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Subcloning

Subcloning is a core technique in molecular biology for transferring a specific DNA fragment, or insert, from a parent vector to a destination vector, enabling targeted analysis, expression, or manipulation of the genetic material in appropriate host systems.^[1] This process is essential for adapting cloned DNA to new experimental contexts, such as changing expression hosts from bacteria to mammalian cells or incorporating regulatory elements like promoters and tags.^[2] The primary method of subcloning involves restriction enzyme digestion to excise the DNA insert from the parent vector and linearize the destination vector, followed by ligation using enzymes like T4 DNA ligase to join the compatible ends.^[1] Directional cloning is often achieved with two different restriction enzymes producing incompatible sticky ends, ensuring the insert orients correctly, while blunt-end ligation can be used for fragments without suitable restriction sites by employing polymerases such as T4 DNA polymerase.^[2] Alternative approaches, including recombination-based systems like Gateway cloning, utilize site-specific recombinases to facilitate seamless transfer without relying on restriction sites, which is particularly useful for large or complex inserts.^[2] Following ligation, the recombinant vector is introduced into competent host cells via transformation, typically using bacterial strains like E. coli JM109, and colonies are screened for successful insertion through methods such as colony PCR, restriction analysis, or sequencing.^[1] Subcloning's versatility supports diverse applications, from protein production and functional genomics to constructing gene fusions and targeting vectors for gene therapy.^[3]

Overview

Definition and Purpose

Subcloning is a core technique in molecular biology that entails isolating a specific DNA fragment, referred to as the insert, from a source vector and transferring it into a destination vector to enable improved functionality, such as increased copy number, specialized promoters, or compatibility with particular host systems.^[1] This process refines the genetic construct by repositioning the insert within a new plasmid backbone, facilitating more targeted experimentation or propagation.^[2] The primary purposes of subcloning include enhancing gene expression through integration into vectors with optimized regulatory elements, constructing expression libraries to screen gene functions on a large scale, preparing refined DNA fragments for high-throughput sequencing, and adapting inserts for diverse host organisms, for instance, moving bacterial-optimized sequences to mammalian expression systems.^[2]^[4] These applications support advanced studies in protein production, functional genomics, and cross-species genetic engineering.^[5] Subcloning relies on foundational concepts of cloning, particularly the formation of recombinant DNA, which involves the enzymatic joining of DNA segments from different origins to create hybrid molecules that can be replicated and expressed in host cells like bacteria.^[6] This technique was first described in the early 1970s as part of the pioneering work in recombinant DNA technology, revolutionizing scalable DNA manipulation and laying the groundwork for modern biotechnology.^[7]

Historical Context

Subcloning emerged in the mid-1970s alongside the pioneering recombinant DNA experiments of Stanley Cohen and Herbert Boyer, who in 1973 successfully cloned antibiotic resistance genes into the low-copy-number plasmid pSC101 in Escherichia coli, establishing the foundation for plasmid-based cloning.^[8] Early vectors like pSC101, with only 5–10 copies per cell, yielded insufficient recombinant DNA for downstream applications, necessitating subcloning techniques to transfer inserts into higher-copy-number plasmids for enhanced production and analysis.^[9] This approach addressed key limitations in yield and scalability, transforming initial cloning proofs-of-concept into practical tools for gene manipulation. The 1980s saw further innovations with the development of shuttle vectors, which allowed inserts to be propagated across species; notably, in 1978, Albert Hinnen, John Hicks, and Gerald Fink introduced the first yeast-E. coli shuttle vector, facilitating eukaryotic cloning and cross-host transfers that expanded subcloning's utility beyond prokaryotes.^[10] By the 1990s, subcloning integrated with polymerase chain reaction (PCR) technology—developed by Kary Mullis in 1983 and commercialized in the mid-1980s—to generate precise inserts without dependence on natural restriction sites, streamlining workflows and reducing labor-intensive steps.^[11] This period marked a shift from purely restriction enzyme-reliant methods toward more versatile amplification-based strategies. The technique evolved further in the early 2000s with recombination systems, exemplified by Invitrogen's Gateway cloning platform launched in 1999, which employed bacteriophage lambda site-specific recombination for directional, scarless transfer of inserts between vectors, significantly improving efficiency, throughput, and fidelity over traditional ligation.^[12] Subcloning's advancements proved instrumental in the Human Genome Project (1990–2003), where it enabled the fragmentation and transfer of large genomic inserts from bacterial artificial chromosomes into specialized sequencing vectors, supporting high-throughput assembly and analysis of the human genome.^[13]

