Femto Pulse

The Femto Pulse System is a novel tool for genomics and molecular biology research. Winner of a 2016 R&D 100 Award, the Femto Pulse is shattering analytic barriers for nucleic acid separation and detection.

FEMTO Pulse Awards

What is the Femto Pulse?

The Femto Pulse System is a remarkably flexible instrument. Quantify, qualify, and size DNA and RNA samples with unstoppable accuracy and precision. Perfect for low concentration and/or large size nucleic acid samples, the Femto Pulse easily analyzes diverse sample types including: cfDNA, total RNA, genomic DNA, large fragment DNA, messenger RNA (mRNA), and more.

Using a pulsed-field power supply, the Femto Pulse is the first ever parallel capillary electrophoresis instrument able to resolve DNA smears and DNA fragments through 200,000 bp. A meticulously designed optical detection platform enables unprecedented sensitivity, detecting nucleic acids into the lower femtogram range.

Femtogram Level Sensitivity
Achieve 10 times higher sensitivity for nucleic acid smears and up to 100 times for nucleic acid fragments.
Large Fragment Resolution
Separate large DNA fragments (through 200 Kb) and smears (through 165 Kb) in about an hour.
Simple Sample Preparation
Minimize sample degradation with fewer pipetting steps and stable reagents.
Powerful Analysis Software
One intuitive software program automates analysis of diverse samples types.
The Benefits of the Femto Pulse.
Conserve Precious Sample
Unparalleled sensitivity allows you to use less precious samples and achieve superior detection.

How Flexible is the Femto Pulse?

A powerhouse instrument, the Femto Pulse provides laboratories with true versatility in sample analysis. DNA and RNA samples are effortlessly separated on the same capillary array. Furthermore, two different gel matrices can be loaded, enabling the unattended, sequential separation of RNA and DNA samples (e.g. mRNA followed by genomic DNA), without cumbersome array swaps or cleaning.

Flexible enough to handle any workflow senarios

Unlock the analytic potential of nucleic acid workflows with the award-winning Femto Pulse.
Pulsed-field capillary electrophoresis and an optimized optical platform enable the sizing of DNA fragments through 200 Kb and DNA smears through 165 Kb.
Up to three, 96-well sample trays can be loaded at a time for the unattended analysis of up to 288 samples.
Two gel bottle locations allow users to set distinct and diverse separation methods for automated operation.

ProSize Data Analysis Software

The Femto Pulse is a remarkable instrument, requiring appropriately powerful analysis software. ProSize Data Analysis Software effortlessly quantifies, qualifies, and sizes DNA and RNA samples run on the Femto Pulse. Further analysis is quickly done through an intuitive interface, providing users with crucial results sooner.

The Femto Pulse is a versatile instrument with various applications across many research disciplines. Capable of separating large DNA fragments and smears, BAC clones, and total RNA with unmatched speed, the list of potential applications of the Femto Pulse goes on and on. Imagination is the only limiting factor for the Femto Pulse.

Superior Sizing

Figure 1

165 Kb Ladder separated on the Femto Pulse System using the Ultra-Short Capillary Array (22-40).

Superior Sensitivity

Figure 2

Dilution series of a 300 bp fragment showing the 5 fg/µL sensitivity of the Femto Pulse System using the Ultra-Short Capillary Array (22-40). Concentrations listed are after dilution into the sample well.

The Femto Pulse is a groundbreaker, with no equivalent on the market. It is future-proofed for the new waves of long-read technology and will be seen as a vital piece of kit in the coming years.

Harbans Marway, Earlham Institute, UK


The Femto Pulse is redefining analytic boundaries and promises to revolutionize nucleic acid based applications, from NGS to the detection of foreign DNA in vaccines. With sensitivity into the lower femtogram range and a sizing capacity through 200,000 bp, the Femto Pulse will generate new applications too.


NGS library QC is essential to the generation of successful sequencing results. Several solutions have been developed to deal with the QC challenges of various types of NGS libraries, from short-read to long-read sequencing platforms, ChIP-seq, RNA-seq, and beyond.

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Genomic DNA

An accurate understanding of genomic DNA quality, quantity, and size is important for numerous methodologies including evaluating isolation success and NGS. Methods of evaluating the quantity, quality, and size of gDNA exist, though many are unable to reliably resolve challenges associated with genomic DNA analysis.

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PCR Fragments

Determination of amplicon size and concentration is a crucial aspect in post-reaction analysis of PCR. Traditional methods of PCR fragment analysis lack the sensitivity and resolution demanded by many applications.

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Active in myriad biological processes, RNA is the target of many applications, from microarrays to NGS. With diverse types of RNA, small RNA, mRNA, rRNA, and more, unique analytic challenges are posed. Several solutions for the quantification, qualification, and sizing of RNA samples have been developed, though many do not fully address the analytic challenges.

