Best Types of Agarose Gels for DNA Electrophoresis – Buyer’s Guide
by Gold Biotechnology, Inc.
Using the wrong agarose can lead to smearing or poor separation. The good news is that once you know how to evaluate agarose and choose the right type for your work, you’re all set.
The best agarose for DNA gels depends on your application. Agarose LE is ideal for routine electrophoresis. Low melt agarose is best for DNA recovery, and high-resolution agarose is meant for fine separation. Agarose specifications are also important to evaluate when choosing for your lab.
In this article, you’ll get an easy review of the common types of agarose out there, when each is most appropriate, and how to choose what is right overall.
What are the types of Agaroses for DNA Electrophoresis?
The most common types of agaroses used for DNA gel electrophoresis are standard agarose, Agarose LE (low EEO), low melt agarose, and high-resolution agarose. Each type is optimized for specific applications such as routine DNA electrophoresis, DNA recovery, or for separating fine fragments.
· Routine DNA Analysis: Routine DNA analysis or routine gels are when running gels to visualize nucleic acid fragments. These would include gels for PCR products, restriction digests, or plasmid screens, and no DNA recovery is involved.
· DNA Recovery: DNA recovery involves excising DNA bands from a gel for use in downstream applications like cloning, ligation, or sequencing. Here, it is important to preserve DNA.
· Fine DNA Fragment Separation: Fine fragment separation involves resolving DNA fragments that are very close in size. Here, higher resolving power is needed to perceive small differences between each fragment.
Standard Agarose
Standard agarose is used for routine DNA gel electrophoresis. These would be situations where high-resolution or DNA recovery is not going to be needed.
A good way to think of what standard agarose is for is when you simply need a presence or absence check: did you get DNA or not? Did you get about what you would expect?
The drawback to standard agarose is that you may get higher background and less consistent migration compared to other agarose types.
Agarose LE (Low EEO)
Agarose LE is a low electroendosmosis (EEO) agarose for routine DNA gel electrophoresis. The low EEO reduces that background you might get with standard agarose, and it improves DNA migration consistency.
Agarose LE is going to give you sharper, more reproducible bands. It’s commonly used for PCR analysis, cloning and general DNA visualization.
To some extent, agarose LE can be used for other downstream applications. However, you may want to select another specialty agarose depending on what those applications are.
For any type of agarose, you’ll want to adjust the agarose concentration in your gel depending on the size of DNA that you are trying to visualize or isolate (Table 1).
Table 1. Recommended agarose concentrations based on DNA size.
|
Concentration (%) |
DNA Size (bp) |
|
0.5 |
1,000 – 25,000 |
|
0.8 |
800 – 12,000 |
|
1.0 |
500 – 10,000 |
|
1.2 |
400 – 7,500 |
|
1.5 |
200 – 3,000 |
|
2.0 |
50 – 1,500 |
Another advantage of Agarose LE is that lower agarose percentage gels are stronger, and therefore easier to handle without breaking. So, if you’re working with large DNA molecules such as plasmids, then Agarose LE may be your best option.
For a deeper understanding about Agarose LE, we have a great article that explains more about what it is, how it works and why it leads to more consistent results.
Low Melt Agarose
Low melt agarose melts at a lower temperature than standard agarose. The advantage of this is that it allows DNA fragments to be excised from the gel without being exposed to higher heat.
Reduced heat helps DNA recovery because higher temperatures can damage DNA and reduce downstream performance.
Something to note about low melt agarose is that it tends to have a lower gel strength. This means that the gel matrix is more fragile and is prone to tearing during excision.
High-Resolution Agarose
High-resolution agarose was designed to improve separation from DNA fragments that differ very slightly in size because it has a more uniformed gel matrix.
High-resolution agarose has finer pores than standard agarose, which creates more resistance for DNA movement. Think of it like a sieve with a finer mesh, or like comparing a cheese cloth to a coffee filter.
By tightening the gel matrix, DNA migration is slowed, which improves fragment separation that would otherwise appear as a single band in a standard gel.
The improved resolution is especially important for visualizing subtle differences between smaller DNA fragments such as PCR products.
There are some tradeoffs with high-resolution agarose though. The first is that reduced migration speed means you will have to increase your runtime. Casting can also take some practice and precision in order to avoid bubbles and uneven gels. This type of agarose also usually costs more than the standard agarose.
What Agarose Should I Use for DNA Electrophoresis?
Agarose LE is ideal for routine DNA analysis when you want less background and more consistent results. Standard agarose is good for very simple analysis (presence/absence check). Low melt agarose is best to use for DNA recovery, and high-resolution is ideal for finer DNA separation.
As you’re seeing, different agarose types were designed for different electrophoretic needs such as resolution, recovery, or lower background. When it comes to choosing which type to use, it all depends on your goals and the characteristics of these agaroses that are most important to you.
Let’s look at each type of agarose and the more direct reasons behind what they’re appropriate for.
Standard Agarose
Appropriate for: Basic DNA gel electrophoresis where the goal is really to confirm the presence or absence of DNA. Or to get an approximate size of your fragments. A quick PCR check is a good example of when standard is a good choice.
Considerations: Standard agarose has a practical gel matrix that allows DNA to migrate and separate based on their sizes. However, this type of agarose can have higher electroendosmosis (EEO) and greater variability. Therefore, it isn’t the best choice when you need consistent, reproducible results.