Molecular Principles

Role of Vectors and Inserts

In subcloning, vectors serve as the essential DNA backbone that enables the replication, maintenance, and selection of recombinant molecules within host cells, while inserts represent the specific genetic sequences of interest that are transferred into these vectors for further manipulation or expression. Destination vectors, such as high-copy plasmids from the pUC series, are widely used for efficient propagation of inserts in Escherichia coli due to their mutated ColE1 origin of replication, which supports copy numbers exceeding 500 per cell, facilitating high-yield DNA production. These vectors include key features like a multiple cloning site (MCS)—a polylinker region containing unique restriction enzyme recognition sites for precise insert integration—an origin of replication (ori) for autonomous propagation, and selectable markers such as the ampicillin resistance gene (bla) to identify transformed hosts. Expression vectors like the pET series, which incorporate the T7 promoter for inducible high-level protein production in T7 RNA polymerase-expressing strains, extend this functionality by providing regulatory elements for downstream applications in protein studies. Shuttle vectors, designed with multiple origins of replication (e.g., one for E. coli and another for yeast or mammalian cells), allow seamless transfer and propagation of inserts across diverse host organisms, enhancing versatility in multi-host experiments.^[14]^[15] Inserts in subcloning are DNA fragments carrying the genetic cargo, such as genes, promoters, or regulatory elements, that are excised or amplified from source material like PCR products, genomic libraries, or existing recombinant clones, and then incorporated into the destination vector to confer new properties or enable functional analysis. These inserts typically range in size from 100 base pairs (bp) to 10 kilobases (kb), balancing ease of manipulation with the complexity of the sequence; smaller inserts (under 1 kb) are common for regulatory elements, while larger ones (up to 10 kb) suit full genes or operons, though efficiency decreases beyond this due to recombination risks in bacterial hosts. Sources of inserts include polymerase chain reaction (PCR) amplification for targeted sequences or restriction digestion of parental plasmids, ensuring the fragment ends are compatible with the vector's MCS.^[1]^[16]^[3] Compatibility between vectors and inserts is governed by principles that ensure efficient and directional ligation, primarily through matching cohesive or blunt ends generated by restriction enzymes at the MCS and insert termini. For instance, using enzymes like EcoRI or HindIII creates compatible sticky ends that anneal precisely, while linkers or adapters can bridge incompatible sites by adding tailored restriction motifs. To prevent vector self-ligation, which would yield empty recombinants, alkaline phosphatase treatment dephosphorylates the vector's 5' ends, blocking recircularization without affecting the insert's phosphorylated termini. Overall, vectors provide the structural and selective framework for stable propagation, whereas inserts deliver the functional payload, forming the core of subcloning's modular design.^[1]^[16]^[15]

