Zymo Reagents

<h2>What are microbial and environmental DNA isolation kits?</h2>
&nbsp;
Microbial and environmental DNA isolation kits purify DNA from soil, sediment, freshwater, marine water, feces, and other complex environmental matrices using lysis and purification chemistry designed to remove humic acids, metal compounds, and other inhibitors that interfere with PCR and sequencing, supporting 16S/18S rRNA amplicon profiling and shotgun metagenomic sequencing. Related entities include "kitome" and "splashome" contamination controls, alpha diversity and microbial community composition analysis, and compatibility with both short-read (Illumina) and long-read (Oxford Nanopore) sequencing platforms. Choose a kit validated for your specific sample matrix (soil, sediment, water, or feces), since benchmarking studies consistently show kit performance varies by matrix rather than one kit being universally best.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" role="presentation">Spin-column fungal and bacterial kits for rapid DNA purification using rapid silica-membrane technology&nbsp;</li>
<li dir="ltr" role="presentation">Parallel extraction of soil, fecal, and environmental samples using high-throughput 96-well microplates&nbsp;</li>
<li dir="ltr" role="presentation">Automated&nbsp; purification of complex microbial and environmental specimens using Magnetic bead isolation systems</li>
<li dir="ltr" role="presentation">Scalable microprep and midiprep columns tailored for concentrated low-volume elution demands and diverse sample inputs</li>
</ul>
&nbsp;
<h2>How to choose a microbial and environmental DNA isolation kit</h2>
&nbsp;
Matrix-specific kit performance
Benchmarking studies comparing multiple commercial kits across sediment, water, soil, oyster gut microbiome, and mammalian feces have found that the best-performing kit varies by matrix - kits ranked highly for sediment did not necessarily perform best for water or host-associated samples. Rather than assuming a single "universal" kit, match your kit choice to published benchmarking results for your primary sample type where available.
Inhibitor removal for downstream PCR and sequencing
Environmental samples, especially sediments and soils, contain organic and metal compounds that inhibit PCR amplification if not removed during extraction; kits designed for these matrices integrate inhibitor-removal steps as part of the standard protocol. If your samples have historically produced low PCR amplification efficiency with general-purpose kits, an environmental-matrix-specific kit with built-in inhibitor removal is the first thing to evaluate.
Short-read vs. long-read sequencing compatibility
For long-read metagenomic sequencing, DNA fragment length and integrity from the extraction kit directly affect achievable read lengths, though longer extracted fragments don't always translate consistently into longer sequencing reads - kit choice affects both fragment length and downstream classification rate and reproducibility. If long-read metagenomics is your goal, prioritize kits with published long-read benchmarking data over kits validated only for short-read amplicon work.
Contamination control (kitome/splashome)
Kit-derived contamination ("kitome") and cross-sample contamination during processing ("splashome") can affect microbial community composition results, particularly for low-biomass samples; benchmarking studies evaluate kits specifically for these contamination sources alongside yield and diversity metrics. For low-biomass environmental samples, prioritize kits with documented low kitome contamination in published comparisons.
&nbsp;
<h2>Specifications context</h2>
&nbsp;
The key specs for microbial and environmental DNA isolation are matrix-specific validation (soil vs. sediment vs. water vs. feces), built-in inhibitor removal for PCR-ready output, and fragment length/integrity for long-read sequencing compatibility where relevant. Since benchmarking studies repeatedly show no single kit performs best across all matrices, identifying your primary sample type before selecting a kit is the most impactful decision. Labs running metagenomic surveys across multiple matrices (e.g., soil and water from the same field site) often need separate matrix-optimized kits rather than a single universal kit. The parent <a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/dna-extraction-kits/genomic-dna">genomic DNA extraction kits hub</a>&nbsp;links to related sample-type categories, including&nbsp;<a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/dna-extraction-kits/genomic-dna/insect">insect genomic DNA kits</a>&nbsp;and&nbsp;<a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/dna-extraction-kits/genomic-dna/plant">plant genomic DNA kits</a>&nbsp;for organism-associated environmental work, and&nbsp;<a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/dna-extraction-kits/high-molecular-weight-dna">high molecular weight DNA kits</a>&nbsp;for long-read metagenomics requiring larger fragment sizes. For cell-free DNA in environmental water samples (eDNA detection), see&nbsp;<a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/dna-extraction-kits/cell-free-dna">cell-free DNA kits</a>.&nbsp;
<section class="mbp-contact-cta">
&nbsp;
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>

Microbial & Environmental DNA Isolation

DataSheet

MSDS

YeaStar™ Genomic DNA Kit

D2002 by Zymo Research is the YeaStar™ Genomic DNA Kit, a 40-prep spin-column kit designed for simple, total genomic DNA purification from a broad spectrum of Zymolyase-susceptible fungal species, including Saccharomyces cerevisiae, Candida, Pichia, and more than a dozen additional genera. Each prep yields up to 25 µg of high-molecular-weight fungal gDNA (35–60 kb) at A260/A280 ≥ 1.8, processed in approximately 1.5 hours from culture to elution.

