Nucleic Acid Cleanup Kits

Sanger DTR

<h2 data-section-id="vnaphp" data-start="0" data-end="28">What are Sanger DTR kits?</h2>
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Sanger DTR (Dye Terminator Removal) kits are post-sequencing cleanup products used to remove excess fluorescent dye terminators, unincorporated nucleotides, salts, and short primer fragments from completed cycle sequencing reactions before capillary electrophoresis. During Sanger sequencing, a large excess of fluorescently labeled dideoxynucleotide terminators (ddNTPs) is required to generate DNA fragments of varying lengths. After the reaction, most of these labeled terminators remain unused.
If these contaminants are not removed, they produce strong fluorescent signals known as dye blobs at the beginning of the electropherogram. Dye blobs can obscure the first portion of the sequence, reduce base-calling accuracy, and increase sequencing failure rates. DTR cleanup kits solve this problem by separating the desired labeled DNA fragments from smaller unwanted molecules prior to loading the sample onto a sequencing instrument.
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<h2 dir="ltr">What you will find:</h2>
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HighPrep DTR Magnetic Reagents: A robust paramagnetic bead-based system designed for the rapid removal of BigDye&trade; terminators, primers, and non-targeted amplicons to ensure reliable, high-resolution DNA readings.
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Scalable Purification Formats: Flexible volume options ranging from 1mL to 500mL, optimized for both manual workflows and seamless integration into fully automated liquid handling workstations for high-throughput sequencing labs.
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</ul>
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<h2 data-section-id="109ahyv" data-start="1462" data-end="1499">How to choose a Sanger DTR product</h2>
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Cleanup chemistry
Gel-filtration cleanup remains one of the most commonly used approaches for Sanger sequencing purification. Products such as Performa DTR remove excess dye terminators, salts, nucleotides, and short primers without introducing additional chemicals that may affect downstream analysis. Optima DTR products use proprietary resin technology to achieve similar purification performance while offering additional format flexibility.
Processing format
Single-sample spin cartridges are suitable for laboratories performing occasional sequencing runs or troubleshooting individual samples.
Eight-well strip formats provide a practical solution for laboratories processing small to medium batches without requiring a full 96-well workflow.
Ninety-six-well plate formats are the preferred option for sequencing cores and high-throughput facilities because they allow simultaneous purification of large sample sets and direct transfer into sequencing plates.
Throughput requirements
Laboratories running a few sequencing reactions per week often prioritize convenience and flexibility. High-volume sequencing facilities generally select plate-based DTR systems that minimize handling time and support automated workflows.
Alternative cleanup methods
Ethanol precipitation is a low-cost cleanup method but requires multiple reagent additions, centrifugation steps, and careful sample handling. While effective, it is more labor-intensive and can introduce variability.
Bead-based systems such as BigDye XTerminator offer rapid purification with minimal hands-on time. These systems are often selected when workflow speed is more important than maximizing read length.
Read quality and read length
For laboratories focused on obtaining the longest possible sequence reads and minimizing retests, gel-filtration DTR methods remain the preferred choice. These systems consistently produce high-quality sequence traces with strong early-read performance and reduced dye contamination.
Chemistry compatibility
Most DTR products are compatible with multiple dye-terminator sequencing chemistries, including BigDye Terminator v1.1, BigDye Terminator v3.1, DYEnamic ET, WellRED terminators, and related sequencing reagents. This broad compatibility makes them suitable for both current and legacy sequencing workflows.
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<h2 data-section-id="1fljvas" data-start="4992" data-end="5017">Specifications context</h2>
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Modern Sanger DTR products are designed for compatibility with major capillary electrophoresis platforms and sequencing chemistries. Gel-filtration systems typically use hydrated matrices that require no additional preservatives or buffer exchanges and allow purified sequencing products to be loaded directly into sequencing plates after centrifugation.
As of 2026, gel-filtration DTR cleanup in 96-well plate format remains the most widely adopted purification method in academic, clinical, and commercial Sanger sequencing facilities because of its strong performance in read length, sequence quality, and retest reduction. Bead-based purification systems continue to gain adoption in laboratories where rapid turnaround and high-throughput processing are primary workflow priorities.
Optimize your sequencing cleanup&mdash;&nbsp;<a href="https://mbpinc.net/contact-us" style="color: #236fa1; text-decoration: underline;">contact the MBP team</a> today for a quote on our professional HighPrep DTR solutions.