Key Enzymes and Reactions

Type II restriction endonucleases serve as the primary tools for preparing DNA inserts and vectors in subcloning by recognizing specific short DNA sequences and cleaving the phosphodiester backbone at precise locations. These enzymes, such as EcoRI and HindIII, are classified as Type II, meaning they require only Mg²⁺ as a cofactor and cut within or near their 4- to 8-base-pair palindromic recognition sites, producing either sticky (cohesive) or blunt ends depending on the stagger of the cut. For instance, EcoRI recognizes the sequence 5'-GAATTC-3' and cleaves between the G and A residues, generating 5' sticky ends with a 4-base AATT overhang; HindIII recognizes 5'-AAGCTT-3' and cleaves between the first A and A, also producing 5' sticky ends with an AGCT overhang. This cleavage specificity allows for the generation of compatible ends that facilitate precise fragment assembly without random cuts.^[17]^[18] DNA ligase, most commonly T4 DNA ligase from bacteriophage T4, is essential for joining the prepared DNA fragments by catalyzing the formation of phosphodiester bonds between the 5'-phosphate and adjacent 3'-hydroxyl groups on double-stranded DNA substrates. The reaction is ATP-dependent and occurs in three enzymatic steps: first, the ligase forms an enzyme-AMP intermediate by reacting with ATP; second, the AMP group is transferred to the 5'-phosphate terminus of the DNA; and third, the activated 5'-phosphoryl attacks the 3'-hydroxyl, sealing the nick and releasing AMP. Optimal conditions for this ligation include incubation at 16°C overnight to maximize efficiency with cohesive ends, though higher temperatures like 25°C can be used for shorter times with blunt ends.^[19]^[20] Additional enzymes support subcloning by modifying ends to prevent artifacts or enable alternative strategies. Alkaline phosphatase, such as calf intestinal alkaline phosphatase (CIP), dephosphorylates the 5'-ends of linearized vectors by hydrolyzing the phosphate group, thereby preventing recircularization during ligation since T4 DNA ligase cannot join dephosphorylated ends without a 5'-phosphate donor from the insert. For blunt-end subcloning, when sticky ends are absent or incompatible, polymerases like T4 DNA polymerase or the Klenow fragment (lacking 5'→3' exonuclease activity) of Escherichia coli DNA polymerase I are used; these fill in 5' overhangs via 5'→3' polymerase activity or excise 3' overhangs via 3'→5' exonuclease activity, creating flush ends for non-directional ligation.^[21]^[22] The core reaction principles in subcloning emphasize compatibility and stoichiometry to ensure efficient recombinant formation. Directional cloning exploits asymmetric sticky ends from enzymes like EcoRI and HindIII at opposite insert termini, allowing compatible pairing with the vector in only one orientation and reducing inverted inserts. Blunt-end reactions, while less directional, rely on the same ligase mechanism but achieve specificity through dephosphorylation. To promote insert incorporation over vector self-ligation, a molar ratio of insert to vector DNA of approximately 3:1 is standard, as it saturates vector ends while minimizing multimers.^[23]^[24]

