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.

<h2>What are DNA Sequencing Cleanup Reagents?</h2>
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DNA sequencing cleanup reagents purify double-stranded DNA at every enzymatic step in genomic library preparation workflows - after end-repair/A-tailing, after adapter ligation (to remove adapter dimers), and after PCR amplification of indexed libraries - removing primers, dNTPs, adapter dimers, buffer salts, and enzymes that inhibit downstream sequencing steps. Adapter dimer removal is the most critical cleanup step: dimers formed during ligation efficiently cluster on Illumina flow cells and produce non-informative reads that reduce effective genome coverage and waste sequencing cost. The Zymo ZR DNA Sequencing Clean-up Kit (D4050) and ZR-96 DNA Sequencing Clean-up Kit (D4052) use Zymo-Spin silica-membrane column technology to remove dye terminators, unincorporated dNTPs, salts, enzymes, and short oligonucleotides from sequencing reactions in under 10 minutes, eluting purified DNA ready for capillary electrophoresis or downstream NGS steps. Perform cleanup after every adapter ligation step in Illumina library preparation - skipping this step and proceeding to amplification will amplify adapter dimers exponentially, and the resulting library cannot be rescued by cleanup after PCR.
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<h2 dir="ltr">What you will find: </h2>
<ul>
<li dir="ltr" aria-level="1">
ZR DNA Sequencing Clean-up Kit&trade;: A rapid-velocity spin-column system designed to isolate ultra-pure templates without the risk of ethanol carryover or inhibitory salt precipitation.
</li>
<li dir="ltr" aria-level="1">
ZR-96 DNA Sequencing Clean-up Kit: A high-throughput 96-well platform optimized for automated liquid handlers, delivering reproducibility-tested results across massive genomic cohorts.
</li>
</ul>
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<h2>How to Choose a DNA Sequencing Cleanup Reagent</h2>
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Individual Tube vs. 96-Well Plate Format
The Zymo ZR DNA Sequencing Clean-up Kit (D4050) processes individual reactions in a standard microcentrifuge - the right format for low-volume sequencing labs running 1-24 reactions per session. The ZR-96 DNA Sequencing Clean-up Kit (D4052) processes 96 samples simultaneously using a 96-well spin plate with a centrifuge, reducing per-sample hands-on time for high-throughput sequencing workflows. Choose the 96-well format when running 48 or more sequencing reactions per session.
Dye Terminator Removal
Both ZR kits are validated for removal of BigDye Terminator v3.1 and equivalent fluorescent dideoxy terminator chemistries - the most common source of dye blob artefacts in Sanger electropherograms. The silica-membrane column binds sequencing extension products while unincorporated terminators, dNTPs, salts, and short oligonucleotides pass through in the wash steps, producing clean sequencing product ready for capillary injection.
Elution Volume
For Sanger sequencing, elute in the minimum recommended volume (6-10 ul) to maximize sequencing signal per injection. For NGS post-ligation cleanup where DNA concentration must be quantified by Qubit HS before library pooling, elute in 20-25 ul to ensure sufficient volume for quantification and downstream steps. Avoid over-eluting in large volumes that dilute the cleaned product below Qubit HS detection limits.
Post-Cleanup QC
For Sanger cleanup: confirm a clean electropherogram from base 30 onward with no dye blob artefacts and read length exceeding 700-800 bases. For NGS library cleanup: confirm with Bioanalyzer or TapeStation that the correct peak insert size is present, no adapter dimer peak is visible at 120-130 bp, and library concentration is &gt;=1 ng/ul for Qubit HS detection. A visible adapter dimer peak after cleanup signals insufficient wash steps, an overloaded column, or excessively high adapter concentration during ligation.
Throughput Scaling
For programs processing more than 96 reactions per day, run multiple ZR-96 plates sequentially on the same centrifuge. The ZR spin-column formats are optimized for manual and semi-automated workflows.
