공지 SHARP Primer Design & Optimization

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Please find below some general guidance on primer design and troubleshooting that we hope will be helpful.

Primer design: We are continuing to conduct systematic testing on primer design strategies. The answer is not yet definitive and further work is needed, but the best strategy we have found so far is to stay around 20-22 bp and approximately 50% GC content. While this is not a guarantee of success or performance, it appears to give the best chance of a good result. Primers outside of this range have worked for us as well, just not as consistently. Tm does not appear to be a strong predictor in SHARP the way it is in PCR, at least based on our tests to date. We will be sure to keep you updated as we learn more.

Amplicon length: SHARP is capable of amplifying long targets, but the recommended formulation in the user manual is currently tuned for the 200 to 1500 bp range. Amplifying longer sequences can benefit from adjustments to the mix.

Troubleshooting recommendations: We have found the following general tips to be helpful:

  • Match template DNA quantity by molarity (copy number) and NOT mass to the positive control as a starting point. 

  • Vary primer concentration, which often compensates for variation in primer performance.
  • Vary SSB from 1/2x to 2x. Higher SSB may help with longer amplicons.

SSB handling and user manual: We kindly recommend always referring to the latest version of our user manual on our website (https://sharpdx.com/documents) since we regularly update operation and storage instructions as we learn more about the system. The latest version recommends that the SSB protein be briefly heated and thoroughly mixed before every use to promote even pipetting.

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