MagBio Reagents

DNA normalization and Concentration

<h2>What is DNA normalization and concentration for NGS?</h2>
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DNA normalization for NGS is the process of adjusting all individual indexed sequencing libraries to the same molar concentration before pooling them into a single multiplexed sequencing run, so that each library contributes approximately the same number of sequencing reads to the total run output. Concentration may also be needed when a library is too dilute after cleanup or elution. SPRI (solid-phase reversible immobilization) magnetic bead-based cleanup, most commonly using AMPure XP beads, is the standard method for post-library-prep cleanup, size selection, and concentration in NGS workflows.
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<h2 dir="ltr">What you will find:</h2>
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Magbio MagQuant Plus DNA Kit: for automated, high-throughput nucleic acid concentration and normalization workflows
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</ul>
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<h2>How to normalize and concentrate NGS libraries</h2>
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Quantify each library by qPCR to calculate molar concentration accurately
Kapa Library Quantification qPCR kits or equivalent measure the amplifiable, adapter-ligated molecules in a library, providing a molar concentration based on insert size that can be used to pool libraries at equal molar ratios. Fluorometric quantitation gives mass per volume but not molar concentration, and libraries with different insert sizes have different mass-to-moles conversion factors.
Calculate library molar concentration using measured mass and average insert size
If molar quantitation by qPCR is not available, the molar concentration of a library can be estimated from its fluorometric mass concentration and the average insert size from Bioanalyzer or TapeStation: molar concentration (nM) = (mass in ng/&micro;l &times; 10^6) / (insert size in bp &times; 660 g/mol/bp). This converts mass to moles using the average molecular weight per base pair.
Pool indexed libraries at equal molar ratios for balanced depth
After calculating the molar concentration of each library, pool volumes delivering equal moles of each library into the final pool. Even small quantitation errors translate into coverage imbalances between samples in the sequencing output.
Use SPRI bead cleanup to concentrate libraries and remove adapter dimers
SPRI bead cleanup with AMPure XP beads at the appropriate bead-to-sample ratio selects for DNA fragments above a size cutoff while removing smaller adapter dimers and free adapter molecules. The final elution in a smaller volume of buffer concentrates the library. The bead ratio determines the minimum retained fragment size, with higher ratios retaining smaller fragments.
Verify the pooled library before sequencing
After pooling and final SPRI cleanup, measure the pooled library by qPCR and Bioanalyzer to confirm molar concentration and size distribution before loading, since loading concentration determines cluster density and affects sequencing performance.
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<h2>Specifications context</h2>
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AMPure XP SPRI beads use polyethylene glycol and sodium chloride to precipitate DNA onto paramagnetic beads in a size-dependent manner, making the bead-to-sample volume ratio the key parameter for controlling the minimum retained fragment size. As of 2026, automated bead-based normalization kits that combine quantitation and normalization remain available for high-throughput settings, though most academic labs perform manual quantitation and normalization before pooling.
Browse through the catalog and <a href="https://mbpinc.net/contact-us">contact the expert team</a> to book high-quality DNA normalization and concentration products today.

MagQuant_Plus_DNA Kit V2 - Protocol_REV3

Magbio MagQuant Plus DNA Kit V2

MQP-50000 by MagBio Genomics is the MagQuant Plus DNA Kit V2, a magnetic bead kit for DNA normalization and quantitation in NGS, amplicon, and genomic DNA workflows. No centrifugation, no standard curve required; 25–50 µL elution volume; available in 96-, 384-, and 1920-prep sizes.

Starting material (Sample matrix)

DNA input

DNA Purity Requirements

Process method

Purification method

Application

Elution Volume

Manufacturer

MagQuant Plus DNA Kit V2 (10 Preps)

MagQuant Plus DNA Kit V2 (96 Preps)

MagQuant Plus DNA Kit V2 (384 Preps)

MagQuant Plus DNA Kit V2 (1920 Preps)

MagQuant Plus DNA Kit V2 (5000 Preps)