Applicable For

Elution Volume

Equipment

Processing Time

Processing Volume

Purity

Sample Source

Size Range

Type

Manufacturer

YeaStar™ Genomic DNA Kit (40 Preps.)

YD Digestion Buffer (4.8 ml)

YD Lysis Buffer (4.8 ml)

<h2>What are Spin-Column Bacterial and Fungal RNA Extraction Kits?</h2>
&nbsp;
Spin-column bacterial and fungal RNA extraction kits isolate total RNA from Gram-positive bacteria, Gram-negative bacteria, yeasts, filamentous fungi, algae, and protozoa using ultra-high-density BashingBead mechanical cell wall disruption in a chaotropic lysis buffer, followed by RNA binding to a Zymo-Spin silica-membrane column, on-column washing, and elution in 6-100 ul of RNase-free water - all using a standard microcentrifuge. The complete protocol takes under 15 minutes for a batch of 1-12 samples, requiring only a vortex with a microcentrifuge tube adapter, a microcentrifuge, and standard pipetting equipment. No specialized robotics, vacuum manifolds, or magnetic separation racks are needed. Choose a spin-column bacterial/fungal RNA kit for manual extraction of 1-24 samples per run, when existing automation infrastructure does not support magnetic bead formats, or when the fastest possible turnaround from culture to RT-qPCR data is required.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
Pinpoint&trade; Slide RNA Isolation System for targeted extraction of total RNA directly from localized tissue sections on microscope slides
</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
Quick-RNA&trade; Fungal/Bacterial MicroPrep Kit for highly concentrated, low-volume recovery of transcripts utilizing micro-elution spin-column matrices&nbsp;
</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
ZR Fungal/Bacterial RNA MiniPrep for precise cell-wall shattering of yeast and recalcitrant spores&nbsp;
</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
YeaStar&trade; RNA Kit efficiently permeabilizes tough yeast cell walls.&nbsp;
</li>
</ul>
&nbsp;
<h2>How to Choose a Spin-Column Bacterial/Fungal RNA Kit</h2>
&nbsp;
Miniprep vs. Microprep Format
The Zymo Quick-RNA Fungal/Bacterial Miniprep processes up to 2x10^8 bacteria or 2x10^7 fungi per column, eluting in 25-100 ul - the standard choice for typical 1-5 ml bacterial cultures. The Microprep handles smaller inputs (up to 1x10^7 bacteria) and elutes in as little as 6 ul, concentrating RNA for sensitive applications such as single-cell-equivalent samples or very low-input transcriptomics.
Bead Size for Target Organism
Pre-mixed 0.1 mm + 0.5 mm BashingBead tubes in Zymo kits handle bacteria (0.1 mm) and fungi (0.5 mm) without selecting bead size. For pure Gram-negative bacterial cultures that do not require bead beating, direct lysis in buffer is available as a faster protocol option that skips the bead-beating step entirely.
On-Column DNase I Treatment
Include DNase I for all RT-qPCR and RNA-seq applications. Bacterial gDNA is abundant and co-purifies efficiently under silica-membrane binding conditions; without DNase treatment, gDNA contamination produces false amplification in RT-qPCR assays targeting genes with no introns. DNase I Reaction Mix is included in Zymo Quick-RNA Fungal/Bacterial kits.
Elution Volume
Elute in 25-50 ul for standard RT-qPCR (2-5 ul per reaction provides 5-25 RNA equivalents per assay). For RNA-seq library preparation requiring &gt;=200 ng input, use 50-100 ul elution volume to recover more total RNA mass; then measure concentration by Qubit and adjust for library prep.
Storage of Extracted RNA
Store spin-column bacterial RNA at -80C in single-use aliquots; mRNA from bacteria is AU-rich and degrades rapidly through multiple freeze-thaw cycles. Use within 6 months for transcriptomic applications; RT-qPCR targets with high expression levels remain quantifiable for 12+ months at -80C.
&nbsp;
<h2>Specifications Context</h2>
&nbsp;
Target quality metrics for spin-column bacterial/fungal RNA: A260/A280 &gt;= 1.8, A260/A230 &gt;= 1.5, and RIN &gt;= 7 from log-phase cultures processed within 60 seconds of harvest. Zymo Research Quick-RNA Fungal/Bacterial kits use the same Zymo-Spin column technology found across the Quick-RNA product line and are validated for inhibitor-free RNA suitable for NGS, RT-PCR, microarray, and hybridization. The Quick-RNA Fungal/Bacterial Miniprep is one of the most widely used spin-column formats for bacterial and fungal RNA in academic molecular microbiology research, with validated protocols for S. cerevisiae, C. albicans, A. fumigatus, and standard Gram-positive and Gram-negative species.&nbsp;
<section class="mbp-contact-cta"></section>
&nbsp;
<a href="https://mbpinc.net/contact-us">Contact the MBP team</a> for kit selection guidance, bulk pricing, and Zymo Research protocol adaptation for non-standard organisms.

