FEMTO Pulse™

FEMTO Pulse™ Automated Pulsed-Field CE Instrument

Introduction

Winner of a 2016 R&D 100 Award, the FEMTO Pulse Automated Pulsed-Field CE Instrument is shattering analytic barriers for nucleic acid separation and detection. 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. With a meticulously designed optical detection platform unprecedented sensitivity is achieved, detecting nucleic acids into the lower femtogram range.

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

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

Overview

Technology Applications Features and Benefits Specifications Array

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

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.

The FEMTO Pulse Automated Pulsed-Field CE Instrument has innumerable applications and supports researcher innovation. With sensitivity in the femtogram range and sizing through 200,000 bp, new measurements can be made and novel applications developed. The FEMTO Pulse is poised to have a significant impact on various applications including:

Single Cell Analysis Low quantity NGS Library Preparations
Exosomes
Small RNA
cfDNA
QC Genomic DNA
QC Large DNA Fragments
BAC Clone Sizing
Detect Foreign DNA in Vaccines
Biobanking
Eliminate Performance Based Qualitative Tests
Run Low Cycle PCR to Reduce Amplification Bias
Count Virus
Microbial Metagenomics
Microbial Metatranscriptomics
QC Ancient DNA
FFPE Nucleic acids

The FEMTO Pulse does not require amplification with fluorescently-labeled probes to achieve a remarkable level of detection sensitivity, instead a sensitive intercalating dye is used to detect DNA and RNA. This strategy allows the FEMTO Pulse to analyze nucleic acids without prior knowledge of the samples; in turn broadening the analytic scope of the instrument. What could you do with an instrument as sensitive and powerful as the FEMTO Pulse

High sensitivity
Large DNA fragment and smear resolution
3 sample drawers allow the loading of up to 288 samples
Barcoded Reagents
12 Capillary Ultra-Short Array (22-40)
Pulsed-Field Power supply can function as constant power supply for standard nucleic acid fragments and smears

The FEMTO Pulse Automated Pulsed-Field CE Instrument is a novel tool for genomics and molecular biology research. A remarkably flexible instrument, the power of CE is combined with pulsed-field electrophoresis and an enhanced optical detection system. Pulsed-field capillary electrophoresis (PFCE) supplies researchers with the means to quickly and efficiently separate large DNA fragments and smears. A methodically designed optical detection platform gives the FEMTO Pulse the sensitivity to detect DNA and RNA samples down to the single femtogram level. The pulsed-field power supply is versatile, enabling both PFCE and standard capillary electrophoresis.

PFCE with the FEMTO Pulse provides a streamlined and easy to use alternative to pulsed-field gel electrophoresis (PFGE). The FEMTO Pulse is able to separate smears in about one hour and DNA fragments in less than 2 hours, while PFGE separation time can extend beyond 20 hours.

Maximum Sample Throughput: 12 samples per run

Maximum Unattended Sample Capacity: 288 samples

Minimum Sample Volume: 20 μL of liquid for injection

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 (in well concentration)

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® 3.0 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 38 cm W x 51 cm D (24 x 14 x 20 in)

Instrument Weight: 40 Kg (88 lbs)

A custom 12 Capillary Ultra-Short Array is employed with the FEMTO Pulse

Automated Pulsed-Field CE Instrument. 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 Automated CE System or the Fragment Analyzer INFINITY Automated CE System. 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.

Resources

FEMTO Pulse™ Video