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<h2>Specifications Context</h2>
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The Zymo ZR DNA Sequencing Clean-up Kit (D4050) and ZR-96 DNA Sequencing Clean-up Kit (D4052) use Zymo-Spin column technology to remove dye terminators, dNTPs, salts, enzymes, and unincorporated primers from sequencing reactions, delivering cleaned product ready for capillary electrophoresis or NGS loading. Both kits are validated for BigDye Terminator v3.1 and produce clean electropherograms with read lengths exceeding 800 bases when input cycle-sequencing reactions are prepared under standard conditions. Column-based sequencing cleanup is the standard method for individual and plate-scale Sanger sequencing verification, clone confirmation, and plasmid sequencing at academic molecular biology laboratories at institutions including Howard Hughes Medical Institute, Vanderbilt University, and MD Anderson Cancer Center.
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Purify your pathway to discovery&mdash;<a href="https://mbpinc.net/contact-us">reach out to our technical team</a> today to secure a quote for your DNA cleanup reagents.

<h2>What are Sequencing Cleanup and Size Selection Reagents?</h2>
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Sequencing cleanup and size selection reagents purify nucleic acid libraries and reaction intermediates throughout next-generation sequencing (NGS) workflows by removing enzymes, buffer salts, primers, adapter dimers, and unincorporated nucleotides. These reagents are used after enzymatic steps such as end repair, adapter ligation, PCR amplification, cDNA synthesis, and other library preparation procedures to improve library quality and sequencing performance. Size selection workflows can also enrich fragments within a desired size range for downstream sequencing&nbsp;applications.
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<h2>&nbsp;What you will find: </h2>
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<ul>
<li dir="ltr" role="presentation"><a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-cleanup-kits/sequencing-clean-up-and-size-selection/dna">DNA Cleanup:</a> Specialized kits like the ZR DNA Sequencing Clean-up Kit&trade; are designed to remove fluorescent terminators and salts for extended read lengths. </li>
<li dir="ltr" role="presentation"><a href="http://mbpinc.net/reagents/molecular-biology/nucleic-acid-cleanup-kits/sequencing-clean-up-and-size-selection/dna/pcr">DNA/PCR Size Selection:</a> HighPrep&trade; PCR systems offering tunable paramagnetic bead ratios for precise fragment selection and consistent cluster generation. </li>
<li dir="ltr" role="presentation"><a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-cleanup-kits/sequencing-clean-up-and-size-selection/rna/c-dna">RNA/c-DNA Purification:</a> Advanced magnetic bead solutions, including HighPrep&trade; RNA Elite, engineered for rapid recovery while maintaining isoform specificity for transcriptome profiling. </li>
<li dir="ltr" role="presentation"><a href="http://mbpinc.net/reagents/molecular-biology/nucleic-acid-cleanup-kits/sequencing-clean-up-and-size-selection/sanger-dtr">Sanger DTR:</a> A laboratory cleanup technique used to remove unincorporated dye terminators and impurities from DNA samples before sequencing.</li>
</ul>
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<h2>How to Choose a Sequencing Cleanup and Size Selection Reagent</h2>
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Nucleic Acid Type: DNA vs. RNA/cDNA
Select cleanup reagents based on the nucleic acid being processed. DNA-focused cleanup reagents are commonly used for genomic DNA libraries, PCR products, and sequencing reactions, while RNA-specific magnetic bead systems are designed for purification and recovery of RNA and cDNA products generated during transcriptomics and RNA-seq workflows.
Cleanup vs. Size Selection
Cleanup workflows remove reaction contaminants such as enzymes, primers, salts, and unincorporated nucleotides, whereas size selection workflows enrich DNA or RNA fragments within a desired size range. Magnetic bead-based reagents can be used for both cleanup and size-selection applications, depending on the protocol and bead-to-sample ratio employed.
Throughput Requirements
Spin-column formats are well-suited for low- to moderate-throughput workflows, while 96-well plate and magnetic bead formats support higher-throughput processing and integration into automated laboratory workflows.
