Targeted Size Selection for Next-Gen Sequencing
(100bp – 50kb)

Collect DNA Fragments up to 50kb or Size Select Proteins

The BluePippin has the DNA capabilities of the Pippin Prep, plus the extra benefit of pulsed-field electrophoresis for resolving and collecting high molecular weight DNA.  With SDS-agarose gel cassettes, the BluePippin collects targeted protein sizes from complex samples for biomarker or protein modification studies. Target sizes or ranges of sizes are entered in software, and fractions are collected in buffer. Up to 5 samples/gel cassette may be run, with no possibility of cross contamination.

Benefits of the BluePippin System

  • Saves time and effort compared to manual gel purification
  • Sample-to-sample reproducibility streamlines research
  • Higher sample quality improves downstream analysis

Key Downstream Technologies

  • Mate-pair sequencing
  • Single molecule sequencing
  • Protein mass spec

Pre-Cast Agarose Gel Cassettes for DNA Size Selection

Gel cassettes for DNA selections are available in four agarose concentrations to provide a full range of size selection options between 100bp up to 50kb.  For smaller fragment sizes, internal standards may be used for higher accuracy and increased sample capacity (from 4 to 5 samples/cassette).  Higher molecular weight fragments require a dedicated lane to run a calibration marker.  Run times are as little as 30 minutes,  To resolve very large DNA fragments, pulsed-field runs may last several hours. View the BluePippin cassette reference chart to explore the DNA size selection options and run times.

Gel Cassette Types and Target Ranges

  • 3% agarose, 100-250bp
  • 2% agarose, 100-600bp
  • 1.5% agarose, 250bp – 1.5kb
  • 0.75% agarose, 1-50kb

Downstream Technologies

  • miRNA isolation
  • DNA sequencing, RNA-seq, genotyping
  • DNA sequencing, ChIP-seq
  • Mate-pair, single molecule

See the Workflow Summary.

SDS-Agarose Gel Cassettes for Protein Purification

Protein size selection gel cassettes are cast with specially formulated agarose that provides similar resolution to acrylamide gels.  Cassettes are cast with SDS and can run up to 4 samples simultaneously. One lane (each cassette has 5 lanes) must be dedicated to running a size standard to calibrate the timing of collections.  Samples are collected in 0.1% SDS-electrophoresis buffer.

Gel Cassette Types and Target Ranges:

  • 5% Agarose, 18-80kDa

Downstream Technologies:

  • Mass spec


The BluePippin instrument includes a monitor, keyboard, and mouse. A CPU is built in; an external PC is not required.

Blue Pippin Specs
Electrophoresis voltage25V, 100V or 150V constant, 100V pulsed field
Optical detection470 nm excitation, 525 nm emission
Power requirements100-240 VAC, 2.5 A, 50-60 Hz
Weight15 lbs / 7 kg
Dimensions7h x 11w x 21d (in) | 18h x 28w x 53 d (cm)

Cassette Kits

Kits include 10 ea. disposable pre-cast gel cassettes.  All necessary standards and reagents are included with the purchase.

Brochure and Datasheets


Posters and Presentations

Application Notes

Case Studies

BluePippin Citations

BluePippin Blog Posts