Siau Xuan Chong

Separation can be affected by hydration and gel formation. It all depends on the concentration of DNA and dye. In addition, there may be a complex influence of the quantum nuclear effect.

https://www.nature.com/articles/s42005-022-00881-8

There are several possible reasons why your supercoiled DNA ladder smeared and not separated well on the gel. Some of them are:

• Degradation of the DNA due to contamination with DNases or improper handling. This can cause the DNA ladder bands to have thin tails or smears1.
• Loading too much of the ladder onto the gel. This can cause the DNA ladder bands to have wide and bright smears1.
• Contamination of the DNA with proteins, such as restriction enzymes or ligases, used in cloning. This can cause the DNA to run as a high molecular weight band with a strong smear1.
• Inadequate running conditions, such as voltage, agarose concentration, buffer type, or run time. This can affect the rate and resolution of the DNA migration on the gel12.

To troubleshoot these issues, you can try the following solutions:

• Use DNase-free pipette tips and tubes, and handle the DNA ladder carefully to avoid degradation1.
• Load the recommended amount of DNA ladder on the gel, usually between 3-5 μl/well for most ladders1.
• Use a fresh DNA ladder or check for protein contamination by running a protein gel or using a protein assay kit1.
• Optimize the running conditions by adjusting the voltage, agarose concentration, buffer type, or run time according to the size range and resolution of your DNA ladder12.

Some references for more information on how to troubleshoot DNA ladders are:

• Troubleshooting DNA Ladders | GoldBio, a web page that explains some common issues and solutions for DNA ladders.
• Having some problem with DNA ladder. Please help? : r/labrats - Reddit, a Reddit thread that discusses some possible causes and tips for DNA ladder smearing and separation.

Learn more:

1. goldbio.com2. reddit.com3. goldbio.com4. reddit.com

Good luck