Automation Compatibility
Magnetic bead-based cleanup reagents are commonly used in automated sequencing library preparation workflows because they eliminate centrifugation steps and can be integrated with liquid handling platforms and magnetic separation devices.
Library Quality Assessment
Following cleanup or size selection, library quality is commonly evaluated using capillary electrophoresis systems such as Agilent Bioanalyzer, Agilent TapeStation, or similar fragment analysis platforms to confirm fragment size distribution and detect residual adapter dimers or other unwanted products.
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<h2>Specifications Context</h2>
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Sequencing cleanup and size selection reagents remove enzymes, primers, adapter dimers, unincorporated nucleotides, salts, and other contaminants from DNA, RNA, cDNA, PCR amplicons, and NGS library intermediates. Available formats include silica-membrane spin columns, 96-well plates, and magnetic bead-based purification systems for both manual and automated workflows. Zymo Research ZR DNA Sequencing Clean-up Kits and ZR-96 DNA Sequencing Clean-up Kits provide purification of DNA sequencing reactions and library intermediates, while MagBio HighPrep PCR and HighPrep RNA Elite reagents support cleanup, concentration, and size selection of DNA, RNA, cDNA, and PCR products. RNA Purification Magnetic Beads provide recovery and purification of RNA products for transcriptomics and RNA sequencing workflows. These reagents are widely used in NGS, amplicon sequencing, metagenomics, transcriptomics, and gene expression studies where contaminant removal, reproducible recovery, and workflow scalability are important for library quality and sequencing performance. MBP supplies sequencing cleanup and size selection reagents to registered vendors at Howard Hughes Medical Institute, Vanderbilt University, and MD Anderson Cancer Center.
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Optimize library quality and sequencing workflow performance&mdash;request a quote by contacting <a href="mailto:customerservice@mbpinc.net">customerservice@mbpinc.net</a>.

Sequencing Clean up and Size Selection

<h2>What Are Sequencing Reagents?</h2>
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Sequencing reagents are the enzymes, buffers, clean-up reagents, and library preparation components used to prepare nucleic acids for DNA and RNA sequencing workflows. These products support both Sanger sequencing and next-generation sequencing (NGS) applications by enabling sample preparation, library construction, sequencing reaction setup, and post-reaction clean-up. Sanger sequencing remains widely used for plasmid verification, clone confirmation, PCR product analysis, and targeted sequencing, while NGS enables high-throughput analysis of genomes, transcriptomes, and other complex nucleic acid samples. Choose Sanger sequencing reagents for low-throughput sequence verification workflows and NGS library preparation reagents for large-scale sequencing projects requiring parallel analysis of multiple samples or targets.
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<h2 dir="ltr">What you will find:</h2>
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<ul>
<li dir="ltr" aria-level="1">
<a href="https://mbpinc.net/reagents/sequencing/next-generation-sequencing-ngs" title="Next-generation Sequencing (NGS)">Next-generation Sequencing (NGS):</a> kits include size selection reagents and library preparation to optimize acquisition of high-throughput genomic data&nbsp;
</li>
<li dir="ltr" aria-level="1">
<a href="https://mbpinc.net/reagents/sequencing/sanger-sequencing" title="Sanger Sequencing">Sanger Sequencing:</a> high-purity clean-up reagents and dye terminators to ensure reliable electrophoresis screening.
</li>
</ul>
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<h2>How to Choose Sequencing Reagents</h2>
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Sanger vs. NGS
Sanger sequencing is commonly used for plasmid verification, PCR product sequencing, clone screening, and sequence confirmation. NGS enables simultaneous analysis of many targets or samples and is the preferred approach for high-throughput genomic and transcriptomic studies. The appropriate workflow depends on sample volume, throughput requirements, and research objectives.
Sanger Sequencing Clean-Up Reagents
Sequencing reaction clean-up is an important step before capillary electrophoresis. Products such as Magbio HighPrep DTR are designed to remove excess dye terminators, primers, salts, and other reaction components that can interfere with sequencing quality. These reagents support efficient purification of sequencing reactions prior to downstream analysis.
