Fragment Analyzer Systems

5300 Fragment Analyzer System

The 5300 Fragment Analyzer system is a capillary electrophoresis instrument that can separate up to 48 or 96 samples in parallel. This system is designed to improve lab efficiency and workflow allowing you to automate the analysis of large numbers of samples and focus on results.

The 5300 Fragment Analyzer system performs DNA QC and RNA QC for a broad range of samples including, gDNA, small RNA, cfDNA, large DNA fragments, and total RNA. The diversity of sample types these systems can separate make these instruments ideal for individualized workflows, including NGS library QC and CRISPR workflows.


  • Separate 48 or 96 samples in parallel with a single simple dilution step and easy instrument set up
  • Reduce sample analysis time by using batch processes features post electrophoresis to automatically generate results reports
  • Load and separate up to 288 samples for unattended and automated analysis of large numbers of samples
  • Easily adapts to changes in your workflow with flexible option like maximizing your runs or speed or resolution of individual samples by choosing a shorter or longer array
  • Minimize hands on time with no daily array handling and room-temperature stable reagents
  • Change priority of runs to fit your lab’s needs
  • Use quality metrics for RNA (RQN) and genomic DNA (GQN) to remove subjective quality assessments
  • See clear results with the high sizing accuracy and precision along with separation resolution as good as 3 bp from fragments under 300 bp
  • Kits provide a wide dynamic range covering two orders of magnitude
  • Achieve accurate molarity calculations with reliable smear analysis
  • IQ/OQ services available for use in GMP environments
  • Desktop PC supplied with a comprehensive 3-year warranty through HP


Ambient Temperature 20-23 °C
Dimensions (WxDxH) 35 cm x 61 cm x 86 cm
Line Frequency 47-63 Hz
Line Voltage 100-240 VAC
Number of Samples per Run 96
Operating Environment Relative Humidity 20-80 %
Power Consumption 150 VA
Weight 38.5 kg

How It Works


The broad range of kits available for the 5300 Fragment Analyzer system allow you to qualify and quantify DNA and RNA samples such as plasmids, genomic DNA, total RNA, small RNA, CRISPR edits, large DNA fragments, and much more. The quantitative kits provide measurements of both sample size (bp or nt) and concentration. Similarly, the qualitative DNA kits offer accurate sizing and provide relative quantification.


In busy laboratories, instrument accessibility is critical to reducing time to results. The 5300 Fragment Analyzer system can hold up to three, 96-well plates and process the plates in any order. This unprecedented capability allows for samples to be held on the instrument while awaiting separation. if needed, high-priority samples can be moved to the front of the line. Data files can then be saved to a networked computer for easy post-separation access.


With the unique ability to house two different gel matrices, the 5300 Fragment Analyzer system can run not only more samples, but also different types of samples, unattended. The operational software automates the gel switching and filling between different applications, eliminating unnecessary wait times.


NGS library QC with the 5300 Fragment Analyzer system

Next generation sequencing (NGS) library preparation is a critical step for obtaining high quality sequence data. The 5300 Fragment Analyzer system with its broad kit portfolio for nucleic acid samples offers the objective quality assessment to ensure that the NGS workflow starts withhigh quality input nucleic acid samples. The objective DNA and RNA quality control (QC) can be achieved by using automated parallel capillary electrophoresis.

Automated fragment analysis with the 5300 Fragment Analyzer system

The Agilent 5300 Fragment Analyzer is a powerful system for automated fragment analysis, with high flexibility in sample throughput and application types. The 48 or 96 parallel automated electrophoresis can decrease analysis time and generate reliable and reproducible research data for your DNA and RNA workflows.