA input of < 5 μg, dilute the SR RT Primer 3 1:2 in Nuclease-free Water):
    Nuclease-free Water: 4.5 μl
    SR RT Primer 3: 1 μl
    ------------------------------------------------------------
    Total volume now should be: 25.5 μl

  7. Heat samples for 5 minutes at 75°C. Transfer to 37°C for 30 minutes and then, to 25°C for 15 minutes.

  8. With 5 minutes remaining, resuspend the 5´ SR Adaptor 3 in Nuclease-free Water (For NEB μl Nuclease-free Water and for NEB resuspend NEB #E6162A in 30 "">#E6160L resuspend NEB #E6162AA in 150 μl Nuclease-free Water).

    For total RNA input of < 5 μg, resuspend the 5´ SR Adaptor 3 NEB #E6162A in 60 μl Nuclease-free Water and NEB #E6162AA in 300 μl Nuclease-free Water.

  9. Heat the adaptor at 70°C for 2 minutes.

  10. Transfer tube to ice.

  11. Add the following components to the ligation mixture from step 7 and mix well:
    5´ SR Adaptor 3 (from Step 10): 1 μl
    5´ Ligation Reaction Buffer (10X): 1 μl
    5´ Ligation Enzyme Mix: 2.5 μl
    ------------------------------------------------------------
    Total volume now should be: 30 μl

  12. Incubate for 1 hour at 25°C in a thermal cycler.