DNA/PCR

<h2>What is DNA/PCR Sequencing Cleanup?</h2>
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DNA/PCR sequencing cleanup purifies PCR-amplified NGS library products - indexed Illumina libraries after amplification, amplicon sequencing PCR products (16S rRNA, ITS, targeted gene panels), and long-range PCR products for long-read sequencing - removing residual PCR primers, dNTPs, thermostable polymerase, betaine, DMSO, BSA, and PCR buffer salts that inhibit sequencing cluster generation, flow cell loading, and library quantification. Perform SPRI bead cleanup after every PCR amplification step in library preparation - residual primers generate non-informative sequencing reads, betaine carryover inhibits cluster generation chemistry, and thermostable polymerase coats flow cell surfaces, reducing cluster density and data yield.
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<h2>What you will find</h2>
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<ul>
<li>Magbio HighPrep&trade; PCR: A highly flexible, bead-based reagent that simplifies post-PCR cleanup and dual-sided size selection, fitting seamlessly into your high-throughput automated platforms.</li>
<li>HighPrep&trade; PCR PB Kit: Specifically optimized for the rigorous demands of Pacific Biosciences (PacBio) workflows, this kit ensures you recover the long-read fragments your research depends on.</li>
<li>Selective Contaminant Depletion: Our buffers are engineered to remove salts and polymerases without the stress of centrifugation, delivering transfection-grade purity in every sample.</li>
</ul>
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<h2>How to Choose a DNA/PCR Sequencing Cleanup Reagent</h2>
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Bead Ratio for Target Amplicon Size
The bead-to-sample ratio determines the minimum fragment size retained. At 0.8x: retains &gt;=300 bp; removes primers and adapter dimers; best for amplicons &gt;=300 bp (16S V3-V4, ITS2). At 0.9x: retains &gt;=200 bp; removes primers and adapter dimers; standard for indexed library amplicons. At 1.0x: retains &gt;=150 bp; removes primers; useful for short-insert libraries (100-200 bp). At 1.8x: retains &gt;=100 bp; maximum primer removal; over-cleaning for library amplicons. Always calibrate the bead ratio using a test library at your target amplicon size before processing study samples; empirical calibration is required because bead lot performance and PEG concentrations vary.
Double-Side SPRI After PCR
For amplicon libraries where the PCR product range is wide (multiple bands) or where large amplification artifacts must be removed alongside primers, double-sided SPRI after PCR selects the target amplicon precisely: the first step removes amplification artifacts above the target size; the second step retains the target amplicon and discards primers and primer dimers.
Bead-Based vs. Spin Column After PCR
AMPure XP beads are preferred for high-throughput 96-well plate PCR cleanup in amplicon sequencing workflows where 96-384 individual PCR amplicons must be cleaned before pooling. Spin columns (Zymo DNA Clean &amp; Concentrator-5) are used for small-batch amplicon cleanup when concentrated eluate in 6-30 &micro;l is needed before capillary electrophoresis or other downstream analysis.
Betaine and DMSO Removal
If your PCR protocol includes betaine (1-2 M) or DMSO (1-5%), confirm complete removal by checking that the post-cleanup DNA solution is free of unusual viscosity (indicating residual betaine). At the standard bead ratio, betaine and DMSO are completely removed during the 2x 80% ethanol wash steps. If betaine or DMSO carryover is suspected (reduced sequencing cluster density), add 200 &micro;l ethanol wash before elution.
Amplicon Sequencing Pool Cleanup
After individually cleaning and quantifying each amplicon library by Qubit HS, pool at equimolar ratios before the final SPRI cleanup of the pool. Final pool cleanup at 0.9x removes any residual primer from individual library cleanup steps and normalizes the final pool for sequencing loading.
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<h2>Specifications Context</h2>
HighPrep&trade; PCR uses SPRI magnetic bead technology for post-PCR cleanup and DNA size selection. Adjustable bead-to-sample ratios enable efficient removal of primers, primer dimers, adapter dimers, nucleotides, enzymes, and buffer components while selectively retaining target DNA fragments. Standard ratios support PCR product cleanup, while dual-sided selections provide precise library size distribution for NGS workflows. HighPrep&trade; PCR PB Kit is optimized for PacBio sequencing, maximizing recovery of long DNA fragments while depleting smaller contaminants. The centrifugation-free workflow supports both manual and automated processing and is compatible with Illumina, ONT, and PacBio library preparation.
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Ready to refine your library? The MBP team is here to help&mdash;<a href="https://mbpinc.net/contact-us">contact us</a> today for a personalized quote on our PCR size selection reagents.

Magbio HighPrep PCR

HighPrep PCR by MagBio Genomics is a paramagnetic bead reagent for post-PCR cleanup and NGS-ready DNA size selection, retaining fragments ≥100 bp at 1.8× ratio, with >70% DNA recovery, ≥15 µL elution, 18-month shelf life at 2–8°C, and KingFisher Flex automation compatibility.