Spin-column

Bacterial/Fungal RNA/ Spin-column

Protocol

YeaStar™ RNA Kit (40 Preps.)

YeaStar™ RNA Kit R1002 by Zymo Research — 40-prep yeast RNA isolation kit, ≤25 µg yield, A260/A280 ≥1.8, 30-min protocol, compatible with S. cerevisiae, Candida, Aspergillus, Pichia, and Schizosaccharomyces. Ships from MBP INC to USA, Canada, and international labs.

Yield

Shipping Condition

Storage Condition

<h2 data-section-id="v1drft" data-start="0" data-end="43">What are cloning chemicals and reagents?</h2>
&nbsp;
Cloning chemicals and reagents cover the enzymes, buffers, and molecular biology-grade chemicals used in DNA fragment preparation, modification, and purification within a cloning workflow, including restriction endonucleases, T4 DNA ligase and other DNA-modifying enzymes (phosphatases, polymerases), reaction buffers, and plasmid extraction reagents. Related entities include restriction enzyme digestion, DNA dephosphorylation/phosphorylation, plasmid DNA purification (column-based and magnetic bead-based), and enzyme unit definitions.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Targeted XJa and XJb strains for faster recovery of proteins.</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Mix &amp; Go! solutions for optimized and dependable bacterial transformation.</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Culture Media &amp; Supplements used for yeast research, and include YPD Plus and mating pheromones.</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Extraction and Lysis Reagents include reliable genomic preparation and yeast protein kits.</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Chromogenic Substrates and Enzymatic Inducers with highly pure X-GAL and IPTG for cloning and blue-white screening.</li>
</ul>
&nbsp;
<h2 data-section-id="1daajgc" data-start="866" data-end="913">How to choose cloning chemicals and reagents</h2>
&nbsp;
Restriction enzyme selection and buffer compatibility
Restriction enzymes require specific reaction buffers, and many modern enzyme lines use a single universal buffer compatible across multiple enzymes to simplify double-digest reactions; confirm buffer compatibility when combining enzymes from different suppliers or using older single-buffer-per-enzyme formulations.
Enzyme unit definitions and reaction scale
Restriction enzyme and ligase activity is defined in units per microliter, with one unit typically defined as the amount needed to digest or ligate a defined quantity of standard substrate DNA under specified conditions in a set time; scale enzyme quantity to the amount of DNA being processed rather than assuming a fixed volume works for all reaction sizes.
Plasmid purification grade
Plasmid DNA extraction reagents range from molecular biology grade, suitable for general cloning and sequencing, to transfection-grade or endotoxin-free formulations required for applications such as lentiviral packaging or mammalian cell transfection, where endotoxin contamination can reduce transfection efficiency or cause cell stress.
Dephosphorylation for preventing vector self-ligation
Alkaline phosphatase treatment of a linearized vector before ligation removes 5' phosphate groups, preventing vector self-ligation and improving the ratio of recombinant clones; this step is particularly useful when the vector and insert share compatible sticky ends that could otherwise religate without insert incorporation.
&nbsp;
<h2 data-section-id="1fljvas" data-start="3459" data-end="3484">Specifications context</h2>
&nbsp;
Restriction enzymes and ligases are supplied at defined unit concentrations (commonly 10&ndash;20 units per microliter for restriction enzymes), with reaction buffers formulated for specific pH and salt conditions optimized for enzyme activity. Plasmid purification kits are differentiated by yield (micrograms of DNA recovered), purity (A260/A280 ratio), and endotoxin level (endotoxin units per microgram), with endotoxin-free kits specifying levels below a defined threshold suitable for transfection applications.&nbsp;
This sub-category is part of MBP's cloning catalog alongside ligation independent cloning kits and transformation kits and competent cells, used downstream of enzyme-based fragment preparation. Labs producing custom lentivirus for immortalization can also review MBP's cell immortalization catalog. MBP's specialist team can help confirm enzyme buffer compatibility and plasmid purification grade for a specific downstream application before order placement.
<a href="https://mbpinc.net/contact-us">Contact the expert team </a>at MBP today to request a quote for high-purity chemicals and reagents.

