How Gel Electrophoresis Works & How We Save You Time & Money

Excedr - Gel Electrophoresis Equipment

Despite the diversity in applications and methods, our lease program is able to source any instrument type for your laboratory, and can accommodate whichever brand preferences you or your end-user might have. Request a lease estimate today and learn more about the benefits of leasing your next gel electrophoresis instrument or chamber.

All equipment brands/models are available

The Advantages of Excedr’s Gel Electrophoresis System Leasing Program:

  • Eliminates the upfront cost of purchasing equipment by spreading its cost over time
  • Minimizes equipment downtime with included complete repair coverage and preventive maintenance
  • Takes advantage of potentially 100% tax deductible* payments, providing you significant cash-savings
  • Expedites the administrative work needed for instrument procurement and logistics
  • Conserves working capital,  enabling you to reinvest in your core business and operations (staffing, inventory, marketing/sales, etc.)
  • Accommodates all manufacturer and model preferences

*Please consult your tax advisor to determine the full tax implications of leasing equipment.

a cell, a microplate well, antibodies, and a dot with 6 lines through it

Electrophoresis is used in the life sciences and biotechnology to separate and extract DNA fragments, RNA, and proteins, based on their size and charge, in order to analyze them.

It is used as a preparative technique in laboratories for PCR, Southern blotting, genome mapping, and DNA sequencing, and is also used in DNA fingerprinting and plant breeding. Scientists studying molecular biology, microbiology, and biochemistry utilize electrophoresis for studies and experiments in medicine, forensic science, and conservation biology, just to name a few.

Gel electrophoresis is one of the most common electrophoresis methods used.

In these systems, molecular samples are loaded into the electrophoresis apparatus, a type of box or chamber referred to as a gel box. The gel box is filled with an agarose or polyacrylamide gel and is equipped with a gel comb, as well as a negative electrode, or anode, on one side, and a positive electrode, or cathode, on the other. The comb helps form the wells where the samples are placed, and the negative and positive electrodes create an electrical current that generates electrophoretic separation.

The electrical current generated separates the DNA fragments based on their size or charge because, even though DNA molecules have the same amount of charge per mass, longer DNA fragments tend to have a higher molecular weight compared to shorter DNA pieces. That difference means segments move at varying speeds through the gel medium, grouping up according to size.

After gel electrophoresis is performed, the gel is stained with a fluorescent binding dye, which eventually allows the groups that formed to be more easily observed. Having stained the gel, a light source is then used to excite the fluorescent dye so that the DNA bands are visible for post-separation and analysis.

A well-defined group or line of DNA is referred to as a separation band. These separation bands tell us more about the DNA fragments size or charge.

Gel Types, Techniques, Buffers, & Automation

an outstretched hand face up holding the end of a DNA double helix

There are different types of gel used for different tasks, and the amount used can vary depending on the size of macromolecules in the sample.

The gel interacts with a buffer that affects the porousness of the gel matrix. Depending on the application, you’ll want to use a certain gel.


Agarose gels are made from the natural polysaccharide polymers found in seaweed. Agar is extracted by heating seaweed for several hours. After washing and alkaline pre-treatment, the seaweed is submerged in boiling water.

The agar dissolves into the water and the mixture is filtered to remove any residual seaweed matter. It is easily handled and cast compared to other matrices because the casting is done physically rather than with the assistance of chemicals. It is also capable of being stored for later use.

Because agarose gel does not have a uniform pore size, it is ideal for testing that involves molecules that are larger than 200 kDa, or 200 kilodaltons. The percent of agarose in the gel influences the distances between DNA bands of different lengths.

Precast agarose gels are also available, and do away with messy and time-consuming prep work. They run up to twice as fast as traditional handcast gels and come in a variety of agarose percentages, well formats, and throughput capacities.



While most modern techniques involve agarose gel, polyacrylamide gel can also be used for specific applications in similar ways. The uniformity of polyacrylamide gel allows for better accuracy, and is controlled using acrylamide and bis-acrylamide powder to create the gel.

Varying the percentage of polyacrylamide in the gel affects the pore size. Because polyacrylamide gel is biologically inert, modulating the stiffness of the gel using the powder does not affect its biochemical properties. This allows for observations that can be made based on the stiffness of the gel and no other competing changes in cellular functions.