Main functions

Starting amount

RNA recovery

Instrument

RNA Purity

HighPrep PCR (1 mL)

HighPrep PCR (5 mL)

HighPrep PCR (50 mL)

HighPrep PCR (250 mL)

HighPrep PCR (500 mL)

Mag Beads

<h2>What Are Magnetic Bead HMW DNA Extraction Kits?</h2>
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A magnetic bead HMW DNA extraction kit uses Solid Phase Reversible Immobilization (SPRI)-type magnetic beads to bind genomic DNA released by gentle lysis, with a magnetic separator handling wash and elution steps in place of centrifugation, columns, or vacuum manifolds, producing fragment sizes in the 50-150 kb range depending on how beads are resuspended during elution. Related entities include PacBio Nanobind-type bead chemistry, KingFisher-compatible automated magnetic particle processors, A260/280 and A260/230 purity thresholds above 1.8, and downstream long-read sequencing library preparation for PacBio and Oxford Nanopore platforms. Choose magnetic bead HMW kits when fragment sizes in the 50-150 kb range meet your long-read sequencing needs, and you want to avoid centrifugation-based shearing.
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<h2>What you will find:</h2>
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<ul>
<li>Low-shear high molecular weight DNA isolation solutions using advanced paramagnetic bead technology, including the Magbio HighPrep HMW DNA Kit.</li>
<li>High-throughput magnetic bead-based extraction systems for simultaneous recovery of intact genomic DNA, including the Quick-DNA&trade; HMW Kit.</li>
<li>Workflow-friendly HMW DNA purification kits designed to preserve long DNA fragments for long-read sequencing applications.</li>
<li>Solutions compatible with manual and automated sample processing for efficient genomic DNA recovery.</li>
<li>HMW DNA extraction products suitable for genome assembly, structural variant analysis, and other advanced genomics workflows.</li>
</ul>
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<h2>How to Choose a Magnetic Bead HMW DNA Kit</h2>
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Bead Resuspension Method and Fragment Size Tradeoff
Fragment size from magnetic bead HMW kits depends on how beads are resuspended after washing: gentle tube tapping typically yields fragments in the 50-150 kb range, while vortexing produces somewhat smaller fragments (around 40-100 kb) but may improve recovery consistency. If your sequencing application benefits from the largest possible fragments (e.g., resolving large structural variants), prioritize tapping-based resuspension protocols even if yield is marginally lower.
Sample Input and Expected Yield
Magnetic bead HMW kits for blood, cells, and tissue typically specify inputs such as 200 ul of fresh/frozen whole blood, 1 million cells, or up to 8 mg of tissue, with a minimum yield around 3 ug of HMW gDNA&mdash;matching the input requirements of PacBio library preparation (around 1 ug above 30 kb) and Oxford Nanopore ligation kits (100 ng to 1.5 ug). Confirm your sample type matches a documented protocol within the kit family rather than assuming a single universal protocol.
No Centrifuge, Column, or Vacuum Required
Unlike silica spin-column or 96-well plate HMW approaches, magnetic bead HMW kits eliminate centrifugation, columns, and vacuum manifolds entirely, relying only on a magnetic separator for all wash and elution steps. This simplifies equipment requirements for labs without access to specialized centrifuge rotors, though a magnetic stand or automated magnetic particle processor is still required.
Purity Ratios and RNA Removal
A260/280 and A260/230 ratios greater than 1.8 are generally preferred for HMW DNA from magnetic bead kits, with near-complete RNA removal reported as a feature of bead-based HMW chemistry. Ratios below this threshold can indicate protein or salt contamination requiring troubleshooting before proceeding to expensive long-read library preparation.
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<h2>Specifications Context</h2>
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The defining specifications for magnetic bead HMW DNA extraction are the fragment size achievable via the bead resuspension method chosen, sample-specific input requirements relative to the kit's documented minimum yield, and purity ratios above 1.8 for both A260/280 and A260/230. A kit yielding around 3 ug of DNA in the 50-150 kb range from 200 ul whole blood, 1 million cells, or up to 8 mg tissue meets standard PacBio and Nanopore library preparation inputs without centrifugation.&nbsp;
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<section class="mbp-contact-cta">
MBP's specialist team can help match kit chemistry, format, and throughput to your sample type and downstream application.&nbsp;<a href="https://mbpinc.net/contact-us">Contact the MBP team</a> for personalized guidance.
</section>

Magbio HighPrep HMW DNA Kit

HighPrep HMW DNA Kit by MagBio Genomics is a magnetic bead-based system that isolates high molecular weight DNA (50–300+ kb) with A260/A280 and A260/A230 &gt;1.7 from blood, tissue, cells, and bacteria — yielding ≥10 µg from 10 mg tissue — for long-read sequencing, nanopore, microarray, and genotyping applications.

