Description
DNA clean-up beads for NGS
GeniePure DNA Clean-up Beads are paramagnetic SPRI (solid-phase reversible immobilisation) beads for size-selective purification and clean-up of DNA. They remove primers, nucleotides, salts and enzymes after PCR, library preparation and enzymatic reactions. Adjustable bead-to-sample ratios give tunable size selection with high, reproducible recovery.
The beads support DNA purification and size selection for next-generation sequencing fragment libraries, and suit DNA and RNA library preparation protocols from kit manufacturers and the published literature. They are used in the same way as other commercial SPRI beads, with no need to re-optimise conditions, and give highly consistent library yield and size distribution. Every lot undergoes strict quality control. For research use only.
Key Features
| Drop-in protocol | Used in the same way as other commercial SPRI beads, with no need to test new conditions. | |
| Consistent results | Recovery and library size distribution are highly consistent with other SPRI beads. | |
| Broad compatibility | Suitable for DNA and RNA library preparation and compatible with many library prep kits. | |
| Tunable size selection | Bead-to-sample ratios select fragments from ≥100 bp to ≥1 kb, or narrow windows from 170 bp to 700 bp. | |
| Strict quality control | Every lot is tightly quality-controlled. |
Specifications
| Technology | SPRI (solid-phase reversible immobilisation) paramagnetic beads |
| Applications | DNA purification and size selection for DNA or RNA NGS library preparation |
| Purification cut-offs | 0.5× (≥1 kb) to 2.2× - 3.0× (≥100 bp) |
| Size selection range | Average fragment length 170–700 bp (double-sided selection) |
| Shelf life | 2 years |
Components
| Components | Amount |
| GeniePure DNA Clean-up Beads | 5 ml / 60 ml / 450 ml |
Storage
Store at 2 ~ 8°C.
DNA purification
- Equilibrate the beads
- Take the beads out of 2–8°C storage and leave at room temperature for more than 30 min.
- Bind DNA
- Mix the beads thoroughly by vortexing or inverting. Add beads at the ratio in Table 1 and mix with the sample by pipetting 10 times.
- Incubate at room temperature for 10 min.
- Separate
- Place the tube on a magnetic rack for about 5 min until the supernatant is clear, then carefully discard the supernatant.
- Wash
- Keeping the tube on the rack, add 200 μl of freshly prepared 80% ethanol without disturbing the beads. Incubate at room temperature for 30 sec and carefully discard the supernatant.
- Repeat for two washes in total.
- Dry
- Keeping the tube on the rack, air-dry the beads for 5–10 min.
- Elute
- Remove the tube from the rack, add an appropriate volume of nuclease-free ddH2O and resuspend the beads by pipetting or vortexing. Incubate at room temperature for 2 min.
- Place the tube on the rack until the supernatant is clear (~5 min) and transfer the supernatant to a new PCR tube.
Table 1. Reference conditions for DNA purification (bead volume = ratio × sample volume)
| Fragment size retained | Reference ratio |
| ≥1 kb | 0.5× |
| ≥400 bp | 1.0× |
| ≥300 bp | 1.2× |
| ≥200 bp | 1.5× |
| ≥100 bp | 2.2× - 3.0× |
DNA size selection
- Equilibrate the beads
- Leave the beads at room temperature for more than 30 min, then mix thoroughly by vortexing or inverting.
- First-round binding (removes large fragments)
- Add the 1st-round bead volume from Table 2 and pipette 10 times. Incubate at room temperature for 10 min.
- Place on the magnetic rack for about 5 min until clear, then transfer the supernatant to a new PCR tube.
- Second-round binding (captures target fragments)
- Add the 2nd-round bead volume from Table 2 to the supernatant and pipette 10 times. Incubate at room temperature for 10 min.
- Place on the magnetic rack for about 5 min until clear, then discard the supernatant.
- Wash, dry and elute
- Wash twice with 200 μl of freshly prepared 80% ethanol (30 sec each), air-dry for 5–10 min and elute in nuclease-free ddH2O as for DNA purification.
Table 2. Reference conditions for DNA size selection (volume ratios are beads : initial sample)
| Average selected fragment length (bp) | 1st-round ratio | 2nd-round ratio |
| 170–200 | 1 | 0.3 |
| 220–250 | 0.9 | 0.2 |
| 260–280 | 0.8 | 0.2 |
| 290–310 | 0.8 | 0.15 |
| 310–340 | 0.7 | 0.2 |
| 340–360 | 0.7 | 0.15 |
| 360–390 | 0.7 | 0.1 |
| 390–420 | 0.65 | 0.1 |
| 410–440 | 0.6 | 0.15 |
| 410–450 | 0.6 | 0.1 |
| 530–570 | 0.55 | 0.1 |
| 570–600 | 0.5 | 0.15 |
| 660–700 | 0.45 | 0.15 |
Q1: Which bead ratio should I use for clean-up?
- Bead volume = ratio × sample volume. Use 0.5× to retain fragments ≥1 kb, 1.0× for ≥400 bp, 1.2× for ≥300 bp, 1.5× for ≥200 bp and 2.2× - 3.0× for ≥100 bp.
Q2: Why is my DNA recovery low?
- Make sure the beads have equilibrated at room temperature for more than 30 min and are fully resuspended before use. Avoid over-drying the beads: if they look cracked, they are too dry and DNA elution will be poor.
Q3: What causes high-molecular-weight tailing in my fragment analysis?
- This is usually due to residual beads in the eluate. Use a magnetic rack with strong magnetic force and avoid disturbing the beads when taking the final supernatant.
Q4: Can I use these beads with my existing library prep kit?
- Yes. The beads suit DNA and RNA library preparation protocols from kit manufacturers and the published literature, and are used in the same way as other commercial SPRI beads.
