The application data presents a comparative analysis of plasmid DNA yield and quality using both the new (V1.01.04.01) and old (V1.01.02.08) versions of the AmMag Quatro software. Both software versions were evaluated for their efficiency in processing pcDNA 3.1 (+) plasmids, which contain an ampicillin resistance gene transformed into DH5α competent E. coli cells.
Experimental Conditions:
Plasmid: pcDNA 3.1 (+) with ampicillin resistance
Host Cells: DH5α competent E. coli
Media: TB media
Purification Kits: AmMag Quatro Kit - Elution H2O - Cat. No. L00882
Software Versions: Old and New AmMag Quatro software
Old software (V1.01.02.08)
Table 1. Test Protocol Parameters - Old software (V1.01.02.08)
| Mix S1 Time | 600 s | S1 S2 S3 vol | 12 ml | Lysis Conditions | High |
| Mix S2 Time | 300 s | S4 vol | 9 ml | S3 Mix Cycles | 14 |
| Binding Time | 1500 s | MagClear Vol | 4 ml | Separation elution | yes |
| Mix W2 Time | 180 s | Binding Volume | 1.5 ml | Remove Endotoxin | yes |
| Mix Elution | 300 s | Elution Vol | 1.5 ml | ||
| Wait Elution | 600 s |
Table 2. Comparative analysis of plasmid DNA yield, endotoxin levels, and quality parameters processed with the old AmMag Quatro software.
| Sample | Pellet mass (g) | Conc. (ng/µl) | 260/280 | 260/230 | Final Vol (µl) | Yield (µg) | Endotoxin (EU/mL) |
Endotoxin (EU/µg) |
Super coil (%) | gDNA |
|---|---|---|---|---|---|---|---|---|---|---|
| Sample 1 | 1.40 | 715.05 | 1.897 | 2.147 | 1000 | 715 | 138 | 0.19 | 93 | negligible |
| Sample 2 | 1.36 | 701.30 | 1.894 | 2.139 | 980 | 687 | 171 | 0.24 | 90 | negligible |
Figure 1. Agarose gel electrophoresis image showing the supercoil ratio and restriction digestion analysis using the old software.
New software (V1.01.04.01)
Table 3. Test Protocol Parameters - New software (V1.01.04.01)
| Mix S1 Time | 600 s | S1 vol | 12 ml | Lysis Conditions | High |
| Mix S2 Time | 300 s | S2 S3 vol | 12 ml | S3 Mix Cycles | 14 |
| Binding Time | 1500 s | S4 vol | 9 ml | Separation elution | yes |
| Mix W2 Time | 180 s | MagClear Vol | 4 ml | Remove Endotoxin | yes |
| Mix Elution | 300 s | Binding Volume | 1.5 ml | ||
| Wait Elution | 600 s | Elution Vol | 1.5 ml |
Table 4. Comparative analysis of plasmid DNA yield, endotoxin levels, and quality parameters processed with the new AmMag Quatro software.
| Sample | Pellet mass (g) | Conc. (ng/µl) | 260/280 | 260/230 | Final Vol (µl) | Yield (µg) | Endotoxin (EU/mL) |
Endotoxin (EU/µg) |
Super coil (%) | gDNA |
|---|---|---|---|---|---|---|---|---|---|---|
| Sample 1 | 1.38 | 683.90 | 1.888 | 2.134 | 890 | 609 | 91.4 | 0.13 | 93 | negligible |
| Sample 2 | 1.39 | 715.25 | 1.888 | 2.146 | 950 | 679 | 70.1 | 0.10 | 92 | negligible |
Figure 2. Agarose gel electrophoresis image showing the supercoil ratio and restriction digestion analysis using the new software.
Results:
Both the old and new versions of the software performed comparably in terms of plasmid yield, concentration, and quality. Key parameters such as the A260/280 and A260/230 ratios, as well as the percentage of supercoiled plasmid, showed consistent results across both versions.
However, the new software demonstrated a significant improvement in endotoxin levels, where a reduction of approximately twofold was observed. This improvement can be attributed to a modified reagent addition sequence in the new software, which increases the efficiency of endotoxin removal.