Nucleic Acid Electrophoresis

This technique is used to separate and analyze DNA or RNA fragments by size and reactivity. It involves segmenting the molecules using a restriction enzyme.

After segmentation, the samples are placed in the gel for size and charge separation, and are then dyed using a fluorescent dye specifically for DNA. This allows for easy observation. Agarose gel is most often used in systems that perform nucleic acid gel electrophoresis.

Some applications of agarose gel electrophoresis include:

  • Analysis of PCR (polymerase chain reaction) products. Examples include genetic fingerprinting, molecular cloning, or molecular genetic diagnosis
  • Separation of restricted genomic DNA before Southern transfer, or Southern blot
  • Separation of DNA fragments for extraction and purification
  • Estimation of the size of DNA after digestion using a restriction enzyme

There are a variety of nucleic acid-specific devices available, including vertical electrophoresis systems, which are available in midid or mini gel electrophoresis format. Vertical systems are more ideal for proteins, unlike horizontal systems which are well suited for DNA and RNA.

The vertical systems utilize a discontinuous buffer system, where the top chamber contains the cathode and the bottom chamber contains the anode, and a thin gel is poured between two glass plates that are mounted. This submerges the bottom of the gel in one chamber, while the top of the gel is submerged in buffer in the top chamber.

After applying an electrical current, a small amount of buffer migrates through the gel from the top chamber to the bottom chamber. This allows for precise control of voltage gradients during separation, and results in greater separation and resolution.


Protein Electrophoresis

Polyacrylamide gel is often used in gel electrophoresis of proteins, and is ideal for protein separation and analysis. This method is commonly used in the field of immunology. It is typical for polyacrylamide gel electrophoresis (PAGE) systems to run vertically, so that the stacking and resolving gels form a continuous gel, which would be much more difficult in a horizontal gel.

It also allows a much greater protein amount to be loaded onto the gel. Protein Electrophoresis analyzes the proteins in a fluid or extract. Because of practical limitations, protein electrophoresis is generally not suited as a preparative method.

PAGE applications include:

  • Peptide mapping
  • Estimation of protein size
  • Protein quantitation
  • Measuring molecular weight
  • Comparison of the polypeptide composition of different samples
  • Analysis of the number and size of polypeptide subunits


Buffers are used to help transmit the electrical charge through the gel, and maintain a stable pH level to minimize any change that may occur. The buffer may also help with the extraction of DNA.

There are a number of buffers used for agarose electrophoresis, some of which include TAE and TBE. TAE contains a mixture of Tris base, acetic acid, and EDTA (Ethylenediaminetetraacetic acid), while TBE contains a mixture of Tris base, boric acid, and EDTA.

These buffers contain EDTA to inactivate many nucleases which require divalent cation for their function, providing good conductivity while producing less heat.


Power Supply

The power supply of your gel electrophoresis equipment can be just as important as your gels and buffers. There are various electrophoresis power supplies available for you to use, including


Automated Systems

Automated systems are an easy-to-use alternative to traditional gel electrophoresis instruments that provide an increase in throughput and a decrease in turnaround time.

Automated electrophoresis is best suited for a lab that wants to perform repetitive analyses, wishes to cut down on high labor cost, and has small amounts of precious samples to work with. The speed and convenience offered by an automated system that includes digital data storage for any recording is an important advantage to consider.

They incorporate DNA microfluidic kits and Chip (chromatin immunoprecipitation assay) systems for separation, sizing, and quantification of nucleic acids and proteins. The process is simplified so that minimal volumes of sample are required and results are produced in less than an hour, in contrast to manual processes that typically require substantial amounts of a sample and take over an hour to produce any results.

However, it should also be noted that being able to perform both manual and automated electrophoresis is a realistic approach for almost any laboratory, because each method offers specific advantages.


Gel Conditions Explained

There are two different types of gel conditions: denaturing and native. Denaturing gels operate under conditions that disrupt the natural structure of an analyte, which causes it to unfold into a linear chain. Because of this, the mobility of a macromolecule only depends on its length and mass-to-charge ratio. Because the biomolecular structure is disrupted, the only structure left to be analyzed is the primary.

