| NucleoSpin Gel and PCR Clean-up |
NucleoSpin Gel and PCR Clean-up Midi | NucleoSpin Gel and PCR Clean-up Maxi | |
| Technology | Silica membrane | Silica membrane | Silica membrane |
| Format | Mini spin columns | Midi spin columns | Maxi spin columns |
| Starting material | <400 µl PCR reaction mixture <400 mg TAE/TBE agarose gel |
<4 ml PCR reaction mixture <4 g TAE/TBE agarose gel |
<10 ml PCR reaction mixture <10 g TAE/TBE agarose gel |
| Fragment size | 50 bp–20 kb | 50 bp–20 kb | 50 bp–20 kb |
| Typical recovery | 70–95% | 70–95% | 70–95% |
| A260/280 | 1.8–1.9 | 1.75–1.85 | 1.75–1.85 |
| Elution volume | 15–30 µl | 200–400 µl | 1 ml |
| Preparation time | 10 min/6 preps | 25 min/6 preps | 30 min/6 preps |
| Binding capacity | 25 µg | 75 µg | 250 µg |
Tech Note
PCR cleanup and gel extraction—the two-in-one kit
- One kit for PCR cleanup and gel extraction
- High recoveries for a wide range of fragment sizes (50 bp to 20 kb)
- Low and standard elution volumes—as little as 15 µl (mini), 200 µl (midi) or 1 ml (maxi)—result in highly concentrated DNA
- Binding buffer with pH indicator for confirmation of optimal kit performance
- Separate buffers available for single-stranded DNA or SDS-containing samples
- Suitable for all gel buffer systems (e.g., TAE, TBE)
- Also available for QIAcube; contact technical support for information
The NucleoSpin Gel and PCR Clean-up procedure is the easiest way to purify DNA fragments from agarose gels as well as to perform direct purification of PCR products. The kit includes one buffer for both applications, which contains a pH indicator displaying the correct pH for optimal kit performance. The purification procedure from enzymatic reactions (e.g., PCR, restriction digestion) allows fast and easy removal of enzymes, nucleotides, salts, and other impurities. You can isolate fragments ranging from 50 bp–20 kb in minimal elution volumes (as low as 15 µl for the mini kit, 200 µl for the midi kit, and 1 ml for the maxi kit) with typical recovery rates of 70–95%.
At-a-glance
Binding buffer with pH indicator
The optimal pH to bind even small DNA fragments to the silica membrane is about 5–6. Binding Buffer NTI is sufficiently buffered to maintain this pH. However, to be sure that the pH is right even for samples with extreme alkaline pH or high buffer concentration, a pH indicator has been added (Figure 1). The pH indicator does not interfere with DNA binding and is completely removed during the purification. The yellow color is also beneficial for gel extractions, making it easy to identify undissolved pieces of agarose. To restore the correct conditions, add more Buffer NTI or 4 M sodium acetate (NaAc, pH 5.0), or small amounts of hydrochloric acid (HCl) until the color switches back to yellow.
Figure 1. The range of colors displayed by the pH indicator in Binding Buffer NTI.
PCR cleanup data
High recovery rates
The NucleoSpin Gel and PCR Clean-up kit showed a high recovery rate for a wide range of fragment sizes, down to 50 bp (Figure 2). DNA fragments of different sizes were purified from a standard PCR buffer using the kit, with elution volumes of 15 μl, 30 μl, and 50 μl. DNA was analyzed and quantified using an Agilent Bioanalyzer 2100.
Figure 2. High recovery rates for PCR cleanup of fragments down to 50 bp.
Consistent performance with different polymerase buffer systems
Recovery rates and efficiency of primer removal using the NucleoSpin Gel and PCR Clean-up kit were shown to be comparable for three different polymerase buffer systems, unlike competitor kits which showed lower recovery and/or inefficient primer removal (Figure 3). A 165-bp PCR fragment was amplified using different DNA polymerase reaction mix formulations (a–c). Additional primers were added and the mixture was purified using competitor kits from Q, S, and R. The elution volume was 25 μl. For analysis, the complete eluate was loaded onto a 1% TAE agarose gel (u: unpurified). In comparison to MN (the NucleoSpin Gel and PCR Clean-up kit), the other kits all showed lower recovery or inefficient removal of primers. The Competitor Q kit showed a comparable recovery rate but inefficient removal of primers.
Figure 3. The NucleoSpin Gel and PCR Clean-up kit provides comparable recovery rates with different polymerase buffer systems.
Reliable sequencing results
50 ng of a 1,730-bp PCR product purified using the NucleoSpin Gel and PCR Clean-up kit was cycle-sequenced with standard BigDye-Terminator chemistry using an ABI PRISM 3130 Genetic Analyzer. The reading length of up to 750 bp was excellent, and up to 900 bp could be analyzed (data not shown). Data kindly provided by Dr. A. Kocyan, Systematic Botany, Ludwig Maximilian University Munich, Germany.
High recovery with low elution volumes
The NucleoSpin Gel and PCR Clean-up kit provides high recovery rates with elution volumes as low as 15 µl (Figure 4). A PCR fragment (782 bp) was purified from a 1% TAE agarose gel according to the standard NucleoSpin Gel and PCR Clean-up kit protocol using different elution volumes as shown. All eluates were adjusted to 25 μl plus 4.5 μl loading dye. For analysis, the mixture was loaded onto a 1% TAE agarose gel. Recovery was estimated against reference samples (Lanes 1–4). Even with an elution volume as low as 15 μl, recoveries of up to 75–100% can be achieved.
Figure 4. High recovery with low elution volumes.
Optimal recovery for small fragments
The NucleoSpin Gel and PCR Clean-up kit showed optimal primer removal and high recovery rates for 50-bp and 100-bp PCR fragments (Figure 5). A sample containing 50-bp and 100-bp PCR fragments and a 27-nt primer was purified using the NucleoSpin Gel and PCR Clean-up kit. The eluate was analyzed on a Agilent Bioanalyzer 2100 and compared to the input before purification. The 15-bp peak displays the internal Bioanalyzer marker. The results showed an optimal removal of the 27-nt primer and a very high recovery (>90%) of the 50-bp and 100-bp PCR fragments.
Figure 5. Optimal recovery for small fragments. Red graph: sample before purification. Blue graph: eluate after purification.
Gel extraction data
Gel extraction of a wide size range of DNA fragments
The NucleoSpin Gel and PCR Clean-up kit showed high recovery of a wide size range of DNA fragments extracted from agarose gels (Figure 6). DNA fragments of different sizes were purified from a 1% TAE agarose gel using the kit. DNA was analyzed and quantified using an Agilent Bioanalyzer 2100.
Figure 6. Gel extraction of a wide range of DNA fragment sizes.
Protocol schematic
- For PCR clean-up: after addition of Binding Buffer NTI, the mixture is applied to the silica membrane. Contaminants are removed by a simple washing step with ethanolic Buffer NT3.
- For gel extraction: the agarose gel slice is dissolved in high-salt Buffer NT and applied to a NucleoSpin Gel and PCR Clean-up Column, followed by centrifugation and a subsequent washing step. Pure DNA is eluted under low ionic strength conditions with slightly alkaline Buffer NE (5 mM Tris/HCl, pH 8.5).
Figure 7. The NucleoSpin Gel and PCR Clean-up protocol.
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