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SageELF Automates Multiple Size Fractionation of DNA, Proteins; PacBio Among Early Access Users


NEW YORK (GenomeWeb) — Sage Science has developed a new gel electrophoresis system, called SageELF, that automates the separation and preparation of DNA and proteins of different sizes.

The SageELF, short for Sage Electrophoretic Lateral Fractionator, promises to save time and labor for next-gen sequencing users who want to prepare DNA or RNA-seq libraries with different insert sizes from the same sample. Proteomics researchers can prepare protein samples for mass spectrometry without the need for lengthy in-gel digestion.

The instrument separates DNA or proteins by size and automatically extracts 12 fractions along the gel using electroelution. It has a list price of $20,000 and can take up to two precast agarose gel cassettes per run, which each cost $25 and take one sample. The cassettes can be loaded with up to 5 micrograms of DNA — though it works with smaller amounts — down to tens of nanograms. Including the elution step, each run takes between 1.5 and 3.5 hours, depending on the sample and gel type.

A number of beta customers are currently testing the SageELF for various applications, including Pacific Biosciences, which already co-markets another DNA fractionation system from Sage, the BluePippin.

Sage, based in Beverly, Mass., plans to launch the SageELF commercially in June in the US and elsewhere in August.

According to Sage CSO Chris Boles, the SageELF was originally designed for the protein analysis market. But when the firm started showing it to their existing customers, mostly DNA researchers, "they were much more enthusiastic than we had anticipated," so it now expects the instrument to be used about equally for DNA and protein applications. "We're thinking it's actually going to solve unique problems on both sides," he said.

For DNA, the SageELF will likely be most useful for researchers wanting to prepare several mate-pair libraries with different insert sizes from the same sample, which increases the sensitivity for detecting structural variations. Compared to manually extracting DNA fractions from a preparative gel, the system could save several hours per sample, Boles said.

PacBio researchers are testing the system for fractionating cDNA for RNA-seq applications, which allows them to characterize new isoforms and alternative splice sites. Earlier this year, the company presented a new transcriptome sequencing method for its sequencer, the PacBio RS II, which uses a new bioinformatics pipeline, called Iso-Seq, and Sage's BluePippin. However, the BluePippin is not designed for collecting multiple fractions from the same sample, Boles said.

Edwin Hauw, PacBio's senior director of product management, told In Sequence that he and his colleagues are co-developing library prep methods with Sage that involve the SageELF. "We believe that the ELF holds great promise to make the workflow for full-length cDNA preparation more efficient," he said.

Researchers have also suggested using the SageELF to separate a sample into a fraction for short-read libraries with insert sizes below 1,000 base pairs and another fraction for a mate-pair library with an insert size above 2 kilobases, Boles said.

At launch, Sage will offer the instrument with two DNA gel cassettes; a 0.7 percent gel to fractionate DNA between 300 base pairs and 18 kilobases, and a 2 percent gel to separate DNA between 100 base pairs and 2.2 kilobases. These come with two protocols, one for cDNA fractionation and one for mate pair library preparation.

The company is working on new gel cassettes and protocols that will allow it to fractionate DNA up to 50 kilobases, and it expects to be able to go up to 100 kilobases "without too much trouble," Boles said.

This could be useful for long-read applications, both from PacBio and nanopore sequencing platforms. "If you have a whole bunch of different DNA sizes in your prep, your sequencer is not going to be used very efficiently because the small fragments kind of waste time on your sequencer," he explained.

The company also believes the SageELF will be of interest to proteomics researchers for fractionating proteins for mass spec analysis, using agarose gel cassettes with SDS, which denatures proteins. The process takes about half a day, Boles said, compared to a day and a half to two days using standard polyacrylamide gels and in-gel digestion.

Initially, Sage will sell two types of protein gel cassettes; a 5 percent gel for proteins from 10 to 100 kilodaltons, and a 3 percent gel for proteins from 50 to 500 kilodaltons.

Going forward, protein researchers might also be able to use the SageELF to separate native protein complexes, such as proteasomes or ribosomes, using non-denaturing gels. Sage is currently testing this application with bacterial ribosomes, Boles said.

One advantage of the system is that all fractions of a precious sample are preserved and nothing goes to waste. Oftentimes, the size of DNA or proteins in a sample is not known ahead of time, Boles explained, and as long as an approximate size range can be estimated, the SageELF ensures that at least some useful material will be recovered.

Sage Science already has two automated preparative gel electrophoresis systems on the market – the Pippin Prep, which selects DNA up to 1.5 kilobases in size and has a list price of about $10,000, and the BluePippin, which fractionates DNA up to 50 kilobases and has a list price of $15,000 – but the company believes these systems, which process up to five samples per gel cassette, will complement rather than compete with the SageELF.

While it is possible to collect several fractions from both the Pippin Prep and the BluePippin, they were not designed for this and the process is "a little cumbersome," Boles said. As such, most SageELF customers will likely be users of manual preparative gel electrophoresis systems.

Sage Science says it has no competition for the automated fractionation of several DNA sizes from the same sample at the moment. For protein fractionation, Expedeon offers a somewhat similar instrument called the Gelfree 8100 Fractionation System.