Native gels perform in non-denaturing conditions so that the analyte’s natural structure remains intact. This allows for the molecule’s physical size to affect its mobility, and be more easily analyzed on all four levels of its biological structure. The separated molecules in a native gel differ in molecular weight and charge, but also experience different electrophoretic forces based on its overall shape.


Gel Documentation System Leases to Fit Every Need

a petri dish with a sample inside

Electrophoresis is a commonly used preparative technique essential in any biotechnology company that’s focused on molecular biology, microbiology, or biochemistry.

Worried about the upfront costs of gel electrophoresis equipment, or any other analytical separation technique, such as liquid chromatography or western blotting? Leasing with Excedr might be the option for you.

Spreading out the cost of an acquisition can help you keep daily operations going, and with our preventative maintenance and repair coverage, you can have peace of mind that any instrument downtime is being actively minimized.

We offer leases that can be customized to your financial and operational needs.  Let us know how we can help and request a lease estimate today.

Operating Lease

This off-balance sheet financing structure provides three options at the end of the term. The lessee has the option to return the equipment to the lessor, renew at a discounted rate, or purchase the instrument for the fair market value. Monthly payments are also 100% tax deductible which yields additional monetary savings.


If you recently bought equipment, Excedr can offer you cash for your device and convert your purchase into a long-term rental. This is called a sale-leaseback. If you’ve paid for equipment within the last ninety days, we can help you recoup your investment and allow you to make low monthly payments. This also frees up money in your budget rather than tying it down to a fixed asset.

Gel Electrophoresis Instrument Manufacturers & Models on the Market
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Thermo Fisher Scientific:
Invitrogen XCell SureLock Mini-Cell, Invitrogen Mini Gel Tank, Invitrogen XCell4 SureLock Midi Cell, Owl Electrophoresis Systems, Owl Horizontal Systems, Owl A-Series, Owl C-Series, Owl D-Series, Owl EasyCast B-Series, Owl Vertical Systems, Owl Sequencing Gel systems, Owl P-Series, E-Gel Precast Agarose Electrophoresis System, Invitrogen E-Gel Power Snap

Fisher Scientific:
Fisherbrand Horizontal Electrophoresis Systems, Fisherbrand Horizontal Mini Gel

Bio-Rad Laboratories:
Mini-PROTEAN Tetra Vertical Cell, Mini-PROTEAN Tetra Handcast Systems, Mini-PROTEAN 3 Dodeca Cell, Criterion Vertical Cell, Criterion Dodeca Cell, Large Format 1-D Chambers, Mini-Sub Cell GT, Wide Mini-Sub Cell GT, Sub-Cell GT

LabChip GXII Touch, LabChip GXII Touch 24, LabChip GX Touch Nucleic Acid Analyzer

4150 TapeStation System

Mupid One System, Mupid 2Plus System, Mupid exU system

Labnet International:
ENDURO 96 Horizontal, ENDURO VE10, ENDURO VE20, ENDURO Modular, ENDURO GDS Touch Gel Documentation System, ENDURO GDS II, ENDURO GDS Touch II, ENDURO GDS

Accuris Instruments:
MyGel Mini

Analytik Jena:
Biometra Compact, Compact X/XS, Compact M, Compact L/XL, Biometra Compact Multi-Wide, Biometra Horizon Family, Biometra Eco-Line, Biometra Minigel-Twin


Operating Capital Benefits

Operating Capital Benefits

Excedr's operating lease structure allows you to keep your business credit line open for expansions, staffing, and other operational expenses. Additionally, it strengthens the cash flow of your business and keeps cash reserves free for business development opportunities.

Effects on Credit

Effects on Credit

Leasing / renting provides you with non-dilutive financing and does not hinder your future borrowing ability. You're able to acquire the equipment you need without the baggage associated with traditional financing.

Speed of Approval

Speed of Approval

Excedr's program allows you to respond quickly as your need for equipment and technology arises. You can be approved with minimal documentation and have the equipment you need in operation and generating revenue for your business quickly.

Refurbished Equipment

Refurbished Equipment

Unlike traditional financing and leasing companies, the Excedr program can accommodate refurbished equipment in addition to demo units. If you are looking for additional cost-savings, we recommend considering this option.