Chemicals/Reagents

Yeast Protein Kit (200 Preps)

Yeast Protein Kit (Y1002) by Zymo Research — 200 preps for enzymatic lysis of Zymolyase-susceptible yeast and fungi (S. cerevisiae, C. albicans, Kluyveromyces, and others) in approximately 35 minutes. Lysates suitable for Western blot and PCR. Y-Lysis Buffer refill available separately (Y1002-1-6).

<h2>What is a 1 kb DNA ladder?</h2>
&nbsp;
A 1 kb DNA ladder is a gel electrophoresis size standard containing a defined set of double-stranded DNA fragments spaced at or near 1-kilobase intervals, produced by digesting proprietary plasmids with restriction enzymes to generate typically 10 or more bands spanning 0.5 to 10 kb. One band, commonly at 3.0 kb, is supplied at higher concentration to serve as a bright reference band for rapid gel orientation. The 1 kb ladder is one of the most widely used size standards for routine molecular biology applications, covering the size range commonly encountered in PCR products, restriction digests, and cloned inserts.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" role="presentation">ZR 1 kb DNA Marker for gel electrophoresis analysis and routine DNA fragment sizing&nbsp;</li>
<li dir="ltr" role="presentation">Azura PureView&trade; 1kb DNA Ladder for the detection of DNA bands with high visibility in agarose gel systems</li>
<li dir="ltr" role="presentation">1kb Plus Opti-DNA Marker for cloning verification workflows and a wide range of DNA fragment analysis&nbsp;</li>
<li dir="ltr" role="presentation">1kb Opti-DNA Marker used in nucleic acid analysis and PCR for standard molecular weight reference&nbsp;</li>
<li dir="ltr" role="presentation">Accuris SmartCheck&trade; 1kb DNA Ladder for quality assessment of gel and DNA sizing with high precision</li>
<li dir="ltr" role="presentation">1 KB DNA Marker for routine DNA electrophoresis&nbsp;</li>
</ul>
&nbsp;
<h2>How to choose a 1 kb DNA ladder variant</h2>
&nbsp;
Choose a standard 1 kb ladder for routine PCR and restriction digest analysis
A standard 1 kb ladder with fragments spanning approximately 0.5 to 10 kb is suitable when most expected DNA fragments fall within this range, making it ideal for routine PCR verification and restriction digest analysis.
Choose a 1 kb Plus ladder when samples include smaller fragments below 500 bp
The 1 kb Plus format extends coverage down to 100 bp while maintaining the upper size range, making it useful when both small PCR products and larger DNA fragments need to be analyzed on the same gel.
Choose a 1 kb Extend ladder when samples include very large DNA fragments
The 1 kb Extend ladder expands coverage up to approximately 48.5 kb and is appropriate for large plasmids, BAC clones, and other high-molecular-weight DNA fragments analyzed on low-percentage agarose gels.
Use the recommended loading volume for accurate mass estimation
Loading the ladder according to the manufacturer's recommended amount helps ensure that any provided band mass references can be used for approximate comparison of DNA quantity based on staining intensity.
Confirm the tracking dye is compatible with your staining and imaging setup
Different ladder formulations use different tracking dyes. Some dyes may partially obscure nearby bands under UV visualization, while alternative formulations are designed to minimize interference and improve visibility across the entire ladder range.
&nbsp;
<h2>Specifications context</h2>
&nbsp;
Standard 1 kb DNA ladders are generated from defined DNA templates digested to produce fragments of known sizes. Enhanced-intensity reference bands are included to provide a readily identifiable orientation marker during gel analysis.
Ready-to-load 1 kb ladder formats with reduced-shadow tracking dyes are commonly used in routine agarose gel electrophoresis workflows because they simplify preparation and improve overall band visibility.
<a href="https://mbpinc.net/contact-us">Contact the expert team at MBP</a> to book high-quality 1Kb DNA Ladders for your lab today.

