Here are some tips for optimization when using the Monarch Gel Extraction Kit.
1. For increased efficiency try to excise the agarose as close to the DNA fragment as possible. excess agarose will result in higher volume samples which may require more than 1 centrifugation step in order to load the sample onto the column.
2. Optimize quality of DNA Try to limit UV exposure of your DNA to avoid damage.
3. Do not incubate the gel slice above 60°C as this may denature the DNA.
4. When removing the column from the collection tube after the last wash, make sure that the tip of the column doesn't touch the walls of the collection tube. If you observe that the tip of the column came into contact with the collection tube wall, then we would recommend an additional 30 second centrifugation step prior to the elution step.
Optimizing yield from gel extractions
5. Make sure that the agarose is completely melted before loading the sample onto the column. Undissolved agarose still containing DNA will result in lower yields and may also clog the column.
6. Ensure that you add the elution buffer to the center of the matrix without puncturing it. The elution buffer needs to be in contact with the column matrix for efficient elution.
7. Be sure to incubate the elution buffer in the column for the full minute before centrifugation.
Optimizing yield for large DNA fragments
8. For fragments that are 8 Kb or larger, we recommend that you add 1.5 volumes of water after the agarose is dissolved. This mitigates tighter binding of the larger DNA pieces to the matrix allowing easier elution off of the column.
9. For plasmids that are larger than 10 Kb, heating the elution buffer to 50°C prior to adding it to the column can improve yields.
10. Please note that sequential elutions may be performed for quantitatively higher recovery but will result in lower final DNA concentration.
Time saving tips
11. To save time, the binding and elution spin steps can be reduced to 30 seconds.
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