This section 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 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: Regular (L00882) and Endo-free (L01031) kits
Software Versions: Old and New AmMag Quatro software
Old software (V1.01.02.08)
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|
| Standard kit | 1.40 | 715.05 | 1.897 | 2.147 | 1000 | 715 | 138 | 0.19 | 93 | negligible | Standard kit | 1.36 | 701.30 | 1.894 | 2.139 | 980 | 687 | 171 | 0.24 | 90 | negligible |
| Endo-free kit | 1.37 | 651.25 | 1.900 | 2.087 | 960 | 625 | 7.08 | 0.01 | 92 | negligible |
| Endo-free kit | 1.39 | 713.40 | 1.889 | 2.154 | 1020 | 728 | 7.47 | 0.01 | 92 | negligible |
Table 1. Comparative analysis of plasmid DNA yield, endotoxin levels, and quality parameters processed with the old AmMag Quatro software using Regular and Low-Endo kits.
Figure 1. Agarose gel electrophoresis image showing the supercoil ratio and restriction digestion analysis using the old software.
New software (V1.01.04.01)
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|
| Regular kit | 1.38 | 683.90 | 1.888 | 2.134 | 890 | 609 | 91.4 | 0.13 | 93 | negligible | Regular kit | 1.39 | 715.25 | 1.888 | 2.146 | 950 | 679 | 70.1 | 0.10 | 92 | negligible |
| Low-endo kit | 1.34 | 670.05 | 1.889 | 2.100 | 880 | 590 | 11.0 | 0.02 | 88 | negligible |
| Low-endo kit | 1.38 | 649.60 | 1.892 | 2.116 | 980 | 637 | 16.7 | 0.02 | 93 | negligible |
Table 2. Comparative analysis of plasmid DNA yield, endotoxin levels, and quality parameters processed with the new AmMag Quatro software using Regular and Low-Endo kits.
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, particularly with the standard kit, 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.
