What is the difference between magnetic bead based isolation and spin columns isolation?

The filter based method (also known as spin columns) has been the golden standard for Nucleic Acid isolation for a long time. Spin columns and filter plates are easy to process, and prep time is relatively short. Yield and purity are consistent and high. So why use magnetic beads for your DNA or RNA isolation? Spin columns besides the ease of use, have some downsides as well. For example spin columns/filter plates are not easy to automate. There are a few manual steps involved in these processes which simply cannot be automated. Secondly, the filters in spin columns and/or filter plates are made from silica. Silica binds DNA and/or RNA in the presence of chaotropic salts. As a result, the final isolated and/or purified sample will contain traces of chaotropic salts which affect downstream processes such as sequencing, PCR, etc.

Magnetic bead based kits have been designed for automation since all steps are easy to automate using a liquid handler (robot). In some cases the automation of a magnetic bead based process can be implemented on a liquid handler already present in the laboratory or core-facility.
If no liquid handler is available at your disposal, you might consider a package deal with the magnetic bead kit supplier. Some suppliers offer interesting package deals including a liquid handler in a reagent contract. Biggest advantage is the supplier will provide an all in solution, including the kits, the liquid handler with pre-programmed and validated protocols.

In regards to the quality of your DNA isolation, modern magnetic bead based kits offer you the same of even better results compared to spin column technology.

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