n any laboratory, versatility matters. Whether it’s a disposable kit or a monster instrument, scientists need to get as much use out of it as possible. We understand — we’ve been there! That’s why we strive to develop each of our products with optimal versatility in mind.
Our sparQ PureMag Beads are a great example. These magnetic beads bind to nucleic acids and perform high-quality cleanup for both DNA and RNA. We’ve even engineered them to remain stable at room temperature to make them as useful as possible. A series of application notes lays out some important details about these methods. We recommend reading them in full, but here are some highlights to tide you over.
DNA Cleanup and Size Selection
In this application note, we demonstrate the use of sparQ PureMag Beads specifically for cleanup and size selection of DNA, testing an accelerated binding protocol for a range of target fragment size ranges. In each case, we compared the performance of sparQ PureMag Beads to the Beckman Coulter SPRIselect™ beads. Experiments were carried out in triplicate; for size selection, we performed three sets of size selection ratios.
In this evaluation, we showed that magnetic bead cleanup provides a reliable and accurate method for post-ligation and post-PCR DNA products. The quantification of eluted DNA from each condition demonstrated equivalent performance between sparQ PureMag Beads (58.1% recovery) and SPRIselect (56.8% recovery) with 1 minute incubation. When incubation time was extended to 5 minutes, DNA recovery increased to 63.5% with sparQ PureMag Beads. These results suggest that sparQ PureMag Beads can be used in place of SPRIselect for DNA cleanup with no change in incubation time, but that increased incubation time can increase DNA yield with sparQ PureMag Beads.
For size selection, we found that in all three conditions we tested, sparQ PureMag Beads gave equivalent size selection to SPRIselect. For example, for selection of fragments in the region of 450 bp to 600 bp, sparQ PureMag Beads gave a peak fragment size of 477 bp with range of 753 bp and SPRIselect gave a peak fragment size of 474 bp with range of 745 bp. Overall, we observed that sparQ PureMag Beads delivered accurate and reproducible size selection at varying sample-to-beads ratios, highlighting their wide utility for various sequencing applications.
RNA Cleanup and Size Selection
In a separate application note, we evaluated sparQ PureMag Beads for RNA cleanup — an important step for a growing number of applications, such as RNA-seq, purification of probes and in vitro transcription experiments. Our results demonstrated that sparQ PureMag Beads are also a highly efficient and reproducible method for RNA cleanup and size selection, further validating their flexibility and performance.
An important consideration is that reagents are free from RNases that could degrade the RNA sample. We assessed the efficiency of ssRNA cleanup with sparQ PureMag Beads, using a low range ladder as the template to assess the capture of different RNA fragment lengths. After 4 hours of incubation at room temperature, the bands of the ssRNA ladder were clearly visualized with no detectable smearing; this indicates the absence of detectable RNase in sparQ PureMag Beads.
Two input concentrations of ssRNA ladder were purified using 1.8X sparQ PureMag Beads or RNAClean XP, and the output concentration was measured. Average percentage recovery was similar from the two bead types at both input RNA concentrations tested. For example, with 500 ng input RNA, average recovery was 81% for purification with sparQ PureMag Beads and 77% with RNAClean XP. Therefore, sparQ PureMag Beads provide a highly efficient RNA cleanup method.
We also evaluated the ability to alter the ratio of beads in the mixture to use sparQ PureMag Beads for highly flexible fragment size selection. After trying various ratios, we found that all cleanup ratios provided high-quality RNA, with no visible sample degradation. These beads enable effective size selection of RNA and can be optimized for specific input RNA conditions or sample matrixes.
sparQ PureMag Beads provide a fast, flexible and cost-effective alternative for RNA purification. They can easily be incorporated into a range of manual or automated RNA workflows to provide superior RNA recovery and quality for downstream applications.
Stability at Room Temperature
The final application note in our series looks at performance or sparQ PureMag Beads when stored at room temperature instead of at the recommended 4°C. For this evaluation, we stored beads at room temperature for six months, and then used them for a standard DNA cleanup and size selection workflow, comparing results to beads stored at 4°C.
Results showed that DNA recovery was high, and that consistency of DNA recovery was maintained even after long-term storage at ambient temperatures. There was no significant difference between performance of the cold-stored or room temp-stored beads. The same held for size selection: outcomes were similar for both bead sets.
Overall, we found that room temperature storage of sparQ PureMag Beads for up to six months had no impact on the performance of the beads, efficiency of DNA recovery or size selection. That makes the product an excellent choice for applications where cold storage isn’t possible, such as those requiring transport or involving workflow automation instruments.