Detailed Procedure

Insert and Vector Preparation

The preparation of the insert in subcloning begins with the isolation of the desired DNA fragment, typically through restriction enzyme digestion of the parent vector, or alternatively through polymerase chain reaction (PCR) amplification from a template such as a cDNA library or existing plasmid when necessary to introduce restriction sites.^[25] For PCR-based preparation, primers are designed to incorporate restriction enzyme recognition sites at their 5' ends, flanking the target sequence, to generate compatible overhangs for subsequent ligation; for example, sequences like AAGCTT (HindIII) or GTCGAC (SalI) are added to enable precise directional cloning.^[26] The PCR reaction employs high-fidelity DNA polymerase to minimize errors, with typical conditions including an initial denaturation at 98°C for 2 minutes, followed by 18–30 cycles of denaturation (98°C, 10 seconds), annealing (55–65°C, 15–30 seconds), and extension (72°C, 30 seconds per kb), ending with a final extension at 72°C for 1–5 minutes.^[26] After amplification, the product is verified and purified via agarose gel electrophoresis on a 0.8–1.5% gel stained with ethidium bromide or safer alternatives like SYBR Safe, allowing separation based on size (100 bp to 25 kb range) and excision of the specific band to isolate the insert from primer dimers or non-specific products.^[27] Gel purification of the insert involves dissolving the excised agarose slice in a chaotropic salt buffer (e.g., guanidine thiocyanate), binding the DNA to a silica column, washing away contaminants, and eluting in low-salt buffer (e.g., 10 mM Tris-HCl, pH 8.0) for recovery yields of 50–80%.^[28] Quantification follows using UV spectrophotometry, where the concentration is calculated as 50 μg/mL per absorbance unit at 260 nm (A260) for double-stranded DNA, with purity assessed by an A260/A280 ratio of approximately 1.8 indicating minimal protein contamination and an A260/A230 ratio near 2.0–2.2 showing low organic contaminants.^[25] Vector preparation entails digestion of the plasmid with one or two restriction enzymes to linearize it and create ends compatible with the insert, using manufacturer-recommended buffers and incubation at 37°C for 1–2 hours (or overnight for complete digestion).^[29] To prevent self-ligation, the linearized vector is treated with alkaline phosphatase (e.g., calf intestinal phosphatase, CIP, at 0.01 U/pmol ends) for 30 minutes at 37°C, followed by heat inactivation or purification to remove the enzyme.^[1] For vectors with internal restriction sites, partial digestion may be employed by limiting enzyme amount or time to ensure only the multiple cloning site is cleaved, preventing fragmentation.^[30] Post-digestion and dephosphorylation, the linearized vector is separated from uncut supercoiled plasmid via agarose gel electrophoresis (1% gel), followed by extraction of the linear band using silica-based kits to achieve >90% purity and remove enzymes or buffer salts.^[31] Quality control for both insert and vector includes agarose gel electrophoresis to confirm fragment size against a DNA ladder (e.g., 100 bp to 10 kb markers) and assess purity by the absence of smearing or extraneous bands, ensuring integrity for ligation.^[32] Contaminants such as RNases, which can co-purify from cellular sources and degrade any residual RNA or affect downstream steps, are minimized by using RNase-free reagents, disposable gloves, and dedicated workspaces to prevent skin-derived enzyme introduction.^[33] To optimize ligation efficiency, yields are calculated based on molar ratios, typically using ~100 ng of vector (e.g., 3 kb plasmid, ~0.05 pmol) with ~50 ng of insert (e.g., 1 kb fragment, ~0.15 pmol) to achieve a 3:1 insert:vector molar ratio (calculated as pmol insert / pmol vector, using approximate MW = bp × 660 g/mol), promoting directional insertion while avoiding excess that could favor concatemers.^[29]^[34]

Ligation and Transformation

The ligation process in subcloning begins with the assembly of the prepared insert and linearized vector DNA fragments in a reaction mixture containing T4 DNA ligase enzyme and 10x ligase buffer, which provides necessary cofactors such as ATP and Mg²⁺ for enzymatic activity.^[35]^[34] Typical reaction volumes range from 10-20 μL, with 50-200 ng of vector DNA and a calculated amount of insert DNA to achieve the desired molar ratio.^[36] To promote the formation of recombinant molecules through phosphodiester bond formation, the insert-to-vector molar ratio is optimized, commonly at 3:1, to favor insert incorporation over vector self-ligation or insert multimers, thereby increasing the yield of desired circular plasmids.^[34]^[37] For cohesive ends typically generated in restriction enzyme-based subcloning, incubation occurs at room temperature (20-25°C) for 10 minutes to 4 hours or at 16°C overnight, allowing efficient annealing and ligation while minimizing non-specific reactions.^[19]^[38] Vector-only ligation controls are routinely included to quantify background religation rates, which should be low (e.g., <1% of total transformants) for effective subcloning.^[31] Following ligation, the recombinant DNA is introduced into host cells through transformation, a critical step that delivers the ligated plasmids into competent Escherichia coli for propagation.^[24] Chemical transformation via heat shock is widely used, where 1-5 μL of ligation mixture is added to 50-100 μL of competent cells on ice, followed by a 30-90 second incubation at 42°C to facilitate DNA uptake.^[39] Alternatively, electroporation involves mixing 1-2 μL of DNA with 20-50 μL of electrocompetent cells and applying a high-voltage pulse (e.g., 1.8-2.5 kV in 0.1-0.2 cm cuvettes), offering higher throughput for large libraries.^[40] Transformation efficiencies vary by method and cell strain, typically ranging from 10⁶ to 10⁹ colony-forming units (CFU) per μg of DNA for heat shock and up to 10¹⁰ CFU/μg for electroporation, influenced by DNA quality and cell viability.^[39]^[41] Chemical competence in E. coli is achieved by treating log-phase cells with ice-cold 50-100 mM CaCl₂, which neutralizes negative charges on lipopolysaccharides in the outer membrane, promoting electrostatic binding of negatively charged DNA and altering membrane permeability to enable uptake during heat shock.^[42]^[43] After transformation, cells are immediately placed on ice to stabilize the process, then diluted into 250-1000 μL of pre-warmed SOC medium (a nutrient-rich broth containing tryptone, yeast extract, NaCl, KCl, MgCl₂, MgSO₄, and glucose) and incubated at 37°C with shaking (200-250 rpm) for 45-60 minutes.^[44]^[45] This recovery step allows expression of antibiotic resistance genes from the plasmid, enhances cell viability, and can double transformation efficiency compared to standard LB medium.^[46]^[47]

