Automated Capillary Electrophoresis System
The Fragment Analyzer™ Automated CE System is a fluorescence-based capillary electrophoresis instrument for both sizing and quantifying nucleic acids (DNA and RNA). By using a sensitive intercalating dye coupled with a powerful LED light source, Fragment Analyzer™ Automated CE System obviates the need for fluorescent labeled primers and can be used to separate dsDNA fragments and RNA (mRNA and total RNA). The Fragment Analyzer™ Automated CE System is the most flexible system on the market today, with the greatest sensitivity, the highest separation resolution over a wide range, the widest dynamic range and the fastest separation times.
This instrument comes available for customers who wish to run either 12 samples or 96 samples at a time.
Currently kits are available to:
• quantify and qualify NGS fragments.
• quantify and qualify RNA.
• quantify and qualify genomic DNA.
• do Mutation Detection, also known as TILLiNG, a reverse genetics technique.
The application kits help laboratories to streamline workflow and avoid bottlenecks typically found with competitive lab-on-a-chip methods. Gels formulated to provide high resolution separation are also available for general fragment analysis, such as SSR/microsatellites, small and large PCR fragments (amplicons) and resolve fragments sized between 10 bp and 40,000 bp with resolution down to 2bp.
Each and every kit is performance-tested prior to shipment to ensure quality, accuracy and ease of use for customers. Most kits require a single pipetting step before placement of the sample plate onto the instrument.
An analytical software package, PROSize™, greatly reduces post-separation analysis time. Put them all together — the instrument itself, the QC-tested application kits, and the analytical software — and the combination makes the Fragment Analyzer™ Automated CE System a powerful package for reducing labor and improving lab workflow and throughput.
Contact us today and request an instrument for your free one day trial.
Parallel Capillary Electrophoresis: Description of Technology
Advanced Analytical's parallel capillary electrophoresis (CE) technology enables electro-driven analytical separations of DNA and RNA with on-line, simultaneous LED-based fluorescent detection.
The instrument is designed to handle either a 12 capillary array which can access all wells of a 96-well plate, 12 samples at a time or a 96 capillary array, able to sample all positions in one injection. Standard capillary dimensions are 50μm inner diameter (i.d.) and 200μm outer diameter (o.d.).
Anyone who was worked with agarose or acrylamide gel electrophoresis knows about the trade- off between speed vs. resolution. If you want high resolution; you use a long box. If you want answers quickly, you use a short box. Likewise with the Fragment Analyzer™ Automated CE System: various capillary lengths can be used, depending on the application, required resolution and desired speed of analysis. Longer arrays provide resolution down to 2 bp for fragments under 300 bp in length. Shorter arrays still provide good resolution with run times as fast as 15 minutes.
The inlet side of the capillary array is arranged in an 8 x 12 format with electrodes placed side-by-side with each capillary, allowing for direct injection via vacuum or voltage from standard 96-well plates. The capillaries are aligned in parallel in the detection window, which is positioned between the LED light source and the detector assembly. The outlets of the capillaries are bundled to a common reservoir where they are connected to a ground. The capillary arrays are modular in nature and a new capillary array can be exchanged in less than five minutes.
Room temperature air is circulated around the capillaries to modulate the temperature during the CE separation. Technology Schematic (12 capillary Version shown)
Maximum Sample Throughput (12 capillary array):
Microsatellite (SSR) analysis by PCR is a powerful molecular tool for screening organisms and determining polymorphic loci and genetic profiles. The Fragment Analyzer™ Automated CE System is an equally powerful and flexible fluorescence-based capillary electrophoresis instrument.
It provides size and quantification information for microsatellites and DNA fragments generated using unlabeled PCR primers specific to polymorphic microsatellite regions. With the highest resolution and fastest run times of any dsDNA fragment analysis capillary electrophoresis system, the Fragment Analyzer™Automated CE System improves laboratory throughput and reduces analysis time of microsatellites. Available in either 12-capillary or 96-capillary format.
Genomic DNA Analysis
Genomic DNA (gDNA) extraction from tissues, cells or organisms is a critical first step for all subsequent DNA analyses. Until now, assessing the quantity and quality of genomic DNA has typically required the use of two separate instruments: one for quantity, one for quality.
With the Fragment Analyzer™ Automated CE System platform, both genomic DNA quality and genomic DNA quantity can be assessed at the same time, using the same aliquot of sample and in less time than to do both by traditional methods.
Large Fragment Separation
Human gDNA sample analyzed with AATI’s high sensitivity gDNA kit. Peak is annotated by size. Measured concentration agreed to within 5% of fluorometric assay.
RNA research is the new frontier of discovery in life science. Labs that once analyzed dozens of RNA samples a week may now analyze hundreds or even thousands.
Assessment of RNA quality and RNA quantitation is critical for many molecular biology techniques. Manual assessment methods for both quantity and quality can use large amounts of precious materials and take a considerable amount of time to complete.
Several analytical instruments exist for the evaluation of RNA. However, these instruments either lack acceptable detection sensitivity or require significant hands-on time to complete chip loading and preparation. The Fragment Analyzer™ Automated CE System process for RNA – either for total RNA and/or messenger RNA – is completely automated, requiring minimal hands on time.
The Fragment Analyzer™ Automated CE System provides an RQN measurement to assist with RNA analysis.RQN stands for RNA Quality Number. Derived from PROSize® analytical software, RQN assesses the quality or integrity of total RNA on a scale of 1-to-10, and allows for correlation to legacy data.