1Kb DNA Ladders

MSDS - M5003

MSDS - M5006

ZR 1 kb DNA Marker

M5003-200 by Zymo Research is the ZR 1 kb DNA Marker (200 µg / 400 µL), a 10-band ladder spanning 0.5–10 kb with an enhanced 3 kb reference band, at 500 µg/mL in Tris-EDTA buffer — loaded at 1 µg per lane for sizing PCR products, restriction digests, and linearized plasmids.

ZR 1 kb DNA Marker™ (200 µg/400 µl)

ZR 1 kb DNA Marker™ (50 µg/100 µl)

ZR 1 kb DNA Marker™ (Ready-to-Load) (50 µg/600 µl)

<h2>What is a 100 bp DNA ladder?</h2>
&nbsp;
A 100 bp DNA ladder provides reference bands at 100-base-pair intervals, typically covering 100 bp to 1000 bp or 100 bp to 2000 bp depending on the variant, making it the most commonly used size standard for routine sizing of small PCR amplicons and restriction digest products. Most commercially available 100 bp ladders include a brighter reference band at 500 bp or 600 bp for quick orientation, and many are available in ready-to-load formats pre-mixed with loading dye and glycerol for direct pipetting into gel wells.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
ZR 100 bp DNA Marker (M5002-200) for high-resolution sizing of DNA fragments in routine electrophoresis workflows
</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
PureView 100bp DNA Ladder for precise sizing and enhanced band visualization of small DNA fragments
</li>
</ul>
&nbsp;
<h2>How to choose and use a 100 bp DNA ladder</h2>
&nbsp;
Use a 100 bp ladder when your samples are mostly below 2 kb
A 100 bp ladder provides more resolution than a 1 kb ladder in the small-fragment range, since 100 bp spacing gives reference bands every 100 bp rather than every 1000 bp. If samples span a broader size range, the 1 kb Plus ladder extending down to 100 bp may be a more versatile single-ladder choice.
Run small-fragment gels on 1.5&ndash;2% agarose for best resolution
Fragments in the 100&ndash;500 bp range benefit from 1.5&ndash;2% agarose, which gives tighter, better-defined bands in this small-fragment window and reduces the risk of small bands reaching the gel front before larger fragments are adequately separated.
Look for a 500 bp or 600 bp reference band for easy orientation
Most 100 bp ladders include a brighter band at a convenient midpoint like 500 bp or 600 bp, which serves as a visual anchor for counting up or down in 100 bp intervals to identify the nearest ladder band.
Choose between upper ranges (1000 bp vs 2000 bp) based on sample sizes
Some 100 bp ladders cover only to 1000 bp (10 bands), while extended versions cover up to 2000 bp. If samples occasionally include products above 1000 bp, the extended range provides coverage without switching to a separate 1 kb ladder.
Pair with a 1 kb ladder when samples span both large and small size ranges
If an experiment includes both small PCR amplicons around 100&ndash;500 bp and larger restriction fragments above 2 kb, loading both a 100 bp and a 1 kb ladder in adjacent lanes provides accurate reference coverage across the full size range.
&nbsp;
<h2>Specifications context</h2>
&nbsp;
The 100 bp DNA ladder is one of the two most commonly used DNA size standards in routine molecular biology labs, alongside the 1 kb ladder, and most labs running small PCR products routinely keep a 100 bp ladder on hand. As of 2026, ready-to-load 100 bp ladder formats with a 500 bp or 600 bp bright reference band remain the default choice for routine agarose gel electrophoresis of small PCR products and restriction digest fragments.
<a href="https://mbpinc.net/contact-us">Contact the expert team at MBP</a> for assistance in selecting the right 100bp DNA ladder for your lab.

100bp DNA Ladders

ZR 100 bp DNA Marker

ZR 100 bp DNA Marker by Zymo Research: 12 defined fragments covering 100–1,500 bp, with intensified 500 bp and 1,000 bp reference bands for agarose gel electrophoresis. Endonuclease-digested plasmid DNA. Available in 50 µg and 200 µg quantities. Research use only.