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Cell-free DNA (cfDNA) is of increasing interest to clinicians and researchers alike as a promising biomarker for various disease states. cfDNA requires rigorous assessment of quality prior to use in NGS workflows to ensure successful sequencing results.

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Large Fragment DNA

The advent of next-generation long read sequencing and synthetic genomics has increased interest in large DNA fragment analysis. Ideal for QC steps in the SMRTBell library workflow from Pacific Biosciences®, the large fragment DNA kits for the Fragment Analyzer can quantify and qualify DNA fragments and smears through 50 Kb.

Commonly analyzed nucleic acid samples include:

  • NGS Libraries (Illumina and PacBio)
  • SSR/Microsatellites
  • PCR Amplicons

Technical Information


Agarose gel electrophoresis lacks the capability to resolve DNA fragments and smears starting around 20 Kb, in a phenomena termed, "limiting mobility". Functionally, limiting mobility results in the co-migration of large DNA fragments in excess of the size threshold as they are unable to migrate in a size dependent manner. Pulsed-field gel electrophoresis (PFGE) ameliorates these issues by alternating the direction of the electric field. This technique uses an agarose gel to separate fragments up to 10 Mb in size. While PFGE is a powerful technique, enabling the visual analysis of large DNA fragments and smears – including intact genomic DNA – it is time consuming, requiring days of preparation time, significant amounts of genomic DNA, and electrophoresis times between 15 and 24 hours. The Femto Pulse Automated Pulsed-Field CE Instrument accelerates this workflow significantly, decreasing preparation time and completing pulsed-field capillary electrophoresis (PFCE) runs in approximately 1 hour.

Diagram Parallel Capillary Electrophoresis Array

The Femto Pulse is equipped with a pulsed-field power supply, enabling pulsed-field capillary electrophoresis (PFCE). The power supply is additionally capable of supplying constant voltage for the separation of nucleic acid fragments and smears that do not require PFCE. To separate large nucleic acid smears and fragments, the Femto Pulse periodically changes the direction of the electric field by 180° in a specific type of pulsed-field electrophoresis called field-inversion electrophoresis. Alternating the electric field in such a manner overcomes limiting mobility, forcing the size dependent separation of large DNA fragments and smears.

An optimized optical system facilitates the detection of nucleic acid samples down to 5 fg/µL. A general overview of how nucleic acids are detected on the Femto Pulse is as follows; an LED light source (470 nm) passes through the capillaries in the detection window, exciting the dye intercalated into the DNA or RNA molecules. The emitted fluorescence then passes through a camera lens and specific band pass filters and spatially imaged onto a CCD detector providing results in real-time.


Maximum Sample Throughput 12 samples per run
Maximum Unattended Sample Capacity 288 samples
Minimum Sample Volume 20 µL of liquid for injection; as little as 1-2 µL of actual sample required
Quantitative Kits NGS Library Preparations for Illumina and PacBio, Genomic DNA, cfDNA, Total RNA, mRNA, ribodepleted RNA, microRNA, and DNA Fragments
Resolution Gel Dependent
Sizing Accuracy Typically 5% or better
Detection Sensitivity As low as 5 fg/µL for fragments and 200 fg/µL for a smear
Light Source 2X 700 mA, 10 W LED, 460 nm excitation wavelength
Detector High sensitivity CCD; 500-600 nm emission wavelength
Software Femto Pulse Operational Software, ProSize Data Analysis Software
Data Export Format CSV, PDF, flexible numerical or binary output options
Environmental Conditions Indoor use, normal laboratory environment 20-23°C
Relative Humidity Range <80% (non-condensing)
Electrical 100-200 VAC; 50-60 Hz; 15 A (alternate configurations available)
Instrument Dimensions Fully configured 61 cm H x 35 cm W x 51 cm D (24 x 14 x 20)
Instrument Weight 40 Kg (88 lbs)

Reagent Kits

The reagent kits below are for the quantitative analysis of low concentration DNA and RNA samples and the sizing of gDNA and large DNA fragments.

Genomic DNA 165kb Kit (FP-1002-0275)

Sizing Range: 1.3 Kb - 165 Kb

Ultra-Sensitivity NGS Kit (FP-1101-0275)

Sizing Range: 100 bp - 6000 bp

Ultra-Sensitivity RNA Kit (FP-1201-0275)

Sizing Range: 15 nt - 6000 nt

Capillary Arrays

A custom 12 Capillary Ultra-Short Array is employed with the Femto Pulse System. With an effective length of 22 cm and an overall length of 40 cm, the 12 Capillary Ultra-Short Array is shorter than the capillary arrays used with either the Fragment Analyzer or the 5400 Fragment Analyzer. The shorter length keeps Pulsed-Field Capillary Electrophoresis (PFCE) separation times low without compromising nucleic acid fragment and smear resolution. In addition to a shorter effective length and overall length, the detection window on the 12 Capillary Ultra-Short Array has been modified to reduce crosstalk between capillaries and facilitate enhanced detection sensitivity.

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