Parallel Capillary Electrophoresis:
Description of Technology

Identification of organisms can be a time consuming task. Some genetic based technologies are simple to use but lack throughput and speed to results while other technologies require expert handling and preparation from the sample to the final result. The DNA PROfiler™ was designed to bridge the gap, combining speed with ease of use.

The figure below shows the DNA PROfiler™ process; Organism identification is 4 easy steps.

Step 1: DNA Extraction

Utilizing off the shelf methods for DNA extraction is acceptable. As an amplification-based detection system, extraction of DNA is critical. Currently the majority of the work cited was generated from pure cultures DNA extracts.

Step 2: DNA Amplification

Since nearly any region of DNA can be amplified, designing primers which amplify through a region with sufficient genetic variability is critical to being able to create unique PROfile (DNA fingerprints). Since the technology is amplification-based and database driven, users have the ability to develop fluorescently-labeled primer set for specific regions of specific organisms or universal genes for more broad coverage and then quickly create a database library for screening organisms of interest. Kits for specific organisms are in development see DNA PROfiler™ buffer kits page for more information on future kits.

Step 3: Controlled Cleavage

The controlled cleavage (time and temperature) is responsible for creating the electrophoresis pattern and is at the heart of this technology. The cleaving agent has the possibility of cleaving after each nucleotide, however proceeds in a very predictable manner such that G & A >> C >> T. On the electropherogram, the peak intensity correlates to the amount of DNA cleaved.

Step 4: Multiplex CE Separation

After cleaving the DNA, the DNA fragments are separated through the DNA PROfiler™, an automated capillary electrophoresis. The DNA PROfiler™ instrument is a 2 color LED fluorescent based automated electrophoresis system that generates an electropherogram specific to the nucleotides present in the amplicon The system has the ability to separate 12 samples simultaneously from a 96 well plate. With single base resolution up to 300 nucleotides and the ability to view two fluorescent tags, genetic data points derived from either two different primer sets or both strand coverage off one primer set can be generated simultaneously.

The figure below shows a typical electropherogram of cleaved DNA. All the tall peaks are either G's or A's (red arrows), the small peaks are C's (blue arrow) and the absence of a peak is a T (green arrow). A few nucleotides are highlighted.

The DNA PROfiler™ can be used in many processes that require rapid genotyping including either genus species identification or strain typing and tracking. The features of the system are described below.