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>
&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>
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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

Protocol

Alpha-Factor Mating Pheromone (240 µl)

Alpha-Factor Mating Pheromone (Y1001) by Zymo Research — 240 µl at 10 mM in 0.1 M sodium acetate pH 5.2 (4 mg total); &gt;98% HPLC purity; MW 1684.0 Da. Trp-His-Trp-Leu-Gln-Leu-Lys-Pro-Gly-Gln-Pro-Met-Tyr. G1 cell cycle arrest in yeast. Storage at −20°C.

Amino Acid Sequence

Concentration

Molecular Weight

Product Storage

Purity

Usage

Manufacturer

Shipping Condition

Storage Condition

<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.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<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>
&nbsp;
<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

M3011 - MSDS

M3011-Protocol

Dual Media Set™ (100 ml EB™ & 500 ml OB™)

M3011 by Zymo Research is the Dual Media Set™ — Expansion Broth (EB™, 100 mL) plus Overexpression Broth (OB™, 500 mL) — for high-yield E. coli recombinant protein expression using a two-phase workflow that eliminates IPTG induction and OD monitoring in T7-based systems.

M3012-100 - MSDS

Expansion Broth™ (EB™)

Expansion Broth (EB) by Zymo Research: bacterial growth medium that represses recombinant protein expression during the cell expansion phase. Use with Overexpression Broth (OB) for consistent, high-yield recombinant protein production. Room temperature storage. 100 ml and 500 ml sizes available.

Expansion Broth™ (EB™) (100 ml)

Expansion Broth™ (EB™) (500 ml)

<h2 data-section-id="k59sk3" data-start="0" data-end="52">What are transformation kits and competent cells?</h2>
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Transformation kits and competent cells consist of E. coli strains prepared to take up exogenous plasmid DNA, either through chemical competence (calcium chloride treatment, transformed via heat shock) or electrocompetence (transformed via electroporation), along with associated transformation buffers and protocols. Related entities include transformation efficiency (transformants per microgram), heat-shock and electroporation methods, strain genotype (recA, endA deficiency for plasmid stability), and downstream plasmid recovery for sequencing or transfection.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li>Mix &amp; Go! Transformation Kits, rapid protocols for preparation of competent E. coli in&nbsp;</li>
<li>ProClone&trade; Competent Cells with optimized E. coli strains for cloning and library generation.</li>
<li>Specialized Competent E. coli Strains ready-made JM109, DH5 Alpha, and Zymo 10B cells for regular and complex assembly.</li>
<li>Autolysis Competent Cells: designed for simplified cell lysis and streamlined protein expression using XJa and XJb strains</li>
<li>Frozen-EZ Yeast Transformation Kits for genetic manipulation of yeast strains.</li>
</ul>
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<h2 data-section-id="1ld88i5" data-start="812" data-end="876">How to choose transformation kits and competent cell products</h2>
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Chemically competent vs. electrocompetent cells
Chemically competent cells use a heat-shock protocol and are generally easier to handle for routine cloning, while electrocompetent cells require an electroporator but can achieve higher transformation efficiency for large plasmids, low-copy constructs, or DNA with modifications that reduce chemical transformation efficiency.
General cloning strains vs. protein expression strains
General cloning strains are selected for high transformation efficiency and genetic features (such as recA and endA deficiency) that improve plasmid stability and quality for downstream sequencing, while protein expression strains carry features supporting recombinant protein production, such as T7 RNA polymerase expression for IPTG-inducible systems; using a cloning strain for protein expression (or vice versa) generally gives suboptimal results.
Transformation efficiency requirements
Routine cloning of standard-sized plasmids works well with competent cells rated at 10^6&ndash;10^8 transformants per microgram, while ligation reactions with very low DNA concentrations (such as multi-fragment seamless assembly products) may benefit from higher-efficiency cells rated above 10^8 transformants per microgram.
Transformation kits may include a positive control plasmid and competent cells for validating transformation efficiency before using precious experimental DNA; this is particularly useful when troubleshooting low transformation yields to distinguish competent cell quality issues from ligation or assembly reaction issues.
&nbsp;
<h2 data-section-id="1fljvas" data-start="3947" data-end="3972">Specifications context</h2>
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Competent cell transformation efficiency is reported in transformants per microgram of standard control plasmid DNA, with general cloning strains commonly rated at 10^6&ndash;10^8 and high-efficiency formulations exceeding 10^8 transformants per microgram. Cells are typically supplied as frozen aliquots (e.g., 50&ndash;100 microliters per tube) for single-use transformations, shipped on dry ice and stored at -80&deg;C, with repeated freeze-thaw substantially reducing efficiency.&nbsp;
This sub-category is part of MBP's cloning catalog alongside ligation independent cloning kits and chemicals/reagents, the upstream steps of a cloning workflow. Labs producing custom lentivirus for immortalization can also review MBP's cell immortalization catalog. MBP's specialist team can help confirm strain genotype and transformation efficiency requirements for a specific cloning or expression project before order placement.
<a href="https://mbpinc.net/contact-us">Contact the expert team</a> at MBP today and get high-quality transformation kits and competent cells for your lab.