NGS Library Preparation
NGS library preparation converts DNA or RNA samples into sequencing-ready libraries through a series of enzymatic processing and adapter incorporation steps. Library preparation requirements vary depending on the sequencing platform, input material, and experimental goals. Products such as the Zymo-Seq SwitchFree 3&prime; mRNA Library Kit support RNA sequencing workflows by enabling the preparation of 3&prime; mRNA sequencing libraries.
Sequencing-Grade Sample Preparation
High-quality nucleic acid input is critical for successful sequencing results. Accurate quantification, purity assessment, and sample normalization help improve sequencing performance and library preparation efficiency. Products such as the Magbio MagQuant Plus DNA Kit V2 support DNA quantification workflows used during sequencing sample preparation.
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<h2>Specifications Context</h2>
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The sequencing product category includes NGS library preparation kits, sequencing reaction clean-up reagents, and nucleic acid quantification products that support sequencing workflows from sample preparation through downstream analysis. Products in this category support essential sequencing preparation workflows, including DNA quantification with the Magbio MagQuant Plus DNA Kit V2, post-reaction dye-terminator removal with Magbio HighPrep DTR for Sanger sequencing, and 3&prime; mRNA library preparation with the Zymo-Seq SwitchFree 3&prime; mRNA Library Kit for next-generation sequencing applications. These reagents help streamline sample preparation, improve workflow consistency, and support high-quality sequencing results.
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Contact the <a href="https://mbpinc.net/contact-us">expert team at MBP</a> today and get optimized sequencing reagents for your lab.

Sequencing

<h2>What Is Next-Generation Sequencing?</h2>
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Next-generation sequencing (NGS), also called high-throughput sequencing or massively parallel sequencing, determines the nucleotide sequence of millions to billions of DNA or RNA fragments simultaneously in a single instrument run. Unlike Sanger sequencing, which reads one locus per reaction, NGS uses sequencing-by-synthesis (Illumina), nanopore translocation (ONT), or single-molecule real-time (SMRT) chemistry (PacBio) to sequence an entire genome, transcriptome, metagenome, or targeted panel in hours to days. Choose NGS reagents based on your sequencing application (DNA-seq vs. RNA-seq vs. amplicon), target platform (Illumina, ONT, or PacBio), sample type (fresh, FFPE, cfDNA, low-input), and throughput requirements.
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<h2 dir="ltr">What you will find out:</h2>
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<ul>
<li dir="ltr" aria-level="1">
<a href="https://mbpinc.net/reagents/sequencing/next-generation-sequencing-ngs/ngs-library-preparation-kits" title="NGS Library Preparation Kits:">NGS Library Preparation Kits:</a> Effective options like the Zymo-Seq SwitchFree series and MagQuant Plus DNA kits, tailored to streamline library production while improving molecular diversity and reducing manual effort.
</li>
<li dir="ltr" aria-level="1">
<a href="https://mbpinc.net/reagents/sequencing/next-generation-sequencing-ngs/rna-sequencing" title="RNA-sequencing:">RNA-sequencing:</a> Customized mRNA and total RNA library kits created for exact gene expression assessments, ensuring precise quantification of low-abundance transcripts with limited starting material.
</li>
<li dir="ltr" aria-level="1">
<a href="https://mbpinc.net/reagents/sequencing/next-generation-sequencing-ngs/dna-sequencing" title="DNA-sequencing:">DNA-sequencing:</a> Trustworthy genomic DNA extraction methods designed for high-yield retrieval and uniform coverage, providing a strong foundation for whole-genome sequencing (WGS) and targeted resequencing projects.
