5'/3' RACE Kit, 2^nd Generation Troubleshooting

Rapid amplification of cDNA ends (RACE) is used to rapidly obtain full-length cDNA from partially known sequences. The 5′/3′ RACE kit (Product No. 03353621001) contains transcriptor reverse transcriptase and recombinant terminal transferase. Transcriptor reverse transcriptase transcribes full-length cDNA for the highly sensitive and rapid amplification of either 5′ or 3′ cDNA fragments up to 14 kb. Recombinant terminal transferase is used to add a homopolymeric A-tail to the 3′ end of the cDNA. The poly(A)⁺ tail decreases the likelihood of inappropriate truncation by the oligo(dT)-anchor primer, and overcomes the weaker A-T compared to the G-C hybridization.

Troubleshooting Rapid Amplification of cDNA ends (RACE)

Poor Results

In addition to the troubleshooting provided in the product manual, most probably the efficiency of the tailing reaction performed by Terminal Transferase could be impaired. This could occur due to several reasons, which will affect the control reaction and 5′ RACE in general:

• Improper denaturation
  Check if the denaturation step before the tailing reaction was performed properly according the protocol: Incubate for 3 minutes at +94 °C. Chill on ice.

• Insufficient incubation time
  Note that the incubation period for the tailing reaction can be increased to 30 minutes.

• Incorrect storage of the High Pure PCR Product Purification Kit
  In this case, precipitation within the Binding Buffer may occur. Such precipitates of buffer components can be carried over to the final eluate and inhibit the subsequent Terminal Transferase reaction.

• cDNA purification protocol
  Strictly follow the purification protocol in the product manual of the 5’/3’ RACE.
  In particular, it is important that the centrifugation step after the last washing step (prior to elution) is performed at maximum speed of 13,000 x g for a minimum of 2 min. The filter tube should be completely dry before elution of bound cDNA. Otherwise, residual ethanol inhibits the tailing reaction. All other centrifugation steps should be performed at 6,000 to 8,000 x g, and for these a 30s duration is sufficient.

Stretches of 60 to 100 T Bases in the 5’ Region

When sequencing the final PCR product of the 5´-RACE procedure one can detect stretches of 60 to 100 T bases in the 5´region. Normally the presence of a non-T base at the 3´-end of the PCR-anchor primer prevents this from occurring by forcing the primer to bind to the inner end of the poly(A) tail.
Nevertheless there are several reasons that T-base stretches may occur:

1. If the annealing conditions during the first PCR amplification are not optimal (i.e., the oligo-d(T)-anchor primer is not completely annealed and might bind within the 5´poly(A) tail) and a proofreading polymerase (e.g., Expand High Fidelity PCR System or Expand Long Template PCR System) is used instead of Taq DNA polymerase, the 3´->5´exonuclease activity may remove a non-annealed 3´ non-T anchor base. This can lead to priming of PCR from within the poly-A tail and the introduction of long 5´ T stretches into the PCR product. Stringent annealing conditions are very important for success of this reaction.
2. Correct purification of the first strand cDNA is extremely important to remove residual unincorporated nucleotides. Otherwise in the 5´tailing reaction, other nucleotides than A can be incorporated which leading to internal binding of the oligo-d(T)-anchor primer to the 5´poly(A) tail.

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