Amplification of Recombinant Plasmids

Following successful transformation, recombinant plasmids are amplified by inoculating a small volume of transformed Escherichia coli cells into Luria-Bertani (LB) broth supplemented with the appropriate antibiotic to maintain selective pressure and ensure propagation of plasmid-bearing cells.^[48] The culture is incubated at 37°C with agitation (typically 200–250 rpm) to facilitate oxygen transfer and logarithmic growth, with optical density at 600 nm (OD₆₀₀) monitored to assess cell density; growth is often continued to the late log phase (OD₆₀₀ ≈ 0.4–0.6) if induction of expression is planned, or overnight to stationary phase for maximal biomass accumulation in routine subcloning.^[49]^[50] Plasmid yield per cell varies significantly based on the vector's origin of replication, with high-copy-number plasmids such as pUC19 achieving 500–700 copies per cell under standard conditions, compared to low-copy-number vectors like pBR322, which maintain only 15–20 copies per cell.^[51] This difference directly impacts the amount of recombinant DNA recoverable, as higher copy numbers enable greater amplification efficiency during host cell division. Following growth, plasmids are typically extracted using an alkaline lysis miniprep method, which selectively denatures chromosomal DNA while preserving supercoiled plasmid integrity through neutralization and precipitation steps.^[52] For initial screening in subcloning workflows, amplification is performed on a small scale using 1–5 mL cultures, yielding sufficient DNA (typically 5–50 μg total) for downstream verification without specialized equipment.^[53] Larger-scale production scales to liter volumes in shake flasks or bioreactors/fermenters, where controlled parameters like pH, dissolved oxygen, and nutrient feeding optimize yields; for E. coli hosts, 37°C remains the standard temperature to balance growth rate and plasmid stability.^[54] Post-amplification purification via alkaline lysis or column-based methods routinely yields 5–50 μg of plasmid DNA per mL of culture, with higher outputs from high-copy vectors under optimized conditions.^[55]