<h2>What are Sanger sequencing reagents?</h2>
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Sanger sequencing reagents are the chemical components used in chain-termination DNA sequencing, the method developed by Frederick Sanger in which a DNA polymerase extends a primer along a single-stranded template and is terminated at random positions by the incorporation of fluorescently labeled dideoxynucleotide terminators (ddNTPs) that lack the 3'-OH group needed for further elongation. The reaction produces a nested set of labeled fragments that, when resolved by capillary electrophoresis, gives the DNA sequence. Key reagents include dye-terminator mastermix (BigDye v3.1 or equivalent), template DNA, sequencing primer, and cleanup reagents.
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<h2 dir="ltr">What you will discover:</h2>
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<li dir="ltr" aria-level="1">
<a href="https://mbpinc.net/reagents/sequencing/sanger-sequencing/sanger-dtr" title="Sanger DTR (Dye Terminator Removal):">Sanger DTR (Dye Terminator Removal):</a> Effective purification systems such as Magbio HighPrep DTR employs paramagnetic bead technology to effectively eliminate surplus terminators and salts, guaranteeing clear baselines and extended read lengths.
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</ul>
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<a href="https://mbpinc.net/reagents/sequencing/sanger-sequencing/cycle-sequencing-kit" title="Cycle Sequencing Kits:">Cycle Sequencing Kits:</a> Durable formulations like the SmartDye Terminator 3.1, designed to deliver consistent peak heights and excellent processivity across various DNA templates, including plasmids and PCR products.
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<h2>How to use Sanger sequencing reagents</h2>
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Clean up PCR products before sequencing reactions
Residual PCR primers and unincorporated dNTPs can interfere with the sequencing reaction by competing with the sequencing primer or being incorporated by the polymerase. ExoSAP enzymatic cleanup or column-based purification removes these contaminants before the sequencing reaction is set up.
Set up sequencing reactions with the minimum recommended cycle number
Sanger sequencing cycle sequencing reactions typically require 25&ndash;30 thermocycler cycles, fewer than a standard PCR, since only one primer is used and each cycle synthesizes a new set of terminated fragments rather than doubling the product. Using too many cycles can deplete the dye-terminator terminators and reduce signal quality.
Clean up the completed sequencing reaction before capillary electrophoresis
Unincorporated dye-terminator ddNTPs must be removed before capillary electrophoresis injection, since free fluorescent ddNTPs obscure the first 25&ndash;50 bases of the read. Column purification, ethanol-EDTA precipitation, or size-exclusion spin columns are standard cleanup approaches.
Use 10&ndash;50 ng of purified PCR product as template
Too little template produces weak, noisy signal; too much produces dye blobs from terminator over-incorporation. Typically 10&ndash;50 ng of PCR product or 200&ndash;500 ng of plasmid DNA is appropriate for a single sequencing reaction.
Position the sequencing primer at least 100 bp from the target region
Sanger reads have lower quality in the first 50&ndash;100 bases, with the high-quality window running from approximately base 100 to 900 from the primer. Placing the sequencing primer so that the target region falls within this window gives the best data quality.
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<h2>Specifications context</h2>
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BigDye Terminator v3.1 has been the dominant commercial dye-terminator chemistry since its introduction, incorporating fluorescently labeled ddNTPs with distinct emission wavelengths for reads of consistently high quality up to approximately 1000 bp. As of 2026, Sanger sequencing remains the method of choice for mutation confirmation, plasmid verification, and colony screening, because its per-sample cost and turnaround for single loci is substantially more practical than NGS for these routine targeted applications.
Ensure the precision of your sequence&mdash;<a href="https://mbpinc.net/contact-us" title="reach out to the MBP team">reach out to the MBP team</a> now for a quote on our expert Sanger sequencing services.

Sanger Sequencing

HighPrep™ DTR - Protocol

Flyer

HighPrep™ DTR - MSDS

MSDS

HighPrep DTR - DX IFU

Magbio HighPrep DTR

HighPrep DTR — DT-70000 by MagBio Genomics — is a magnetic bead reagent for Sanger sequencing reaction cleanup that removes dye-labeled terminators and salts from ABI and MegaBACE sequencing reactions in 96-well and 384-well formats. The Bind-Wash-Elute protocol uses 10 µL per sample in 96-well mode and 5 µL per sample in 384-well mode, with elution in low-salt buffer or nuclease-free water suitable for direct injection on capillary electrophoresis systems. Available from MBP in 1 mL, 5 mL, 50 mL, 250 mL, and 500 mL sizes — place orders via <a href="https://www.mbpinc.net/quickorder">Quick Order</a> or contact <a href="mailto:customerservice@mbpinc.net">customerservice@mbpinc.net</a>.

