sparQ PureMag Beads

Fast, reliable DNA purification & size selection for NGS workflows

Features & Benefits

  • High recovery of DNA fragments greater than 100 bp
  • Efficient removal of unwanted components from adapter ligation and PCR reactions
  • Consistent single or double-sided size selection
  • Seamless integration into existing NGS workflows with little or no protocol change
  • Easy-to-use and compatible with manual processing or automated liquid handling robots
  • Cost effective alternative to AMPure® XP with equivalent performance

Description

sparQ PureMag Beads is a fast and reliable nucleic acid purification system for reaction cleanup and size selection in Next Generation Sequencing (NGS) workflows. Based on the reversible nucleic acid-binding properties of magnetic beads, this product can be used to quickly remove primers, primer-dimers, unincorporated nucleotides, salts, adapters and adapter-dimers from NGS library prep reactions to improve downstream sequencing performance. sparQ PureMag Beads allows excellent recovery of fragments greater than 100 bp without centrifugation or filtration. Consistent and reliable size selection can be achieved by simply adjusting the beads to sample ratio. This product is designed for both manual and automated processing, allowing seamless integration into existing workflows.

Workflow for Double-Sided Size Selection

Workflow for Double-Sided Size Selection


Workflow for Double-Sided Size Selection

Double-sided size selection is used to remove smaller and larger fragments from either side of the desired region. The fragment size can be easily adjusted to suit the application by manipulating the sparQ PureMag Beads to DNA volumetric ratio.


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  • Double-sided size selection tunable for specific application
  • Achieve consistent size range by simply manipulating the beads to sample ratio

Performance Data

Bioanalyzer trace of fragmented human genomic DNA pre- and post double-sided size selection


Bioanalyzer trace of fragmented human genomic DNA pre- and post double-sided size selection

Electropherogram of fragmented human genomic DNA pre- and post double-sided size selection. Different sparQ PureMag Beads to DNA ratios were used to achieve various targeted size range.


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Highly reproducible purification across a range of inputs


Highly reproducible purification across a range of inputs

Highly reproducible DNA library profiles were achieved using different lots of sparQ PureMag Beads and a broad range of input amount. Libraries were prepared with sparQ DNA Library Prep Kit from 100 ng and 1 ng of fragmented microbial genomic DNA. sparQ PureMag Beads were used post adapter ligation and PCR amplification to effectively remove adapter-dimers and primer-dimers.


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Efficient recovery of DNA equivalent to AMPure XP


Efficient recovery of DNA equivalent to AMPure XP

sparQ PureMag Beads show equivalent performance to AMPure XP for DNA purification. 50 bp DNA ladder was purified with sparQ PureMag Beads and AMPure XP at different beads to DNA ratios and analyzed on 2% agarose gel.


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Performance Data

Consistent and tunable size selection


sparQ PureMag beads workflow

Double-sided size selection is used to remove smaller and larger fragments from either side of the desired region. The fragment size can be easily adjusted to suit the application by manipulating the sparQ PureMag Beads to DNA volumetric ratio.


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Consistent and tunable size selection


Bioanalyzer trace of fragmented human genomic DNA prior and post double-sided size selection

Electropherogram of fragmented human genomic DNA prior and post double-sided size selection. Different sparQ PureMag Beads to DNA ratios were used to achieve various targeted size range.


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Highly reproducible purification across a range of inputs


Highly reproducible purification across a range of inputs

Highly reproducible DNA library profiles were achieved using different lots of sparQ PureMag Beads and a broad range of input amount. Libraries were prepared with sparQ DNA Library Prep Kit from 100 ng and 1 ng of fragmented microbial genomic DNA. sparQ PureMag Beads were used post adapter ligation and PCR amplification to effectively remove adapter-dimers and primer-dimers.


<
>

Efficient recovery of DNA equivalent to AMPure XP


Efficient recovery of DNA equivalent to AMPure XP

sparQ PureMag Beads show equivalent performance to AMPure XP for DNA purification. 50 bp DNA ladder was purified with sparQ PureMag Beads and AMPure XP at different beads to DNA ratios and analyzed on 2% agarose gel.


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What Customers Say
Beads performed as well in my tests as Ampure XP which I consider to be the gold standard. Impressive results given the lower price... Read More Beads performed as well in my tests as Ampure XP which I consider to be the gold standard. Impressive results given the lower price for sparQ PureMag Beads."
Director of Sequencing Technology
University of Southern California

Details

  • Contents
    Cat. No 95196-005 Size:    5 mL
      95196-060    60 mL
      95196-450 450 mL
  • Storage & Handling

    Store the product in a constant temperature refrigerator at 2°C to 8°C upon receipt. Please do not freeze. For lot specific expiry date, refer to package label, Certificate of Analysis or Product Specification Form.