ZR 100 bp DNA Marker™ (200 µg/400 µl)

ZR 100 bp DNA Marker™ (50 µg/100 µl)

ZR 100 bp DNA Marker™ (Ready-to-Load) (50 µg/600 µl)

<h2>What is a 50 bp DNA ladder?</h2>
&nbsp;
A 50 bp DNA ladder provides reference bands spaced at 50-base-pair intervals, most commonly covering 50 bp to 1000 bp (or up to 1500 bp in some extended formats), making it suitable for gel electrophoresis experiments where samples are very small DNA fragments that a 100 bp ladder cannot resolve accurately because 100 bp band spacing is too coarse. Common applications include microsatellite and STR genotyping, analysis of small restriction digest products, multiplex or nested PCR amplicons, and other short-fragment applications in the 50&ndash;500 bp range where precise size discrimination is needed.
&nbsp;
<h2>What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
ZR 50 bp DNA Marker for precise analysis of smaller DNA fragments&nbsp;
</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
Azura PureView&trade; 50 bp DNA Ladder for high-resolution gel results in electrophoresis
</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
Accuris SmartCheck&trade; 50bp DNA Ladder for size determination of PCR products
</li>
</ul>
&nbsp;
<h2>How to choose and use a 50 bp DNA ladder</h2>
&nbsp;
Use a 50 bp ladder when your fragments differ by less than 100 bp and are below 500 bp
The primary reason to use a 50 bp ladder over a 100 bp ladder is when your samples include fragments with size differences of less than 100 bp that need to be resolved, such as microsatellite alleles or closely-sized PCR amplicons from multiplex reactions.
Run small-fragment gels on 2&ndash;4% agarose or polyacrylamide for adequate resolution
High-percentage agarose (2&ndash;4%) or polyacrylamide gels are needed to resolve very small DNA fragments as distinct bands rather than all migrating together near the gel front, since standard 1% agarose does not provide sufficient resolution for fragments below approximately 200 bp.
Use a reference band at a convenient size for quick orientation
Many 50 bp ladders include a brighter reference band at a convenient, easy-to-remember size such as 250 bp or 500 bp, which serves as an anchor for identifying surrounding bands without counting from the well each time.
Confirm the 50 bp ladder's smallest band is detectable with your staining system
Very small DNA fragments, especially below 100 bp, can be difficult to detect or may run off the gel front quickly, and confirming that the ladder's smallest defined bands are visible under your staining and imaging setup helps ensure the full ladder range is usable.
Consider polyacrylamide gels for the highest resolution of fragments below 200 bp
Polyacrylamide gel electrophoresis provides substantially higher resolution than high-percentage agarose for fragments below 100&ndash;200 bp, making it the preferred format when single-base or very fine size discrimination is needed in this range, such as for SSR or STR genotyping.
&nbsp;
<h2>Specifications context</h2>
&nbsp;
Standard 50 bp DNA ladders typically cover from 50 bp to 1000 bp with bands at 50 bp intervals, and many include a brighter reference band at 250 bp or 500 bp for quick orientation. As of 2026, the 50 bp ladder remains the standard small-fragment size reference for microsatellite and STR genotyping workflows, whether on standard agarose or capillary electrophoresis platforms where defined size standards are loaded alongside samples.
<a href="https://mbpinc.net/contact-us">Contact the expert team of Molecular Biology Products Inc. (MBP)</a> and get premium-quality 50bp DNA ladders for your next experiment.

50bp DNA Ladders

ZR 50 bp DNA Marker

ZR 50 bp DNA Marker by Zymo Research contains 12 defined fragments spanning 50–1,200 bp with an enhanced 300 bp reference band, at 500 µg/mL in Tris-EDTA buffer — used at 1 µg per lane for agarose gel sizing of PCR amplicons and restriction fragments. Available in 50 µg and 200 µg formats.

ZR 50 bp DNA Marker™ (200 µg/400 µl)

ZR 50 bp DNA Marker™ (50 µg/100 µl)

ZR 50 bp DNA Marker™ (Ready-to-Load) (50 µg/600 µl)

