DNA Electrophoresis Common Issues

Gel electrophoresis is one of the major methods used in molecular biology for the analysis of DNA. This method involves the migration of fragments of DNA through a gel, where they are separated based on size or shape. However, have you ever encountered any errors during your electrophoresis experiments, such as smeared bands on the agarose gel, or no bands on the gel? What could be the cause of these errors?

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Our technicians have summarized couples of troubleshooting here for your reference.

1. Smeared bands on agarose gel

smeard bands on gel

The DNA was degraded. Avoid nuclease contamination.

● The electrophoresis buffer is not fresh. After repeated use of electrophoresis buffer, the ionic strength decreases, and its pH value increases, so the buffer capacity weakens, which affects the electrophoresis effect. It is recommended to replace the electrophoresis buffer frequently.

● Improper electrophoresis conditions were used. Do not allow voltage to exceed 20 V/cm, and maintain a temperature <30° C during electrophoresis. For the giant DNA strand electrophoresis, the temperature should be <15° C. Check the electrophoresis buffer has enough buffer capacity.

● Too much DNA was loaded on the gel. Decrease the amount of DNA.

● Too much salt in the DNA. Use ethanol precipitation to remove excess salts in advanced.

● The DNA was contaminated with protein. Use phenol extractions to remove protein in advanced.

● The DNA was denatured. Do not heat before electrophoresis. Dilute DNA in buffer with 20 mM NaCl.

2. Anomalies DNA band migration

● Renaturation of the COS site of λHind III fragment. Heat DNA for 5 minutes under 65° C before electrophoresis, and then cool it on ice unit for 5 minutes.

● Improper electrophoresis conditions were used. Do not allow voltage to exceed 20 V/cm, and maintain a temperature <30° C during electrophoresis. Check the electrophoresis buffer has enough buffer capacity.

● The DNA was denatured. Do not heat before electrophoresis. Dilute DNA in buffer with 20 mM NaCl.

3. Faint or no DNA bands on agarose gel

faint DNA bands

● There was insufficient quantity or concentration of DNA loaded on the gel. Increase the amount of DNA. Polyacrylamide gel electrophoresis is slightly more sensitive than agarose electrophoresis, and sample loading can be reduced appropriately.

● The DNA was degraded. Avoid nuclease contamination.

● The DNA was electrophoresed off the gel. Electrophorese the gel for less time, use a lower voltage, or use a higher percent gel.

● Improper W light source was used for visualization of ethidium bromide-stained DNA. Use a shortwavelength (254 nm) W light for greater sensitivity.

4. DNA bands missing

 The small size DNA was electrophoresed off the gel. Electrophorese the gel for less time, use a lower voltage, or use a higher percent gel.

● Difficult to distinguish the DNA bands of similar molecular. Increase the electrophoresis time, and check the concentration of the gel to make sure correctly percent gel to be utilized.

● The DNA was denatured. Do not heat before electrophoresis. Dilute DNA in buffer with 20 mM NaCl.

● The DNA strands are huge, and conventional gel electrophoresis is not suitable. Analyze on pulse gel electrophoresis.What other issues have you had with agarose gel electrophoresis? We will research more for guides in the future.

Beijing Liuyi biotechnology Co., Ltd (Liuyi Biotech) is a specialized company focusing on electrophoresis related products in China. Its story starts in 1970 when China had not yet entered the reform and opening up time.  Through years’ development, Liuyi Bitotech has its own brand, which is known as the Liuyi Brand in domestic market for electrophoresis products.

The Liuyi brand has more than a 50-year history in China and the company can provide stable and high-quality products all around the world. Through years’ development, it is worthy of your choice!

The horizontal electrophoresis cells (tanks/chambers) of Liuyi Biotech are high quality with good appearance. With different sizes of gel trays, they can meet your different experimental requirements. We have our own technical team and factory. From design to manufacture, the raw materials to the key parts, we can control the whole process. The DYCP 31 series is for DNA electrophoresis, which are model DYCP-31BN, DYCP-31CN, DYCP-31DN, and DYCP-31E. The differences among them are gel sizes and price. We provide full sizes of products for our customers. The model DYCP-32C can make the largest gel 250mm*250mm.

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Meanwhile, we recommend our electrophoresis power supply DYY-6CDYY-6D and DYY-10C for our electrophoresis cells (tanks/chambers) DYCP-31 and 32 series.

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If you want more information about the products, please visit this website to get more, and welcome to contact us via email to let us know what you want, and see if we can provide the solutions for you.

For more information about us, please contact us by email [email protected], [email protected]


Post time: May-09-2022