Cloning

<h2 data-section-id="v1drft" data-start="0" data-end="43">What are cloning chemicals and reagents?</h2>
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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.
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<h2 dir="ltr">What you will find:</h2>
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<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>
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<h2 data-section-id="1daajgc" data-start="866" data-end="913">How to choose cloning chemicals and reagents</h2>
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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.
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<h2 data-section-id="1fljvas" data-start="3459" data-end="3484">Specifications context</h2>
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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

MSDS

DataSheet

Protocol

XJb Autolysis Glycerol Stock (1 Tube)

XJb Autolysis Glycerol Stock (T5041) by Zymo Research — arabinose-inducible autolysis E. coli strain for reagent-free recombinant protein extraction. Lon⁻, OmpT⁻. 80–90% lysis efficiency in ~10 min. 1 Tube, store at −70°C to −80°C.

Autolysis

Cell Growth

DNA Extraction

DNA Stability

Genotype

Processing Time

Product Storage

Protein Expression

Manufacturer

Shipping Condition

Storage Condition

Y-Lysis Buffer

Y-Lysis Buffer by Zymo Research is a specialized buffer for enzymatic yeast and fungal cell wall digestion, used at 25 µl per sample alongside Zymolyase in nucleic acid isolation workflows optimized for Saccharomyces cerevisiae and Candida albicans. Available in 6 ml and 100 ml formats.

Y-Lysis Buffer (100 ml)

Y-Lysis Buffer (6 ml)

YPD Plus

Y1003 by Zymo Research is a specially formulated YPD outgrowth medium that increases yeast transformation efficiency by more than 50% compared to standard YPD. Recommended for mutant strains with poor growth characteristics, library screening, and multi-plasmid transformation experiments. Available in 50 ml (Y1003-50) and 100 ml (Y1003-100) formats.

YPD Plus (100 ml)

YPD Plus (50 ml)

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).

Applicable For

Equipment

Sample Source

<h2 data-section-id="b4wzzk" data-start="0" data-end="47">What is bacterial culture media for cloning?</h2>
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Bacterial culture media for cloning workflows includes LB (Luria-Bertani) broth and agar, the standard general-purpose media for E. coli growth, SOC media used for post-transformation recovery, and Terrific Broth for higher-density culture in plasmid preparation. Pre-made agar plates with antibiotic selection (ampicillin, kanamycin, chloramphenicol, and others matching common selection markers) are used to isolate colonies carrying the desired plasmid. Related entities include antibiotic selection markers matching transformation kit resistance genes, post-transformation recovery time, and plasmid yield scaling with culture volume and media richness.
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<h2 dir="ltr">What you will find:</h2>
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<ul>
<li dir="ltr" role="presentation">ZymoBroth Growth Media for efficient transformation workflows to generate highly competent bacterial cells</li>
<li dir="ltr" role="presentation">Overexpression Broth (OB) optimized for increasing recombinant protein yields with high-density nutrient media.</li>
<li dir="ltr" role="presentation">Expansion Broth (EB) for the faster and more reliable expansion of microbial cultures.</li>
<li dir="ltr" role="presentation">Dual Media Sets for integrated growth and induction workflows with the help of combined EB and OB systems</li>
</ul>
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<h2 data-section-id="9xi4x5" data-start="919" data-end="971">How to choose bacterial culture media for cloning</h2>
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LB broth/agar vs. Terrific Broth
LB broth and agar are the standard general-purpose media for routine cloning, colony selection, and small-scale plasmid preparation, while Terrific Broth provides higher nutrient density supporting higher bacterial cell density, making it useful when maximizing plasmid yield in larger-scale preparations.
SOC media for post-transformation recovery
SOC media is richer than standard LB and supplemented with glucose and magnesium. It is commonly used for a brief recovery incubation immediately after heat-shock or electroporation transformation, helping transformed cells recover before plating on selective agar. Some transformation protocols specifically recommend SOC rather than LB for this recovery step.
Antibiotic selection matching
Pre-made antibiotic-selective agar plates must match the resistance marker carried by the transformed plasmid, whether ampicillin, kanamycin, chloramphenicol, or another selection marker. Using the wrong antibiotic&mdash;or no antibiotic at all&mdash;will not properly select for plasmid-containing colonies and may allow unwanted bacterial growth.
Liquid vs. agar plate formats and shelf life
Liquid media (broth) is used for post-transformation recovery and culture scale-up, while agar plates are used for colony isolation and selection. Pre-made antibiotic plates have a defined shelf life because antibiotics gradually lose activity over time, making expiration dates particularly important for antibiotics with lower stability.
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<h2 data-section-id="1fljvas" data-start="3523" data-end="3548">Specifications context</h2>
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LB broth and agar are formulated with defined concentrations of tryptone, yeast extract, and sodium chloride, with agar plates commonly supplied in standard Petri dish sizes (for example, 100 mm) and containing antibiotic concentrations matched to common resistance markers, such as 100 &micro;g/mL ampicillin or 50 &micro;g/mL kanamycin. SOC recovery is typically performed as a short incubation, often around one hour at 37&deg;C with shaking, before plating cells on selective agar.&nbsp;
This sub-category is part of MBP's cloning catalog alongside transformation kits and competent cells, the immediately preceding step, and chemicals/reagents for enzyme-based fragment preparation. Labs scaling up plasmid production for lentivirus packaging in immortalization workflows can also review MBP's cell immortalization catalog. MBP's specialist team can help confirm antibiotic concentration and media format requirements for a specific selection marker before order placement.
<a href="https://mbpinc.net/contact-us">Contact the expert team</a> at MBP today to request a quote for high-quality culture media.

Culture Media

ZymoBroth

ZymoBroth by Zymo Research: growth medium for highly competent E. coli cell preparation, delivering 5–100× transformation efficiency over standard SOB. Compatible with JM109, HB101, BL21, and other strains. Part of the Mix &amp; Go! Transformation Kit workflow. Room temperature storage. Research use only.

ZymoBroth™ (100 ml)

ZymoBroth™ (500 ml)

a-Factor Mating Pheromone (500 µl)

Y1004-500 a-Factor Mating Pheromone by Zymo Research is a farnesylated dodecapeptide supplied at 1 mg/ml in methanol, 500 µl, purity ≥80% HPLC, MW 1630 Da. Induces G1 arrest and mating response in S. cerevisiae MATα cells; working concentration 0.5 µg/ml for BAR1Δ strains. Store at −20°C short-term or below −70°C long-term. MBP is a registered vendor for Howard Hughes Medical Institute, Vanderbilt University, MD Anderson Cancer Center, and many more leading research institutes, serving labs across the United States, Canada, and internationally.