  • Related Resources
    Product Flyers
    Product Manuals
    Technical Notes
    FAQs
    Can I still use the sparQ PureMag Beads if I left it at room temperature for some time?
    sparQ PureMag Beads is manufactured and tested for the storage temperature indicated on the bottle and we cannot guarantee performance if it was stored outside of the recommended condition.
    Can I still use the sparQ PureMag Beads if it was accidentally frozen?
    sparQ PureMag Beads is manufactured and tested for the storage temperature indicated on the bottle and we cannot guarantee performance if it was stored outside of the recommended condition.
    How do I dry my samples before elution?
    Air-dry the beads on the magnetic stand for 5 min or until the beads are dry and before they start to crack. Do not over-dry the beads as it can reduce the DNA recovery.
    Is there a size limit for the DNA fragments that can be bound with sparQ PureMag Beads?
    sparQ PureMag Beads will bind DNA fragments 100 bp and above and exclude primers 50 bases and below. There will be some recovery for oligo or DNA between 50 and 100 bases.
    What is the recovery rate with sparQ PureMag Beads?
    The recovery rate depends on many factors, including the fragment size, sample volume, sample concentration, and elution volume. Up to 90% recovery rate can be expected under the optimal condition. The yield is also correlated with the ratio of beads to sample, and the lower ratio usually results in lower yield. When the ratio reaches to 1.8X, it generally produces maximal recovery.
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    Publications
    A rapid, low cost, and highly sensitive SARS-CoV-2 diagnostic based on whole genome sequencing
    Brian Glenn St Hilaire, BioRxiv - 2020
    Abstract
    Early detection of infection with SARS-CoV-2 is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom onset1,2. Here, we introduce a low-cost, high-throughput method for diagnosis of SARS-CoV-2 infection, dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), that enhances sensitivity by aiming to amplify the entire SARS-CoV-2 genome rather than targeting particular viral loci, as in typical RT-PCR assays. To achieve this goal, we combine a SARS-CoV-2 enrichment method developed by the ARTIC Network (https://artic.network/) with short-read DNA sequencing and de novo genome assembly. We are able to reliably (>95% accuracy) detect SARS-CoV-2 at concentrations of 84 genome equivalents per milliliter, better than the reported limits of detection of almost all diagnostic methods currently approved by the US Food and Drug Administration. At higher concentrations, we are able to reliably assemble the SARS-CoV-2 genome in the sample, often with no gaps and perfect accuracy. Such genome assemblies enable the spread of the disease to be analyzed much more effectively than would be possible with an ordinary yes/no diagnostic, and can help identify vaccine and drug targets. Using POLAR, a single person can process 192 samples over the course of an 8-hour experiment, at a cost of ~$30/patient, enabling a 24-hour turnaround with sequencing and data analysis time included. Further testing and refinement will likely enable greater enhancements in the sensitivity of the above approach.
    Influence of introduced arbuscular mycorrhizal fungiand phosphorus sources on plant traits, soil properties,and rhizosphere microbial communities in organiclegume-flax rotation
    Yunliang Li, Plant Soil - 2019
    Abstract
    Aims We identify P management strategies combiningarbuscular mycorrhizal fungal (AMF) inoculation withrock phosphate or composted manure for intensive or-ganic grain-production systems.Methods We measured the response of plants traits andsoil properties to the factorial combination of three ratesof organic-approved P sources applied in rotation phase-1of legume–flax cropping systems, and of granular AMFinoculant applied in the first, second, or both rotationphases, or not applied. Treatment combinations effectson the rhizosphere communities of AMF, fungi, andbacteria were tested by amplicon sequencing, in twopedoclimates.Results Inoculation had limited effects in both environ-ments. Composted manure decreased lentil yield, butincreased lentil N and P concentrations and soil P fertilityon the Chernozem, while increasing pea productivity onthe Luvisol. Composted manure applied in rotationphase-1 had a residual effect on flax productivity, N andP concentrations, and soil P fertility in both environ-ments. Rock phosphate reduced soil P fertility and flaxproductivity on the Gray Luvisol. The βdiversity of therhizosphere communities was unaffected by treatments,while the αdiversity of bacteria and AMF was altered byAMF inoculation and fertilization only in the GrayLuvisol. Correlations between microbial species andplant traits or soil properties were inconsistent, reflectingthe complex relationships among microbial community,plant identity, and environmental conditions.Conclusion Here, composted manure was more influ-ential than AMF inoculation and rock phosphate. Giventhe influence of environmental conditions, small fieldtrials are recommended before wide-scale adoption oftheir use.
    Topography of the respiratory tract bacterial microbiota in cattle
    Christopher McMullen, Microbiome - 2020
    Abstract