</li>
</ul>
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<h2>How to Choose NGS Library Prep Reagents</h2>
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Application type
DNA sequencing applications include whole-genome sequencing (WGS), whole-exome sequencing (WES), targeted gene panels, amplicon sequencing (16S/ITS for microbiome, custom amplicons), and epigenetic sequencing (WGBS, RRBS, ChIP-seq). RNA sequencing applications include mRNA-seq (poly-A enriched), total RNA-seq (rRNA depleted), small RNA-seq (miRNA, piRNA), and single-cell RNA-seq. Each application requires a distinct library prep chemistry and kit format.
Platform compatibility
Confirm library prep kit compatibility with the target sequencing platform before ordering. Illumina-compatible kits are the most common and generate short-read libraries with paired-end 150 bp reads on NovaSeq X, NextSeq 2000, or MiSeq instruments. ONT-compatible kits generate long-read libraries for MinION, GridION, or PromethION. PacBio HiFi kits generate ultra-accurate long reads on the Revio or Sequel IIe. Most Zymo Research NGS library prep kits are optimized for Illumina sequencing.
Sample type and input amount
Standard input amounts are 100 ng-1 microgram of gDNA for WGS, 1-100 ng for targeted panels, and 10-100 ng of total RNA for RNA-seq. Low-input kits support 1-100 pg of total RNA (single-cell or ultra-low input). FFPE-compatible kits use specialized fragmentation and repair chemistry to address formalin-induced crosslinks and DNA damage, accepting inputs as low as 10-50 ng of FFPE-extracted DNA. Confirm the minimum input requirement and the DV200 score threshold for FFPE RNA before selecting a kit.
Zymo Research NGS portfolio at MBP
Zymo Research is a key MBP brand with an NGS library prep portfolio spanning: Zymo-Seq RiboFree Total RNA Library Kit (probe-free rRNA depletion, any organism, 10 ng minimum RNA input, cited in 150+ peer-reviewed studies); Quick-16S Plus NGS Library Prep Kits (normalization-free, 30 minutes hands-on time for 96 samples, V1-V2 or V4 16S rRNA region); Zymo-Seq RRBS Library Kit (reduced representation bisulfite sequencing, as little as 2 hours hands-on time); and Zymo-Seq UDI Primer Sets (unique dual index barcodes for multiplexed sequencing). Zymo Research kits are cited extensively in published microbiome, transcriptomics, and epigenomics research.
Automation compatibility
High-throughput genomics cores and biobanks processing hundreds of samples per week benefit from automation-compatible library prep formats. Zymo Research Quick-16S Plus kits are 100% automation ready and require no normalization step between PCR and pooling. Assess liquid-handling robot compatibility (Hamilton, Beckman, Tecan, Agilent Bravo) with the kit vendor before scaling.
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<h2>Specifications Context</h2>
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NGS library quality is assessed by three metrics: concentration (Qubit fluorometry; target 2-10 nM for Illumina clustering), fragment size distribution (Bioanalyzer or TapeStation; target 300-500 bp insert for standard Illumina), and library complexity (assessed by PhiX spike-in error rate and percentage of duplicate reads). Adapter dimer contamination below 5% of total library molecules is recommended before sequencing; size selection with SPRI beads (such as AMPure XP, 0.8-1.0X bead ratio) removes dimers efficiently.&nbsp; PCR-free WGS library preparation is increasingly preferred for high-coverage sequencing to eliminate PCR amplification bias, particularly in GC-rich and AT-rich regions, and requires a minimum input of 200-500 ng of high-molecular-weight DNA (HMW gDNA).&nbsp;
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Boost your genomic knowledge&mdash;<a href="https://mbpinc.net/contact-us">contact the MBP team</a> today for a quote on our specialized NGS preparation services.

Next-generation Sequencing (NGS)

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 &ge;100 bp at 1.8&times; ratio, with &gt;70% DNA recovery, &ge;15 &micro;L elution, 18-month shelf life at 2&ndash;8&deg;C, and KingFisher Flex automation compatibility. Available in 1mL (AC-60001), 5mL (AC-60005), 50mL (AC-60050), 250mL (AC-60250), and 500mL (AC-60500).