Selection of Clones

Selection of clones in subcloning involves distinguishing recombinant plasmids containing the desired insert from non-recombinant vectors and untransformed cells, primarily through phenotypic markers integrated into the cloning vector.^[56] Antibiotic selection serves as the initial step to identify transformed bacterial cells, utilizing resistance genes such as the bla gene encoding β-lactamase for ampicillin resistance, which allows only cells harboring the plasmid to survive on media containing the antibiotic. This method, derived from early cloning vectors like pBR322, ensures high initial enrichment but does not differentiate between self-ligated vectors and true recombinants. To further select for recombinants, blue-white screening exploits the lacZα gene fragment in vectors such as pUC19, where insertion of foreign DNA into the multiple cloning site disrupts α-complementation of β-galactosidase, preventing hydrolysis of X-gal substrate and resulting in white colonies, while non-recombinants form blue colonies on indicator plates. This technique, introduced with the pUC series, provides a rapid visual distinction, with recombinant frequencies often reaching 80-95% under optimized conditions. Insertional inactivation extends this principle to antibiotic resistance markers; for instance, cloning into the tetracycline resistance gene (tetR) of pBR322 disrupts its function, rendering recombinants sensitive to tetracycline while retaining ampicillin resistance from the intact bla gene. For vectors with dual markers, replica plating or patch tests enable sequential screening: colonies are transferred from ampicillin plates to tetracycline media, identifying sensitive patches as potential recombinants.^[57] Without such screening, recombinant yields typically range from 1-10% of total transformants due to prevalent vector religation.^[57] The reliability of these disruption-based methods increases with insert size, as fragments larger than 1 kb more effectively inactivate marker genes by causing significant frameshifts or steric hindrance.^[58]

Verification and Analysis

Screening Techniques

Screening techniques in subcloning serve as initial, low-resolution methods to verify the presence and correct orientation of the inserted DNA fragment in transformed bacterial clones, prior to more definitive analyses. These approaches enable efficient filtering of potential recombinants from a pool of transformants, distinguishing those with the desired subcloned insert from empty vectors or religated backbones. By focusing on rapid, cost-effective assays, researchers can prioritize promising clones for further processing, such as plasmid extraction detailed in amplification protocols. Colony PCR is a widely adopted technique for directly assessing insert presence without requiring plasmid isolation. In this method, a small portion of a bacterial colony is resuspended and lysed, typically by brief boiling, to release the plasmid DNA, which is then used as a template in a polymerase chain reaction with insert-specific primers. The reaction amplifies a region spanning the insert or junction sites, and the products are analyzed by agarose gel electrophoresis to confirm the expected band size corresponding to the insert length. For inserts under 3 kb, this approach provides quick results within hours, making it suitable for screening dozens of colonies. Primers flanking the multiple cloning site on the vector can also be used, where the absence of an insert yields a smaller amplicon than one with the insert. This technique is particularly valuable in subcloning workflows due to its simplicity and ability to detect inserts as small as 100 bp. Restriction digest screening offers a complementary verification step by examining the physical structure of the recombinant plasmid. Following miniprep isolation of plasmid DNA from overnight cultures of selected colonies, the DNA is subjected to double digestion with restriction enzymes that flank the insertion site or cut within the insert. The resulting fragments are separated by gel electrophoresis, revealing expected patterns such as the vector backbone and released insert if ligation was successful; for example, a 3 kb insert in a 5 kb vector might produce bands of 5 kb and 3 kb upon digestion, contrasting with a single ~5 kb band for an empty vector (linearized, assuming negligible multiple cloning site fragment). This method confirms both insert presence and approximate size, though it requires more time than colony PCR due to the need for culture growth and purification. To determine insert orientation, particularly in blunt-end or non-directional ligations, PCR-based checks employ asymmetric primer pairs—one annealing to the vector backbone and the other to an internal sequence within the insert. Amplification occurs only if the insert is in the correct orientation, producing a specific band size on gel analysis; for instance, a forward vector primer paired with a reverse insert primer yields a product solely for the desired direction. This approach, adaptable to colony lysates, rapidly distinguishes forward from reverse inserts without sequencing. It has been demonstrated as a reliable alternative to restriction mapping for orientation verification in various plasmid systems. These techniques support high-throughput screening, often in 96-well formats for large clone libraries, allowing parallel processing of hundreds of candidates via automated PCR or digestion setups. However, they are prone to false positives, such as amplification of residual ligation mixture or incomplete digests, necessitating orthogonal confirmation like sequencing for final validation.