NGS Fragment Analysis
Accurately quantifying and qualifying Next Gen Sequencing (NGS) fragments in a high throughput automated fashion is becoming critically important for more laboratories. The labs are seeing increased demand from researchers who want to sequence smaller amounts of information, but from larger pools of organisms.
Typical NGS Separation
Table shows quantitative information from NGS sample library preparation prior to running on Next Gen Sequencer. Electropherogram overlay plot shows size distribution of the NGS libraries samples, along with a sizing ladder (X-axis).
Overlap of NGS Libraries
Different-sized NGS libraries from various fragmentation methods, such as enzymatic, sonication, etc. Top electropherogram represents the sizing ladder.
Separating the 3 forms of Plasmid DNA can be challenging. Each form -- nicked, supercoiled or linear -- can run differently depending on its' size and dye intercalation. The Fragment Analyzer™ Automated CE System is the only multichannel capillary electrophoresis instrument that can successfully separate the 3 plasmid DNA forms.
Large DNA Fragments
Would you undertake different research projects if you had an automated CE instrument that could separate large fragments?
PCR fragments are not always small in size and sometimes larger amplicons (>1,500bp) need to be analyzed. Some competitive DNA analysis instruments are based on single-strand technology, and are very limited in the fragment sizes they can analyze. The Fragment Analyzer™ Automated CE System platform has several gels for larger fragments, including a gel for efficient separation of fragments <12,000bp and another gel for <40,000bp fragments.
Mutation Detection / TILLiNG
TILLiNG (Targeting Induced Local Lesions in Genomes) is a reverse genetics technique designed to detect unknown mutations in a gene by forming DNA heteroduplex as a result of mixing wild-type and chemically-induced mutated genes.
In order to increase experimental throughput, the genes are pooled first, then PCR amplified. This is followed by heteroduplex formation, then the samples are enzymatically digested. Next, digested cleaved DNA fragments are analyzed for scoring. The enzyme specifically recognizes the mismatched base pairs and cleaves the DNA at the site of mismatch.
Until now, detecting unknown mutations was both a challenging and a time intensive process. Advanced Analytical has developed a streamlined TILLiNG process that requires NO fluorescently labeled primers and NO sample clean-up. Detecting unknown mutations has never been easier, especially with this process developed for the Fragment Analyzer™ Automated CE System platform (see below). In comparison to the traditional method, the Fragment Analyzer™ Automated CE System method requires less than ½ the hands on time and analyses can be completed twice as fast (total time) compared to competitive methods.
Currently, Fragment Analyzer™ Automated CE System customers are using their instruments to do:
• reverse genetics TILLiNG of rice.
• reverse genetics TILLiNG of corn.
• reverse genetics TILLiNG of wheat.
• reverse genetics TILLiNG of lettuce.
• reverse genetics TILLiNG of tomato.
• reverse genetics TILLiNG of soybean.
Regardless of whether your lab wants to do TILLiNG (mutation detection) with diploids, tetraploids or hexaploids, the Fragment Analyzer™ Automated CE System has excellent sensitivity for analyzing medium and large-sized TILLiNG pools.
DNF-900-K0500 dsDNA Reagent Kit, 35-500 bp (500 samples)
DNF-910-K0500 dsDNA Reagent Kit, 35-1,500 bp (500 samples)
DNF-910-15L80M-K0500 dsDNA Reagent Kit, 35-5,000 bp (500 samples)
DNF-920-K0500 dsDNA Reagent Kit, 75-15,000 bp (500 samples)
DNF-930-K0500 dsDNA Reagent Kit, 75-20,000 bp (500 samples)
DNF-479-0500 Standard Sensitivity NGS Fragment Analysis Kit, 500 samples
DNF-486-0500 High Sensitivity NGS Fragment Analysis Kit, 500 samples
DNF-489-0500 Sensitivity RNA Analysis Kit, 500 Samples
DNF-491-0500 High Sensitivity RNA Analysis Kit, 500 samples
DNF-487-0500 Standard Sensitivity Genomic DNA Analysis Kit, 500 samples
DNF-488-0500 High Sensitivity Genomic DNA Analysis Kit, 500 samples
DNF-910-K0500T Mutation Discovery 910 Gel Kit, 500 samples
DNF-920-K0500T Mutation Discovery 920 Gel Kit, 500 samples
DNF-480-3000 dsDNA Cleavage Kit, 3000 samples
DNF-600-U010 Intercalating Dye, 10uL
DNF-475-0100 5X Capillary Conditioning Solution, 100 mL
DNF-490-0060 10-3 M Fluorescein, 60 uL with diluent
DNF-495-0075 Dilution Buffer E, 1X, 75 mL
GP-440-0100 Capillary Storage Solution, 100 mL
P60-20 Fragment Analyzer 96-Well Buffer/Waste Tray, case of 50
A2300-9650-3355 96-Capillary Array Cartridge 50 um (ID) 33 cm (EFF), 55 cm (TOT), 10mL (RES)
A2300-9650-5580 96-Capillary Array Cartridge 50 um (ID) 55 cm (EFF), 80 cm (TOT), 10mL (RES)
A2300-1250-5580 12-Capillary Array Cartridge 50 um (ID) 55 cm (EFF), 80 cm (TOT), 2mL (RES)
A2300-1250-3355 12-Capillary Array Cartridge 50 um (ID) 33 cm (EFF), 55 cm (TOT), 2mL (RES)
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