<h2>What are plasmid miniprep kits?</h2>
&nbsp;
A plasmid miniprep kit uses SDS/alkaline lysis to break open pelleted E. coli cells from a small culture volume (1-10 ml), followed by binding to a silica-membrane spin column, washing, and elution, separating plasmid DNA from genomic DNA, RNA, and protein in roughly 10-15 minutes per prep. Related entities include Buffer P1/P2/P3-style alkaline lysis reagents, color-coded lysis dyes for visual confirmation of complete lysis and neutralization, RNase A for RNA removal, and downstream applications including transformation, restriction digestion, PCR, and sequencing. Choose a miniprep kit for routine, low-volume plasmid prep (cloning screens, sequencing checks, restriction digests) where yields up to roughly 20-100 ug per column are sufficient.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Pellet-free and classic plasmid miniprep kits for high-yield bacterial isolation using rapid spin-column workflows</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">High-throughput 96-well plasmid plates optimized for vacuum manifold processing and parallel automated screening&nbsp;</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Specialized yeast plasmid miniprep systems for fragile fungal hosts using cell-wall digesting chemistries</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">BAC/PAC and large construct isolation units for safer purification of high-molecular-weight vectors</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Endotoxin-free plasmid extraction reagents for sensitive mammalian cell lines, ensuring transfection-grade DNA purity&nbsp;</li>
</ul>
&nbsp;
<h2>How to choose a plasmid miniprep kit</h2>
&nbsp;
Standard vs. high-yield chemistry
Standard silica spin-column minipreps typically recover up to about 20 ug per column, while high-yield formulations using modified alkaline lysis and novel binding chemistry can reach up to 100 ug at concentrations up to 3 ug/ul from the same small culture volume. If your downstream application (e.g., sequencing multiple samples from one prep, or transfection requiring more DNA per prep) benefits from a higher concentration, a high-yield kit reduces the need to scale up to midiprep.
Plasmid copy number and culture volume planning
High-copy plasmids (pUC-based vectors) can saturate a miniprep column from as little as 3 ml of culture, yielding around 20 ug, while low-copy plasmids (pBR322, pET, cosmids) may yield under 2 ug from the same volume and benefit from doubling culture volume to 5-10 ml. Identify your vector's origin of replication before choosing a standard culture volume, since low-copy vectors at standard volumes can produce yields too low for some downstream steps.
Color-coded lysis buffers for visual QC
Some miniprep kits include color-coded lysis and neutralization buffers that allow visual confirmation of complete cell lysis (color change) and proper neutralization before loading the column, helping catch incomplete-lysis failures before they waste a column. This visual QC step is particularly useful for new users or when troubleshooting inconsistent yields across a batch of preps.
Endotoxin-free and large-construct options
For transfection-sensitive downstream applications, endotoxin-free miniprep kits add a dedicated wash step without significantly extending the protocol time; for large plasmids, cosmids, or BAC/YAC/PAC constructs, some miniprep kits are validated up to approximately 200 kb, while standard kits are optimized for constructs up to roughly 25 kb. Confirm both endotoxin status and size compatibility match your specific construct and downstream use before relying on a standard miniprep.
&nbsp;
<h2>Specifications context</h2>
&nbsp;
The key specs for plasmid miniprep selection are expected yield relative to your plasmid's copy number and culture volume, whether color-coded buffers aid visual QC, and whether endotoxin-free or large-construct compatibility is needed for your downstream application. A standard miniprep yielding up to roughly 20-25 ug in 10-15 minutes from 1-10 ml of culture covers most routine cloning workflows, while high-yield kits up to 100 ug reduce the need to scale up for moderately DNA-hungry applications. Labs running both daily cloning screens and occasional larger-scale prep work typically keep <a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/plasmid-dna-extraction-kits/miniprep-kits">miniprep kits</a>&nbsp;on hand alongside&nbsp;<a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/plasmid-dna-extraction-kits/midiprep-kits">midiprep kits</a>&nbsp;for when miniprep yields aren't sufficient. The parent&nbsp;<a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/plasmid-dna-extraction-kits">plasmid DNA extraction kits category</a>&nbsp;and&nbsp;<a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/plasmid-dna-extraction-kits/maxiprep-kits">maxiprep kits</a>&nbsp;cover larger-scale options, while the broader&nbsp;<a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits">nucleic acid extraction kits hub</a>&nbsp;and&nbsp;<a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/dna-extraction-kits/genomic-dna">genomic DNA extraction kits category</a> link to chromosomal DNA workflows.&nbsp;
<section class="mbp-contact-cta">
&nbsp;
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>

Miniprep Kits

ZR BAC DNA Miniprep Kit

D4048 by Zymo Research — ZR BAC DNA Miniprep Kit (25 preps) for rapid isolation of BAC, PAC, fosmid, and cosmid DNA up to ~200 kb from E. coli. 15-minute protocol; elution ≥ 10 µl; yield up to 10 µg per prep; purity A260/A280 ≥ 1.8, A260/A230 ≥ 2.0. Includes colored buffer system for visual lysis confirmation.

ZR BAC DNA Miniprep Kit (25 Preps.)

ZR BAC DNA Miniprep Kit (100 Preps.)