    Background Bacterial bronchopneumonia (BP) is the leading cause of morbidity and mortality in cattle. The nasopharynx is generally accepted as the primary source of pathogenic bacteria that cause BP. However, it has recently been shown in humans that the oropharynx may act as the primary reservoir for pathogens that reach the lung. The objective was therefore to describe the bacterial microbiota present along the entire cattle respiratory tract to determine which upper respiratory tract (URT) niches may contribute the most to the composition of the lung microbiota. Methods Seventeen upper and lower respiratory tract locations were sampled from 15 healthy feedlot steer calves. Samples were collected using a combination of swabs, protected specimen brushes, and saline washes. DNA was extracted from each sample and the 16S rRNA gene (V3-V4) was sequenced. Community composition, alpha-diversity, and beta-diversity were compared among sampling locations. Results Microbiota composition differed across sampling locations, with physiologically and anatomically distinct locations showing different relative abundances of 1137 observed sequence variants (SVs). An analysis of similarities showed that the lung was more similar to the nasopharynx (R-statistic = 0.091) than it was to the oropharynx (R-statistic = 0.709) or any other URT sampling location. Five distinct metacommunities were identified across all samples after clustering at the genus level using Dirichlet multinomial mixtures. This included a metacommunity found primarily in the lung and nasopharynx that was dominated by Mycoplasma. Further clustering at the SV level showed a shared metacommunity between the lung and nasopharynx that was dominated by Mycoplasma dispar. Other metacommunities found in the nostrils, tonsils, and oral microbiotas were dominated by Moraxella, Fusobacterium, and Streptococcus, respectively. Conclusions The nasopharyngeal bacterial microbiota is most similar to the lung bacterial microbiota in healthy cattle and therefore may serve as the primary source of bacteria to the lung. This finding indicates that the nasopharynx is likely the most important location that should be targeted when doing bovine respiratory microbiota research.
    Development of a simplified and inexpensive RNA depletion method for plasmid DNA purification using size selection magnetic beads (SSMBs)
    Xi Wang, Genes and Diseases - 2020
    Abstract
    Plasmid DNA (pDNA) isolation from bacterial cells is one of the most common and critical steps in molecular cloning and biomedical research. Almost all pDNA purification involves disruption of bacteria, removal of membrane lipids, proteins and genomic DNA, purification of pDNA from bulk lysate, and concentration of pDNA for downstream applications. While many liquid-phase and solid-phase pDNA purification methods are used, the final pDNA preparations are usually contaminated with varied degrees of host RNA, which cannot be completely digested by RNase A. To develop a simple, cost-effective, and yet effective method for RNA depletion, we investigated whether commercially available size selection magnetic beads (SSMBs), such as Mag-Bind® TotalPure NGS Kit (or Mag-Bind), can completely deplete bacterial RNA in pDNA preparations. In this proof-of-principle study, we demonstrated that, compared with RNase A digestion and two commercial plasmid affinity purification kits, the SSMB method was highly efficient in depleting contaminating RNA from pDNA minipreps. Gene transfection and bacterial colony formation assays revealed that pDNA purified from SSMB method had superior quality and integrity to pDNA samples cleaned up by RNase A digestion and/or commercial plasmid purification kits. We further demonstrated that the SSMB method completely depleted contaminating RNA in large-scale pDNA samples. Furthermore, the Mag-bind-based SSMB method costs only 5–10% of most commercial plasmid purification kits on a per sample basis. Thus, the reported SSMB method can be a valuable and inexpensive tool for the removal of bacterial RNA for routine pDNA preparations.
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    Customer Profile Stories
  • Testimonials

    “Very good product for NGS library purification and size selection”

    Senior Scientist

    MD Anderson

    "Great product. Useful for many different types of DNA capture applications."

    Associate Professor

    University of South Carolina

    "Worked exactly as advertised. I was able to get complete recovery of my DNA easily and quickly."

    Postdoctoral Fellow

    BC CANCER RESEARCH CENTRE <BCCRC>

    "Very good product for NGS Library purification and size selection"

    Associate Professor

    UNIVERSITY of TEXAS MD ANDERSON CANCER CENTER

    "Very easy to use and really good recovery yield."

    Biologist

    BATJ, Inc

    "Beads performed as well in my tests as Ampure XP which I consider to be the gold standard.  Impressive results given the lower price for sparQ PureMag Beads."

    Director of Sequencing Technology

    University of Southern California

    "We found that size selection with sparQ PureMag Beads was similar to our current vendor for but the amount of size selected library recovered was significantly larger."

    Vice President of Operations

    PHASE GENOMICS

Ordering Information

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