PCR Purification Kit Comparison
Which is the best kit for DNA clean up?Which is the Best Kit for DNA Clean Up?
Our aim was to perform a PCR Purification Kit Comparison from different vendors. At Civic Bioscience, we distribute the Favorprep™ and EasyPure® product lines from FAVORGEN and TransBionovo respectively.
First, the FavorPrep™ GEL/PCR Purification Kit, EasyPure® PCR Purification Kit and NEB Monarch® PCR Purification Kit were compared side-by-side using purification of the Trans2K® Plus II DNA Ladder from TransBionovo (8kb to 100bp range).
Next, the FavorPrep™ MicroElute GEL/PCR Purification Kit from FAVORGEN was compared to the NEB Monarch® PCR Purification Kit.
Monarch® is a registered trademark of New England Biolabs, Inc.
Details
Date: December 26th, 2016
Type of experiment: DNA ladder purification (DNA clean up)
Featured Products: FavorPrep™ GEL/PCR Purification Kit, FavorPrep™ MicroElute GEL/PCR Purification Kit, EasyPure® PCR Purification Kit.
Competitor Product(s): NEB Monarch® PCR Purification Kit. Monarch® is a registered trademark of New England Biolabs, Inc.
PCR Purification Kit Columns specifications
Pictures of each PCR Purification columns were taken to show that each spin-column has different cartridge dimensions.
DNA Purification Kit Comparison protocol for 40ul elution volumes
To compare the FavorPrep™ GEL/PCR Purification Kit, EasyPure® PCR Purification Kit and NEB Monarch® PCR Purification Kit side-by-side, 40 ul of pre-purified Trans2K® Plus II DNA Ladder was mixed 5 volumes of solubilization/binding buffer supplied with each kit.
All centrifugation steps were carried at 16 000 RCF.
Columns from each supplier were washed with indicated volumes of wash buffer (750 ul, 650 ul and 200 ul respectively for the FAVORGEN, TransBionovo and NEB kits).
The final spin to remove residual EtOH was carried for 3 min.
The elution buffer supplied with the NEB kit was used to perform the elution in 40 ul from all supplier columns.
Note: the FAVORGEN kit used herein is a dual-purpose kit, enabling the user to purify DNA from both agarose gels and enzymatic reactions. FAVORGEN also manufactures a PCR Clean Up kit better optimized to clean up DNA from enzymatic reactions.
Results of PCR Purification Kit Comparison with 40 ul
Input before DNA purification : 40ul
Output elution volume : 40 ul
Amount of DNA of agarose gel (before mixing with 6x DNA loading buffer):
- Input : 4 ul and 2 ul
- Eluates: 4 ul and 2 ul
Results
Similar band intensities were obtained using eiher kit as compared to the input amount. The FavorPrep™ GEL/PCR Purification Kit appeared to recover slightly more DNA than the 2 other kits used using a 40 ul elution volume. Overall, all kits performed well.
MicroElute PCR Purification Kit Comparison protocol using 10ul elution volumes
To compare the FavorPrep™ MicroElute GEL/PCR Purification Kit from FAVORGEN to the NEB Monarch® PCR Purification Kit side-by-side, 10 ul of pre-purified Trans2K® Plus II DNA Ladder was mixed with 40ul of water. Then, 5 volumes of solubilization/binding buffer supplied with each kit was mixed with each sample.
All centrifugation steps were carried at 16 000 RCF.
Columns from each supplier were washed with indicated volumes of wash buffer (500 ul and 200 ul respectively for the FAVORGEN and NEB kits).
The final spin to remove residual EtOH was carried for 3 min.
The elution buffer supplied with the NEB kit was used to perform the elution in 10 ul from all supplier columns.
Note: the FAVORGEN kit used herein is a dual-purpose kit, enabling the user to purify DNA from both agarose gels and enzymatic reactions. FAVORGEN also manufactures a MicroElute PCR Clean Up kit better optimized to clean up DNA from enzymatic reactions. Finally, a 96-well GEL/PCR Purification kit is also available for high-throughput requirements.
Results of MicroElute PCR Purification Kit Comparison with 10 ul
Input before DNA purification : 10ul
Output elution volume : 10 ul
Amount of DNA of agarose gel (before mixing with 6x DNA loading buffer):
- Input : 5 ul and 2.5 ul
- Eluates: 5 ul and 2.5 ul
Results
Similar band intensities were obtained using eiher kit as compared to the input amount. The FavorPrep™ MicroElute GEL/PCR Purification Kit was as efficient, if not better, at recovering DNA from only 10 ul of elution buffer as compared to the competitor kit.
Conclusion
The results from our PCR Purification Kit Comparison is that we were able to purify a wide range of DNA bands ranging from 8 kb to 100 bp using 3 different commercial kits and a ‘standard’ elution volume of 40 ul. The FavorPrep™ GEL/PCR Purification Kit appeared to recover slightly more DNA, but overall, all kits performed well.
The results from our MicroElute PCR Purification Kit Comparison is that we were able to purify a wide range of DNA bands ranging from 8 kb to 100 bp using 2 different commercial MicroElute kits and only 10 ul as the elution volume. Both kits performed very well.
A major advantage and feature of both FAVORGEN kits that were used for our PCR Purification Kit Comparison is their dual-purpose, Indeed, the FavorPrep™ GEL/PCR Purification Kit and FavorPrep™ MicroElute GEL/PCR Purification Kit enable the user to purify DNA from both agarose gels and enzymatic reactions, making it the ideal choice for day-to-day DNA purification.
Pricing of PCR Purification Kits
- FavorPrep™ GEL/PCR Purification Kit : 184 $ for 300 rx –> 0.61$/prep
- FavorPrep™ MicroElute GEL/PCR Purification Kit : 240$ for 200 rx –> 1.20$/prep
- EasyPure® PCR Purification Kit : 196$ for 200 rx –> 0.98$/prep
- NEB Monarch® PCR Purification Kit : 560$ for 250 rx –> 2.24$/prep
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