CD DNA Clean Beads is particularly created for DNA purification and is based on SPRI (Solid Phase Reverse Immobilization) technology. With a quick and easy workflow, the Kit can also be utilized to select fragment sizes during the preparation of DNA or RNA next-generation sequencing (NGS) libraries. It has significantly higher amplicon recovery rates for small and large amplicon sizes >100 bp and is substantially more efficient than traditional filtration DNA/PCR clean-up and RNA/cDNA/RNA purification clean-up. It can produce high-quality double-stranded and single-stranded DNA templates while also removing dNTPs, primers, primer-dimers, and contaminants without the use of salt carryover.
Workflow:
Workflow of DNA Purification and Size Selection
Storage:
All the components can be stored at 2-8℃ for one year.
Specifications:
| Application | Applicable for DNA purification and fragment size selection during the preparation of DNA or RNA next generation sequencing (NGS) library. |
| Sample type | DNA |
CD DNA Clean Beads is compatible with almost all brands of kits for library construction and protocol reported in paper.
Notes Before Use
Equilibrate the CD DNA Clean Beads to room temperature before use.
Mix the beads thoroughly by vortexing every time before pipetting.
When rinsing the beads with 80% ethanol, keep the tube static on the magnetic stand, and do not disturb the bead.
When air-drying the beads, do not over-dry it. Over-dried beads with cracks on the surface will lead to reduced elution efficiency of DNA.
Purify the DNA fragments with CD DNA Clean Beads
- Equilibrate the CD DNA Clean Beads to room temperature. Suspend the beads thoroughly by vortexing.
- Pipet beads into the fragmentation products. Mix thoroughly by vortexing or pipetting up and down for 10 times.
- Incubate at room temperature for 5 min.
- Place the sample on a magnetic stand. Wait until the soultion clarifies (about 5min). Keep it on the magnetic stand and carefully discard the supernatant without disturbing the beads.
- Keeping the sample on the magnetic stand, add 200 μl of freshly prepared 80% ethanol to rinse the beads. DO NOT re-suspend the beads! Incubate for 30 sec at room temperature and carefully discard the supernatant without disturbing the beads.
- Repeat the Step 5.
- Keep the tube on the magnetic stand, open the tube, and air-dry the beads for 5 - 10 min.
- Take the tube off from magnetic stand. Add sterile ultra- pure water into the tube to elute DNA. Mix by vortexing or gently pipetting. Collect liquids at the bottom of the tube by a brief centrifugation, and then put the tube back on the magnetic stand. Wait until the solution becomes clear (about 5 min). Transfer supernatant to a new PCR tube carefully. (The volume depends on subsequent experiments).
Reference Conditions for Library Selection
The DNA library with full size of 200 bp-1500 bp was prepared using CD NEXT DNA Library Prep Kit for Illumina (DP002) and purified with 1 × CD DNA Clean Beads. Then, using CD DNA Clean Beads again, the library was sorted into different sizes according to the following conditions. Finally, all the libraries were analyzed with an Agilent 2100 Bioanalyzer.
The Effect of Residual Beads on Library Distribution
When the library is analyzed with an Agilent 2100 Bioanalyzer, the peak may come with a tail on the higher molecular weight side (as shown in the following figure), usually caused by the residual beads in purified PCR products. To avoid this, it is recommended to use a magnetic stand with stronger magnetic force and carefully discard the supernatant without disturbing the beads.
