Capillary Electrophoresis Fragment Analyzer

What is the Capillary Electrophoresis Fragment Analyzer?

A single-capillary or multi-channel fragment analyzer separates nucleic acids in a polymer-filled capillary and reports size, concentration and integrity scores. It is the routine quality control instrument for sequencing libraries, RNA samples and PCR products where reproducible digital results are required.

Overview

The instrument injects a small volume of sample into a polymer-filled capillary and applies voltage so that fragments migrate according to size. Fluorescent dye bound to the nucleic acid is excited by an LED or laser, and the detector records a signal over time. Software converts migration times to base pairs using an internal size standard and calculates concentration from a quantitative marker of known concentration. A 12- or 96-sample plate is usually processed in 40–90 minutes, with sizing accuracy typically within 5% and reproducibility suitable for library quality control. Reported results include peak size, molarity, mass concentration, an integrity score for RNA, and region-based values for libraries. Most instruments accept several gel and ladder kits so the sizing range can be adjusted from small amplicons to long-read libraries.

How does it work?

Fragment analysis separates charged nucleic acid fragments in a sieving matrix and detects them by fluorescence. In capillary systems, samples are injected electrokinetically into a polymer-filled capillary, where smaller fragments migrate faster and reach the detector earlier. A laser excites intercalating dye bound to the DNA or RNA, and the software converts migration times into fragment sizes using an internal ladder and into concentrations using a quantitative marker. Microfluidic chips work on the same principle with shorter separation channels and smaller volumes. Automated agarose gel instruments draw samples through a gel by voltage and image the bands after staining. Because the sizing algorithm depends on the ladder and the polymer lot, run quality flags such as marker height and baseline noise should be reviewed before results are accepted.

What are the key features?

• Capillary or multi-channel format with internal size standard for sizing
• Reports size, molarity, mass concentration and RNA integrity score
• Runs a 96-well plate in under about 90 minutes
• Multiple gel and ladder kits cover 10 bp to 50 kb ranges
• Automatic quality flags for marker peaks and baseline noise
• Result export to laboratory information systems or CSV files

What are the technical specifications?

A typical capillary electrophoresis fragment analyzer configuration offers sizing range of 10 bp–50 kb (kit dependent), sizing accuracy of within ±5% (typical), sizing resolution of approx. 5% of fragment length, sensitivity of approx. 0.01–10 ng/µL (kit dependent), samples per run of 12 or 96 (model dependent) and run time of approx. 40–90 min per plate. Values are indicative of the product class; the exact figures for each configuration are confirmed on the quotation and the calibration documents supplied with the instrument.

Which applications is it used for?

The Capillary Electrophoresis Fragment Analyzer is used in sequencing library size and yield checks, RNA integrity scoring before sequencing, PCR amplicon and restriction digest analysis and plasmid and cloning verification. Across the wider Fragment Analyzers class, laboratories also deploy it for next-generation sequencing library quality control, RNA integrity assessment before expression studies and PCR amplicon and restriction digest checks.

Which standards and certifications apply?

Relevant standards and methods include ISO 20395, ISO 22174, CLSI MM09, IEC 61010-1 and ISO 15189. Certification candidates for this model are CE, ISO 9001 manufacturing and IEC 61010-1 safety; each is to be confirmed for the specific configuration before shipment, and certificates are supplied only where they have been issued.

Install the analyzer on a level bench away from vibration and direct sunlight, because optical alignment and polymer flow are sensitive to movement. Store polymer, ladders and dye kits within their stated temperature range and note lot numbers, since a ladder or polymer change can shift sizing by several percent. Run a ladder and a known control with each batch, and review quality flags before releasing data. Replace polymer and clean electrodes as instructed to prevent carry-over between samples. Keep the instrument in a room with stable temperature to limit baseline drift, and include the analyzer in the laboratory's pipette and instrument calibration schedule. Verify performance after any service or software upgrade.

How do I select the right Capillary Electrophoresis Fragment Analyzer?

Select a capillary fragment analyzer when reproducible sizing and digital results matter for library preparation and RNA quality control. Specify sizing range, sample count per run, kit sensitivity, consumable cost per plate, quality-flag settings and data export format.

How does it compare with other Fragment Analyzers variants?

Choose by the sample type, resolution and throughput you need. Capillary systems give the best sizing accuracy and reproducibility, which matters for sequencing libraries and RNA integrity scoring. Microfluidic chip systems run more samples in less time with microlitre volumes but give approximate sizing. Automated gel systems handle many samples at low consumable cost with lower resolution. Check the sizing range against your fragments: amplicons of 100–1,000 bp behave differently from long-read libraries above 20 kb, and high-sensitivity kits are needed below 1 ng/µL. Confirm sample volume, consumable cost, run time, and whether the software exports results to a laboratory information system. Where quantification must be exact, pair the analyzer with a fluorometric or digital PCR method.