Transformation Kits & Competetent Cells

Frozen-EZ Yeast Transformation II™ Kit (120 Rxns.)

The Frozen-EZ Yeast Transformation II&trade; Kit (T2001) by Zymo Research delivers 105&ndash;106 transformants/&micro;g plasmid DNA across four yeast species in under 15 minutes of hands-on preparation and without a spheroplast step. The 120-reaction kit stores at 0&ndash;4&deg;C; prepared competent cells remain stable for &ge;1 year at &le;&minus;70&deg;C.
Compatible species: Saccharomyces cerevisiae, Candida albicans, Schizosaccharomyces pombe, and Pichia pastoris. No carrier DNA 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>.

Competent Cell Stability

Processing Time

Transformation DNA Input

Transformation Efficiency

DataSheet

IPTG (Isopropyl-β-D-thiogalactopyranoside)

I1001-25 is IPTG (Isopropyl-β-D-thiogalactopyranoside), CAS 367-93-1, MW 238.3 g/mol — supplied as a premade 0.5 M sterile solution (25 mL). The standard non-metabolizable lac operon inducer for recombinant protein expression in E. coli. Typical working concentration: 0.1–1 mM. Store at −20°C.

Isopropyl-β-D-thiogalactopyranoside (IPTG) (5 x 5 ml)

Isopropyl-β-D-thiogalactopyranoside (IPTG) (5 ml)

Mix & Go! 2X Stock Competent Buffer

T3001-3 by Zymo Research is the Mix &amp; Go! 2X Stock Competent Buffer for rapid preparation of highly competent E. coli cells in approximately 20 seconds. Available as T3001-3-10 (10 ml) and T3001-3-30 (30 ml). Store at 0–8°C. Compatible with the Mix &amp; Go! E. coli Transformation Kit and Buffer Set for cloning and plasmid propagation workflows.

Mix & Go! 2X Stock Competent Buffer (10 ml)

Mix & Go! 2X Stock Competent Buffer (30 ml)

Mix & Go! 2X Stock Wash Buffer

Mix &amp; Go! 2X Stock Wash Buffer by Zymo Research — wash buffer component for the Mix &amp; Go E. coli transformation system. Room temperature storage. Available as T3001-2-10 (10 ml) and T3001-2-30 (30 ml).

Mix & Go! 2X Stock Wash Buffer (10 ml)

Mix & Go! 2X Stock Wash Buffer (30 ml)

Mix & Go! Competent Cells - DH5 Alpha

Mix &amp; Go! Competent Cells - DH5 Alpha by Zymo Research — 108–109 transformants/µg pUC19, no heat shock, approximately 20-second transformation. Store at &lt;−70°C; integrity guaranteed 6 months. Available as T3007 (10×100 µl), T3009 (96×50 µl, 12×8-Tube Strips), and T3010 (96×50 µl with PCR plates and Cover Foils).

Additional Info

Genotype

Mix & Go! Competent Cells - DH5 Alpha (10 x 100 µl)

Mix & Go! Competent Cells - DH5 Alpha (96 x 50 µl)

Mix & Go! Competent Cells - DH5 Alpha (96 x 50 µl) w/ 96-well PCR plates and Cover Foils

Mix & Go! Competent Cells - HB101

Mix &amp; Go! Competent Cells - HB101 (T3011 / T3013) by Zymo Research are premade chemically competent E. coli HB101 cells with 10⁸–10⁹ transformants/µg efficiency and a 20-second protocol. Available in 10 × 100 µl (T3011) or 96 × 50 µl (T3013) formats; Dam⁺/Dcm⁺, recA⁻, max 10 kb plasmid, stored at −70°C to −80°C. 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.

Mix & Go! Competent Cells - HB101 (10 x 100 µl)

Mix & Go! Competent Cells - HB101 (96 x 50 µl)

Mix & Go! Competent Cells - JM109

T3003 by Zymo Research is the Mix &amp; Go! Competent Cells - JM109, chemically competent E. coli cells for plasmid transformation without heat shock. Transformation complete in 20 seconds; efficiency 10⁸–10⁹ transformants/µg (pUC19). Supplied as 10 × 100 µl tubes; supports blue-white screening and plasmids up to 10 kb. Store at -70°C to -80°C.

Mix & Go! Competent Cells - JM109 (10 x 100 µl)

Mix & Go! Competent Cells - JM109 (96 x 50 µl)

Mix & Go! Competent Cells - TG1 (10 x 100 µl)

Mix &amp; Go! Competent Cells TG1 T3017 by Zymo Research are ready-to-use chemically competent E. coli cells (10 × 100 µL) with 10⁸–10⁹ transformants/µg, requiring no heat shock. TG1 strain supports blue-white screening (lacZ M15) and plasmids up to 10 kb. Storage at –70°C to –80°C.

Mix & Go! Competent Cells - XJa Autolysis (10 x 100 µl)

Mix &amp; Go! Competent Cells — XJa Autolysis (T3021) by Zymo Research. 10 × 100 µl. Transformation efficiency 108–109 cfu/µg. Built-in autolysis: 80–90% cell lysis in 10 min. No heat shock required.