Oligo Pro II

Fast purity analysis of ssRNA and ssDNA oligonucleotides using UV absorption.


What is the Oligo Pro II?

The Oligo Pro II System is employed in the determination of ssDNA and ssRNA oligonucleotide purity. Parallel capillary electrophoresis coupled with UV detection to provide single nucleotide resolution and direct assessment of oligonucleotide purity eliminating the need for intercalating dyes and fluorescent probes. With 12-capillary, 24-capillary and 96-capillary arrays available, the Oligo Pro II quickly adjusts to meet changing throughput demands.

Simultaneously assess 12, 24 or 96 different samples by parallel capillary electrophoresis with online, fixed wavelength UV absorbance detection. Preloaded and optimized separation and capillary conditioning methods simplify and streamline operation.

Modulate throughput and separate up to 288 samples without human intervention with convenient and simple advanced programming of runs. Post-capillary electrophoresis, intuitive data analysis software provides automated and accurate analysis of oligonucleotide samples.

  • Low cost per sample
  • Single nucleotide resolution from 10-mer to 60-mer lengths
  • Easy and economical use and maintenance
  • Minimal sample preparation and consumption
  • Small instrument footprint
Fast Separations
Complete 12, 24 or 96 separations in about 1 hour.
Improve Product Quality
Monitor synthesis performance to demonstrate purity of ssDNA or ssRNA.
Wide Sizing Range
Achieve single base resolution through 60-mers.
Throughput for all Labs
Variable throughput with the option of 12, 24 or 96 capillary arrays.
Direct Detection of Oligos
No dye labeling needed, uses UV detection.
Simplified Report Generation
Advanced peak integration software and data reporting capabilities.

Accurately characterize the purity of synthetic oligos quickly and cost effectively.

The Oligo Pro II provides researchers with a dependable solution for the quality control analysis of manufactured oligos prior to use in critical applications. Importantly, results are free of sequence and size-dependent variations, giving researchers accurate results, no matter what.

Ensure optimum performance of oligonucleotides in downstream applications with sensitive and accurate analysis of impurities. The Oligo Pro II measures impurities at n-1 resolution on up to 96 samples simultaneously, making it the ideal workhorse for oligonucleotide purity analysis.

The electropherogram depicts the separation of ssDNA oligonucleotides at single nucleotide resolution, across the range of the Oligo Pro II.

The electropherogram depicts the separation of ssDNA oligonucleotides at single nucleotide resolution, across the range of the Oligo Pro II.

Flexible enough to handle any workflow scenarios

The Oligo Pro II is able to quickly determine the purity of ssDNA and ssRNA samples, ensuring oligonucleotide quality for downstream applications.
Superior oligomer resolution: High quality capillary array enables size-based, single nucleotide resolution from 10-mer to 60-mer lengths.
Unattended Operation: Load up to three 96-well plates for automated oligonucleotide analysis. Plates can be loaded and prioritized while the system is running.
Small Instrument Footprint: Save laboratory bench space with the low-profile Oligo Pro II.

Oligo Pro II Data Analysis Software

The Oligo Pro II uses intuitive software packages for the operation of the instrument and the data analysis post-capillary electrophoresis. The operational software allows the programming and prioritization of separation runs, taking full advantage of the three sample drawers. Analytic software provides automated analysis of quality and purity, with sophisticated tools for further data analysis.


The Oligo Pro II enables the confident purity and QC analysis of ssRNA and ssDNA oligonucleotides via parallel capillary electrophoresis and UV detection. Employed in various applications that demand a high degree of ssDNA or ssRNA purity, from PCR primers to construction of RNA ladders, oligonucleotides are essential to molecular biology.

Technical Information


Parallel capillary electrophoresis (CE) technology enables small- to large-scale electro-driven analytical separations of ssDNA and ssRNA oligonucleotides with UV absorbance detection.

The array contains 12, 24 or 96 capillaries of 75 µm inner diameter and 200 μm outer diameter. The inlet side of the capillary array is arranged in a 1 x 12, 2x12, or 8 x 12 format, with electrodes either side of each capillary. This allows direct injection via voltage from standard 96-well plates.

Capillaries are aligned in parallel in the detection window, which is positioned between the UV light source and the detector assembly. The outlets of the capillaries are bundled to a common reservoir, where they are connected to a ground. During capillary electrophoresis, room temperature air is circulated around the capillaries to regulate the temperature. The capillary arrays are modular and can be exchanged in less than five minutes.

The optical platform consists of a UV light source, collimating lens, UV camera lens, and a CCD detector. The UV light is provided by a mercury (254 nm) lamp.

Detection is performed at a fixed, single wavelength determined by the UV lamp and an interference filter. Light from the lamp passes through a collimating lens, the detection windows of the capillaries and a focusing UV camera lens before being spatially imaged onto the CCD. The capillary array is imaged continuously, providing real-time, online UV detection for 12, 24 or 96 different CE separations.

The power supply provides appropriate voltage for electrokinetic sample injection and electrophoresis. The recommended operating limits are -16 kV, 3 mA total current (30 µA per capillary.)

Software automates capillary conditioning, sample injection, electrophoresis separation and data processing. You can visualize results in your preferred format and share reports easily.

Diagram Parallel Capillary Electrophoresis Array


Array Sizes 12, 24 or 96 capillaries
Detection Online, fixed wavelength UV absorbance at 254 nm
Sample Injection Simultaneous electrokinetic injection from a 96-well microplate
Sample Format Desalted to maximize injection efficiency; 1 - 5 µM concentration range
Sample Volume Required Typical volume 100 µL/well (minimum of 20 µL/well)
Oligo Sizing Range Up to 60-mer lengths under appropriate sample load
Software Proprietary Oligo Pro II software for system control/data analysis
Data Export Format : PDF, .csv, .jpeg, .bmp, or .png for individual samples or entire sample set
Environmental Conditions Indoor use, normal laboratory environment; lab temperature 15 - 25°C
Relative Humidity Range 15 - 60% (non-condensing)
Electrical 100 – 200 VAC; 50 – 60 Hz (200 – 230 VAC; 50 – 60 Hz available); 15 A
Instrument Dimensions 67.31 cm H x 48.26 cm W x 61 cm D (26.5 x 19 x 24 in)
Instrument Weight 56 Kg (125 lbs)


  • (DN-415-0250) OLIGEL ssDNA Gel, 250 mL
  • (DN-465-1000) ssDNA OLIGEL Buffer, 1000 mL
  • (DN-475-1000) Capillary Conditioning Solution, 1000 mL
  • (DN-400-0001) Oligo Verification Std 10x Solution

Each lot is prepared under rigorously controlled conditions to ensure reliable, consistent results.

Capillary array cartridges are also stringently tested before shipment. A report displaying the separation of a standard QC mixture is included with every cartridge to verify performance.

Capillary Arrays

Capillary arrays are available in three configurations for the Oligo Pro II:

12 Capillary Array 24 Capillary Array 96 Capillary Array
Oligo Pro II 12-Capillary Array Long, 55 cm (EFF), 80 cm (TOT), 75 µm (ID) Oligo Pro II 24-Capillary Array Long, 55 cm (EFF), 80 cm (TOT), 75 µm (ID) Oligo Pro II 96-Capillary Array Long, 55 cm (EFF), 80 cm (TOT), 75 µm (ID)


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