Is the plasmid extraction kit compatible with an automatic nucleic acid extractor?

You do not necessarily have to use the instrument-matched reagents, but for the first run it is best to use the manufacturer-matched reagents to get the workflow running, then switch to compatible magnetic bead reagents. The program for matched reagents is fixed; after switching reagents, issues such as slow magnetic bead sedimentation, aggregation, or yield fluctuation may occur. For a 96-well deep-well plate protocol, it is recommended to use 2 mL square-well plates. After lysis and neutralization, the centrifugal force must be sufficient; otherwise, the viscous lysate will contaminate the magnetic beads and purity will drop noticeably. The per-sample cost depends on the packaging size. Small packs are more expensive, while large packs bring the cost below column-based extraction or close to it, but automated extraction saves labor. It is recommended to first compare 8 samples in a small batch against column-based extraction and check the A260/280 and agarose gel image.

Whether it is possible to use your 96 channel extractor first depends on whether it is an open program or a closed system. An open type plasmid extraction kit using magnetic beads can be commercially available, but bacterial plasmids require alkaline lysis before magnetic bead binding and cannot be directly processed using genomic DNA or RNA programs. Suggest finding a reagent manufacturer to obtain the protocol for plasmid extraction using the deep hole plate method, and reprogram it according to the parameters of instrument heating, magnetization, and mixing. 1-2 ml of bacterial solution is insufficient for plasmid loading. It is recommended to first centrifuge and enrich to about 1.5 ml per well, then add lysozyme/alkaline lysis and bind with magnetic beads. It is difficult to achieve a yield close to the level of a centrifugal column, PCR、 Enzymatic digestion is generally sufficient, while transfection requires endotoxin testing.

The plasmid magnetic bead extraction method is different from the genome/RNA magnetic bead method in that the key lies in lysis and deproteinization. After conventional alkaline lysis, neutralization is required to form a large amount of protein genome precipitate, which can only be added with magnetic beads after centrifugation or filtration in a deep well plate; If the instrument does not come with centrifugation, it should be processed in advance using a 96 well filter plate or deep hole plate centrifuge. The binding conditions of magnetic beads need to be adjusted by adjusting the proportion of isopropanol or binding solution, otherwise the yield will be low. It is recommended to use high copy plasmids for 1-2 ml of bacterial solution, with a yield of approximately a few micrograms per well. Low copy plasmids may not be sufficient. Before batch extraction, verify the uniformity between the holes, repeat the entire 96 well plate, and measure the CV value.

If your instrument has a fixed program and is not open, you may not be able to directly run a magnetic bead plasmid kit, but you can do it semi-automatically: use deep-well plates for alkaline lysis and neutralization, and use the instrument for magnetic bead binding/washing/elution, or use a multichannel pipette with a magnetic rack for manual processing. This avoids the handling of 96 columns, but the throughput is not as good as fully automated. For reagent selection, you can ask Vazyme, Tiangen, Thermo, etc. whether they have automated plasmid magnetic bead solutions; some of them provide instrument-adapted program packages. In terms of cost, do not look only at the reagent price per well; you also need to calculate consumables such as deep-well plates, magnetic rod sleeves, and filter plates. The actual cost per sample may be higher than column-based methods, but it is more cost-effective at scale.