Features

Main functions

Starting material (Sample matrix)

Starting amount

Process method

Purification method

Application

Elution Volume

Manufacturer

HighPrep DTR (1 ml)

HighPrep DTR (5 ml)

HighPrep DTR (50 mL)

HighPrep DTR (250 mL)

HighPrep DTR (500 mL)

RNA/c-DNA

<h2>What are RNA/cDNA Sequencing Cleanup Reagents?</h2>
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RNA/cDNA sequencing cleanup reagents purify RNA and complementary DNA during RNA sequencing library preparation workflows by removing enzymes, buffer salts, unincorporated nucleotides, short nucleic acid fragments, and other reaction contaminants that can interfere with downstream processing and sequencing. These reagents are commonly used after RNA processing, cDNA synthesis, library construction, amplification, and other enzymatic steps to improve nucleic acid purity and workflow performance.
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<h2>What you will find:</h2>
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<ul>
<li>Magbio HighPrep&trade; RNA Elite: A high-performance magnetic reagent optimized for the selective recovery of RNA and cDNA from complex enzymatic reactions.</li>
<li>RNA Purification Magnetic Beads: High-affinity matrices engineered for rapid, centrifugation-free isolation, delivering reproducibility-tested yields in automated workflows.</li>
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<h2>How to Choose an RNA/cDNA Sequencing Cleanup Reagent</h2>
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RNA vs. cDNA Workflows
Select a cleanup reagent compatible with the nucleic acid being processed. RNA-focused cleanup reagents are designed for purification and recovery of RNA products, while many magnetic bead-based systems can also be used for cDNA cleanup, concentration, and size-selection workflows.
Cleanup vs. Size Selection
Cleanup workflows remove reaction contaminants such as enzymes, salts, and unincorporated nucleotides. Size-selection workflows enrich RNA or cDNA fragments within a desired size range when required by the downstream library preparation protocol.
Throughput Requirements
Magnetic bead-based cleanup systems support both low-throughput manual processing and higher-throughput workflows that benefit from automation and 96-well format compatibility.
Automation Compatibility
Magnetic bead-based purification eliminates centrifugation during the cleanup process and can be integrated into automated liquid-handling and magnetic separation workflows.
Quality Assessment
Following cleanup, RNA and cDNA quality are commonly assessed using fluorometric quantification methods and fragment analysis platforms to verify concentration, integrity, and size distribution prior to sequencing.
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<h2>Specifications Context</h2>
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RNA/cDNA sequencing cleanup reagents provide purification of RNA and cDNA products generated during library preparation and other enzymatic workflows. Magnetic bead-based systems enable cleanup, concentration, and size selection without organic extraction or vacuum filtration and are compatible with both manual and automated processing.&nbsp;MagBio HighPrep RNA Elite supports the cleanup and recovery of RNA and cDNA products used in transcriptomics and sequencing workflows, while RNA Purification Magnetic Beads provide rapid magnetic bead-based purification and recovery of RNA samples without centrifugation.&nbsp;These reagents are widely used in RNA sequencing, transcriptomics, gene expression analysis, and related molecular biology workflows where contaminant removal, nucleic acid recovery, and workflow scalability are important for library quality and downstream sequencing performance.
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Ensure the fidelity of your molecular data&mdash;<a href="https://mbpinc.net/contact-us">contact the MBP team</a> today for a quote on our advanced RNA/cDNA cleanup solutions.

HighPrep RNA Elite - MSDS

HighPrep RNA Elite - DX IFU

HighPrep RNA Elite

Magbio HighPrep RNA Elite

RC-90000 by MagBio Genomics is HighPrep RNA Elite, a paramagnetic bead reagent for manual and automated purification of miRNA, siRNA, aRNA, total RNA, and single-stranded cDNA. Compatible with 96-well and 384-well formats; no centrifugation required. Stable 14 months at 4–8°C.

Storage

Stability

No. of reactions in 96 well format

No.of reactions In 384 Well Format

HighPrep RNA Elite (1 mL)

HighPrep RNA Elite (5 mL)

HighPrep RNA Elite (50 mL)

HighPrep RNA Elite (250 mL)

HighPrep RNA Elite (500 mL)

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.