Automated DNA Size Fractionation

System Overview

The Pippin Prep is a new electrophoresis platform for preparation of size-fractionated DNA samples, using pre-cast agarose gel cassettes. The instrument features a computer-controlled power supply and an integrated optical system, which enables user-defined size fractions to be collected automatically. Product DNA is eluted into liquid buffer - no gel extraction required. The system is especially useful for preparation of next-gen sequencing libraries, yielding higher quality DNA at a fraction of the time and labour of manual protocols.

Size Selection Ranges

Several gel types are currently available. Cassettes are pre-cast and disposable. DNA is optically detected with ethidium bromide. Ethidium bromide-free gel cassettes are also available with pre-labelled DNA markers.

Agarose %	For Ranges Between
2.0	0.1-0.6 kb
1.5	0.3-1.5 kb

How the Gel Cassette Works

Gel Cassettes use an external DNA size standard run in a dedicated sample lane to determine the timing of size-selected collections. Four lanes are used for samples, and one extraction can be collected per lane according to user input size ranges. Samples lanes are physically separate and tapered to shorten run times and improve resolution.

Gel Cassettes

Gel cassettes are pre-cast with agarose gel and are disposable. Each cassette has 4 sample lanes and 1 lane on which an external standard (DNA size markers) must be run. Each cassette order includes sufficient DNA marker for every cassette, loading solution, and spare electrophoresis buffer. A P200 pipettor and tips are also required.

Sample lanes are separated by a physical barrier, and one cut can be automatically extracted per sample. In a less automated fashion, consecutive cuts may collected.

Performance

Narrow Size Ranges
For smaller fragment targets, extracted size distributions may be as low as 3% if expressed as CV. Below is a bioanalyzer result of a 200 bp cut from a 2% gel cassette. Broader size ranges may also be collected.

Run Times

Time to collect DNA from samples run the Pippin Prep take between 45 minutes and 2 hours, depending on the sizes range collected and type of cassette used. Hands-on time is 1-2 minutes per sample. Below, the table show relative guidelines - times may vary up to +/- 5 minutes.

Target Fragment (bp), Minimum Distribution		Approx. Time to Collection (minutes)
2% Agarose	1.5% Agarose
100	300	45
350	900	80
600	1500	115

Recovery

Sample recoveries range between 80-90%, for smaller fractions and 50% for larger fractions on a given cassette.
Minimum Size Range
2% Gel Cassette:
3.5% CV at 100 bp
4.0% CV at 600 bp
1.5% Gel Cassette
3.0% CV at 300 bp
9.0% CV at 1500 bp