Tubes

ZR Bashing Bead Lysis Tubes (2 mm) (50 Pack)

ZR Bashing Bead Lysis Tubes (2 mm) by Zymo Research (S6003-50) are 2 ml impact-resistant screw-cap tubes pre-loaded with 2 mm zirconium oxide beads for mechanical lysis of tough samples including soil, stool, biofilms, and gram-positive bacteria. Supplied in a 50-pack for microbiome and metagenomics workflows, these tubes are compatible with standard bead homogenizers and integrate directly into Zymo Research DNA/RNA extraction kits.

S6012-50-MSDS

ZR BashingBead Lysis Tubes

ZR BashingBead™ Lysis Tubes by Zymo Research are available as S6012-50 (0.1 &amp; 0.5 mm beads, 50 pack) for environmental and microbial samples, and S6014-50 (0.1 &amp; 2.0 mm beads, 50 pack) for disease vectors and tough tissues. Each 2 ml impact-resistant tube contains 0.7 ml of chemically inert, fracture-resistant beads. Made in the USA. Suited to metagenomics, microbiomics, and vector biology labs.

ZR BashingBead Lysis Tubes (0.1 & 0.5 mm) (50 Pack)

ZR BashingBead Lysis Tubes (0.1 & 2.0 mm) (50 Pack)

ZR BashingBead Lysis/Filtration Tubes

S6010 by Zymo Research is the ZR BashingBead Lysis/Filtration Tube with 0.5 mm beads, a 25-pack of 50 mL impact-resistant polypropylene tubes that combine bead-beating lysis and silica-based nucleic acid capture in a single vessel. The integrated silica filtration matrix binds 5&ndash;10 &micro;g of nucleic acid; minimum elution volume is &ge;6 &micro;l. Compatible bead beaters include the Bullet Blender (9 tubes per run), FastPrep-24 (40-second processing), and Geno/Grinder 2010 (12 tubes per run).
The 0.5 mm beads are optimized for disruption of bacteria, fungi, and yeast. For tissue homogenization, use the S6011 (2.0 mm beads). No organic denaturants or proteinases are required.
MBP is a registered vendor for Howard Hughes Medical Institute, Vanderbilt University, MD Anderson Cancer Center, Eurofins, and many other institutes across the USA. Order via <a href="https://www.mbpinc.net/quickorder">Quick Order</a> or contact <a href="mailto:customerservice@mbpinc.net">customerservice@mbpinc.net</a>.

Binding Capacity

Compatibility

Format

Volumetric Capacity

ZR BashingBead Lysis/Filtration Tubes w/ 0.5 mm Beads (50 ml) (25 Pack)

ZR BashingBead Lysis/Filtration Tubes w/ 2.0 mm Beads (50 ml) (25 Pack)

<h2>What are DNA Sequencing Cleanup Reagents?</h2>
&nbsp;
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.
&nbsp;
<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>
&nbsp;
<h2>How to Choose a DNA Sequencing Cleanup Reagent</h2>
&nbsp;
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.
&nbsp;
<h2>Specifications Context</h2>
&nbsp;
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.
&nbsp;
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.

D4050-Data Sheet

D4050-MSDS

D4050-Protocol

ZR DNA Sequencing Clean-up Kit™

D4050 by Zymo Research is a 50-prep dye terminator sequencing cleanup kit using Zymo-Spin IB Columns. Removes unincorporated BigDye terminators, dNTPs, primers, and salts from 5–20 µl sequencing reactions in ~2 minutes; elution in 6–20 µl water or formamide. Reusable columns (up to 10 cycles).

Sample storage

ZR DNA Sequencing Clean-up Kit™ (50 Preps.)

ZR DNA Sequencing Clean-up Kit™ (200 Preps.)

Sequencing Binding Buffer (14 ml)

Sequencing Binding Buffer (500 ml)

Sequencing Binding Buffer (55 ml)

Sequencing Wash Buffer (20 ml)

Sequencing Wash Buffer (500 ml)

Sequencing Wash Buffer (70 ml)

ZR Fungal/Bacterial RNA MiniPrep (50 Preps.)

ZR Fungal/Bacterial RNA MiniPrep (R2014) by Zymo Research isolates up to 50 µg of total RNA (≥17 nt) from gram-positive bacteria, fungi, yeast, spores, and pollen in 10 minutes or less using a bead-beating lysis step followed by spin-column purification. Purity exceeds A260/A280 of 1.8, and purified RNA is ready for RT-qPCR, RNA-seq, and microarray applications. 50-prep format.