DNA Size Selection for Next-Gen Sequencing

Pippin instruments are the best alternative to excising DNA from agarose slab gels and purifying with kits. Aside from significant savings in labor and effort, higher quality DNA is extracted with a better yield. The Pippin instruments are a preparative electrophoresis platform that separates and extracts DNA fragments. Using pre-cast and disposable gel cassettes, DNA is automatically collected in buffer according to software-input size ranges. DNA fractions (typically adapter-ligate NGS libraries) are removed using standard pipettes. Workflow requires about 1-2 minutes of hands on time per sample, and cassettes are available for extractions between 50 bp and 50kb. Typical run times (four samples per run) are between 50 and 100 minutes.

For reproducible collections of smaller fragments, up to 1.5 kb, the Pippin Prep facilitates the construction of next-gen sequencing libraries for applications such as paired-end sequencing, ChIP seq, and preparing templates for emulsion PCR. If the collection of larger fractions is also needed, the BluePippin provides a higher range of size selection (using pulsed-field electrophoresis) and the ability to automatically collect DNA bands or restriction fragments.

How the system works

Pippin gel cassettes are pre-cast with agarose and are disposable. Cassettes have a 4 sample capacity, and a fifth lane is used to run a size marker for calibration. Each sample lane is physically separate, and features a branched configuration to which 3 electrodes are applied. DNA is separated along a gel column until the programmed fragment range reaches the branch point. By switching the active electrode, DNA is diverted into a membrane-bound buffer chamber. When the size range has been collected, the active electrode is switched back to the separation channel, and the sample can be removed with a standard pipette.

Benefits of Pippin vs. Manual Gel Purification

  • Minutes of hands on time, saves time and effort
  • No cross — contamination
  • No UV nicking of DNA
  • No purification of LMW artifacts or unligated adaptors
  • Higher sample recovery
  • More accurate and reproducible

The Advantages of Narrow Size Distributions for Whole Genome Sequencing

Pippin size selection provides a narrow and uniform DNA fragment size distribution, with minimal LMW contamination. This provides key advantages to single-end and paire-end sequencing. For bead-based systems, a tightly sized library reduces amplication bias toward smaller fragments, providing a more efficient sequencing run. For paired-end sequencing, narrow “shoulders” provide informaticists with optimal sequence for identifying indels and other structural variants.

Benefits of the Pippin Prep™ DNA size selection system

  • Minutes of labor saves time compared to manual gel purification
  • Reproducible extractions provide more consistent results
  • Provides narrow fragment size distributions for paired-end sequencing
  • Minimal low molecular weight contamination reduce wasted reads and ambiguous indel calling
  • Individual sample channels eliminate sample cross-contamination

Benefits of the BluePippin™ DNA size selection system

  • extracts DNA or protein from agarose
  • features pulsed-field electrophoresis power which enable accurate collection of kb-sized DNAand protein collections between 25-80 kDa.
  • Pulsed-field electrophoresis collects DNA up to 50 kb
  • Reduces complexity of protein samples for mass spec
  • Minutes of labor saves time compared to manual gel purification
  • Individual sample channels eliminate sample cross-contamination

To learn more about the Pippin Instruments, please contact our application support team at or Toll Free number 18002670607

1800 267 0607

+91-22-2528 1012

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