Agarose LE
Appropriate for: Agarose LE is appropriate for routine DNA gel electrophoresis involving a little more analysis. This could include analyzing PCR products, restriction digest, cloning screens or general DNA visualization.
The low electroendosmosis is an advantage because it reduces background and improves consistency. You will end up with sharper, clearer bands compared to standard agarose.
Considerations: Agarose LE offers a great balance between gel strength, clarity and resolution. It also makes the gels stronger and therefore easier to handle. While it is not a good choice for DNA recovery, it is a good choice for routine analysis, and delivers better performance compared to standard agarose.
Low Melt Agarose
Appropriate for: Low melt agarose is best for DNA recovery from a gel, like gel extraction, cloning and ligation. This is because it melts at a lower temperature than standard agarose, which helps preserve DNA integrity.
While the melting temperature doesn’t matter for casting your gel, it does matter when you’re recovering DNA where melting agarose back down is necessary.
Considerations: Low melt agarose forms a softer gel and has a lower gel strength, which can lead to tears. While low melt agarose is good for DNA recovery, it isn’t suited for routine analysis or when fine separation is needed.
High-Resolution Agarose
Appropriate for: High-resolution agarose is the best choice when you need to separate DNA fragments that are very close in size because of its tighter gel matrix which slows migration.
Considerations: Only choose high-resolution agarose when fine separation is needed. It is not a great choice for routine analysis because slow migration means longer runtimes, and high-resolution agarose tends to cost more.
How To Choose Agarose: Quick Summary Table
|
Agarose Type |
Best For |
Why It’s Appropriate |
Key Considerations |
|
Standard Agarose |
Basic DNA checks |
Forms a workable gel for simple presence or approximate size verification |
Higher background, less consistent migration, not ideal for reproducible or downstream workflows |
|
Agarose LE (Low EEO Agarose) |
Routine DNA electrophoresis |
Low EEO improves band sharpness, clarity, and migration consistency |
Not designed for DNA recovery, but ideal as a daily-use agarose |
|
Low Melt Agarose |
DNA recovery and gel extraction |
Lower melting behavior reduces thermal stress during DNA isolation |
Softer gel with lower strength; requires careful handling |
|
High-Resolution Agarose |
Fine fragment separation |
Tighter gel matrix increases sieving power for closely sized DNA fragments |
Slower runs, more fragile gels, higher cost, often unnecessary for routine gels |
References
Green, M. R., & Sambrook, J. (2012). Molecular cloning: A laboratory manual (4th ed.). Cold Spring Harbor Laboratory Press.
Green, M. R., & Sambrook, J. (2020). Recovery of DNA from low-melting-temperature agarose gels: Organic extraction. Cold Spring Harbor Protocols, 2020(3), pdb.prot100461.
Guo, Y., Li, X., & Fang, Y. (1998). The effects of electroendosmosis in agarose electrophoresis. Electrophoresis, 19(8‐9), 1311-1313.
Helling, R. B., Goodman, H. M., & Boyer, H. W. (2012). Analysis of endonuclease R·EcoRI fragments of DNA from lambdoid bacteriophages and other viruses by agarose-gel electrophoresis. Journal of Virology, 14(5), 1235-1244.
Kirkpatrick, F. H. (1990). Overview of agarose gel properties. Current Communications in Cell and Molecular Biology, 1, 9-22.
Lee, P. Y., Costumbrado, J., Hsu, C. Y., & Kim, Y. H. (2012). Agarose gel electrophoresis for the separation of DNA fragments. Journal of Visualized Experiments, (62), e3923. https://doi.org/10.3791/3923
McDonell, M. W., Simon, M. N., & Studier, F. W. (1977). Analysis of restriction fragments of T7 DNA and determination of molecular weights by electrophoresis in neutral and alkaline agarose gels. Journal of Molecular Biology, 110(2), 119–146. https://doi.org/10.1016/S0022-2836(77)80112-3
Rickwood, D., & Hames, B. D. (1985). Gel electrophoresis of nucleic acids: a practical approach. In Gel electrophoresis of nucleic acids: a practical approach (pp. 242-242).
Serwer, P. (1987). Agarose gel electrophoresis. Current Protocols in Molecular Biology , 51(1), 2.5A.1-2.5A.9.
Voytas, D. (2000). Agarose gel electrophoresis of DNA. Methods in Enzymology, 155, 203–223. https://doi.org/10.1016/0076-6879(87)55018-3
Wilkinson, M., & Hames, B. D. (1998). Gel electrophoresis of nucleic acids: A practical approach (2nd ed.). Oxford University Press.
AI Disclosure
Note that Chat GPT was used extensively for brainstorming and research of this article in addition to basic research. Claude AI was used to help fact check. This article was written by a human and final edits and accuracy checks were performed by a human.
Tags
Related Articles
-
DNA Gel Electrophoresis Introduction & Overview
Electrophoresis is a technique where similarly charged molecules in a mixture flow in the same direction using an electric field, and the molecules are separated...
-
Agarose Gel FAQs
These are some of the top questions surrounding gel electrophoresis and agarose gels. Learn about how to reuse/remelt your gels, how to calculate concentration, what...
-
Agarose LE vs. Agarose – What’s the Difference?
There are several different types of agaroses commercially available, each with unique properties suited for specific applications. However, a common question that comes up is...