Starting Material (Diverse Sample Types)

Process Method

Purification Method

Size Range

Purity

Yield

Automated Extraction on Kingfi sher™ Flex

Manual Extraction

Downstream Applications

HighPrep HMW DNA Kit (5 preps)

HighPrep HMW DNA Kit (96 preps)

HighPrep HMW DNA Kit (984 preps)

MagBead

<h2>What Are Magnetic Bead Plasmid DNA Extraction Kits?</h2>
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Magnetic bead plasmid DNA kits use superparamagnetic nanoparticles, typically silica-coated or anion-exchange-functionalized, suspended in optimized binding buffers to capture plasmid DNA from bacterial lysate. After alkaline lysis of E. coli culture (0.5-5 mL per reaction), the beads bind DNA; an external magnetic field then immobilizes the beads so supernatant, RNA, and proteins are washed away without centrifugation. The purified DNA is eluted in water or low-salt buffer and is ready for downstream use. Throughput scales from single-tube manual processing to 96-well plate automation on KingFisher Duo, MagnetaPure 32, or ASSIST PLUS liquid handlers. Choose magnetic bead kits when your lab runs plasmid minipreps at scale (24+ samples/run) or when centrifuge-free automation is required.
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<h2>What you will find:</h2>
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<ul>
<li>Magbio HighPrep Plasmid DNA Plus Kit for rapid, automated plasmid purification using high-binding paramagnetic particle technology.</li>
<li>Zyppy&trade;-96 Plasmid MagPrep Kit for scalable magnetic separation of high-purity vector constructs.</li>
<li>Zyppy-96 Plasmid MagBead Prep Kit for faster, column-free plasmid isolation.</li>
<li>Magnetic bead-based plasmid purification solutions compatible with high-throughput laboratory workflows.</li>
<li>Column-free plasmid DNA extraction systems that simplify processing and reduce hands-on time.</li>
<li>Products designed for efficient recovery of clean plasmid DNA for cloning, sequencing, and transfection applications.</li>
<li>Automation-friendly plasmid preparation kits suitable for 96-well and large-batch sample processing.</li>
</ul>
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<h2>How to Choose Magnetic Bead Plasmid Kits</h2>
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Automation Platform Compatibility
Bead-based kits are designed for specific magnetic rod or liquid-handler platforms. Confirm compatibility before ordering: NucleoMag Plasmid kits are validated for MagnetaPure and IsoPure Mini; MagJET kits are optimized for the KingFisher series; MagMAX Pro HT kits are designed for high-throughput centrifuge-free workflows. Using a kit outside its validated platform may require buffer volume adjustments and is not supported by the manufacturer.
Bead Type and DNA Binding Capacity
Silica-coated magnetic beads use chaotropic binding chemistry similar to spin columns; anion-exchange-functionalized beads offer higher selectivity for covalently closed circular (CCC/supercoiled) plasmid. Standard miniprep bead kits bind 5-20 ug from 1.5 mL culture; scaled protocols for 5 mL can yield up to 50 ug. Check binding capacity against your expected yield to avoid saturation.
High-Copy vs Low-Copy Plasmid
Most bead-based kits are validated for standard high-copy plasmids (pUC, pBR322 derivatives). Low-copy constructs such as fosmids or BACs require longer lysis times and may need protocol modifications; check the kit's validated plasmid types before purchasing for non-standard vectors.
Elution Volume and Concentration
Bead protocols typically elute in 50-100 uL. If downstream transfection requires high DNA concentration, choose kits that support low-volume elution (50 uL) or perform a secondary concentration step. Check that the eluate is compatible with your downstream assay buffer conditions.
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<h2>Specifications Context</h2>
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Plasmid DNA purity from bead-based kits is evaluated by the A260/A280 ratio (target 1.8-2.0) and the A260/A230 ratio (&gt;1.8). Supercoiling percentage (measured by agarose gel densitometry) should exceed 80% for standard transfection applications. Automated 96-well bead workflows complete plasmid isolation in 30-60 minutes for a full plate, compared to 1-2 hours for centrifuge-based spin-column processing of the same number of samples. All kits are Research Use Only (RUO).
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<section class="mbp-contact-cta"></section>
MBP's specialist team can help match kit chemistry, format, and throughput to your sample type and downstream application.&nbsp;<a href="https://mbpinc.net/contact-us">Contact the MBP team</a> for personalized guidance.

Magbio HighPrep Plasmid DNA Plus Kit

The HighPrep Plasmid DNA Plus Kit by MagBio Genomics purifies plasmid DNA from 1.0–1.5 mL E. coli cultures using magnetic bead technology. High-copy yield ~10–15 µg; 50 µL elution volume; 96 preps completed in under 60 minutes. Supports plasmids, BACs, PACs, cosmids, and fosmids. Compatible with KingFisher™ Flex automation and downstream PCR, sequencing, NGS, and transfection.