Confirmation Methods

Confirmation of subcloned constructs is essential to ensure the integrity, accuracy, and functionality of the transferred DNA insert within the new vector, distinguishing this step from preliminary screening by providing high-fidelity validation of the full sequence and assembly. These methods focus on verifying the precise nucleotide composition, detecting any unintended alterations such as mutations introduced during PCR amplification or ligation errors, and confirming proper integration at the vector-insert junctions. While initial screens like restriction digests offer rapid insights, confirmation techniques deliver definitive proof of the construct's fidelity before proceeding to downstream applications. Sanger sequencing remains the gold standard for validating individual subcloned plasmids due to its high accuracy and ability to resolve sequences up to approximately 1,000 base pairs per read. This chain-termination method involves using vector-specific primers, such as those annealing to flanking regions like T7 or SP6 promoters, to initiate sequencing from known sites adjacent to the insert. Primer walking extends coverage across longer inserts by designing sequential primers based on initial read results, ensuring comprehensive analysis of the insert ends and ligation junctions where scars or mismatches may occur. For instance, primers targeting 20-50 base pairs into the vector backbone allow detection of insertions, deletions, or point mutations arising from enzymatic steps like PCR, with error rates typically around 10^{-6} per base pair when using high-fidelity polymerases, minimizing the introduction of mutations during amplification.^[59] This approach confirms the exact sequence of the subcloned fragment, identifying any discrepancies from the reference design. For high-throughput scenarios involving clone libraries or multiple variants, next-generation sequencing (NGS) technologies provide scalable confirmation by generating millions of short reads that can be assembled into full plasmid contigs. Platforms like Illumina or Oxford Nanopore enable parallel sequencing of numerous constructs, with long-read options from the latter achieving complete plasmid resolution in a single run without the need for extensive primer design. Post-sequencing, de novo assembly software aligns reads to reference vectors, verifying the insert's full length and orientation while quantifying coverage depth—typically aiming for 50-100x to minimize errors. This method is particularly useful for detecting rare variants in diverse subcloning pools, offering greater efficiency than Sanger for projects exceeding dozens of clones. Functional confirmation through transient expression assays complements sequence-based validation by assessing the subcloned construct's ability to produce the intended protein or RNA, thereby verifying molecular integrity beyond nucleotide accuracy. In these assays, the plasmid is transfected into appropriate host cells (e.g., HEK293 for mammalian systems), followed by evaluation of expression via Western blot, immunofluorescence, or reporter gene activity, confirming that the insert is not only correctly sequenced but also transcriptionally active without regulatory disruptions at junctions. Such tests are applied judiciously to subcloning workflows, focusing on constructs destined for expression studies, and typically require 24-48 hours for results. Standard criteria for successful confirmation include achieving 100% sequence identity to the expected reference across the entire insert and vector junctions, with no evidence of frameshifts, stop codons, or ligation artifacts like extra nucleotides. Junction analysis specifically examines the 10-20 base pairs at each insert-vector interface to ensure seamless integration, often using targeted primers for bidirectional sequencing. These benchmarks ensure the subcloned construct is reliable for subsequent experiments, with any deviations prompting re-cloning.

Applications and Variations

In Bacterial Systems

Subcloning in bacterial systems, particularly using Escherichia coli as a host, leverages the prokaryotic cell's simplicity for efficient DNA propagation and expression. These systems offer advantages such as rapid bacterial growth rates, which allow for quick amplification of recombinant plasmids, straightforward transformation protocols via electroporation or heat shock, and cost-effectiveness, making them ideal for large-scale library screening and protein production.^[60]^[61] A typical workflow involves subcloning a gene of interest from a genomic library into an expression vector like pET for E. coli expression. The process begins by isolating the target gene insert from the library plasmid through restriction enzyme digestion or PCR amplification, followed by ligation into the multiple cloning site of the pET vector under the control of the T7 promoter. The recombinant plasmid is then transformed into competent E. coli BL21(DE3) cells, selected using antibiotic markers such as ampicillin resistance, and induced with isopropyl β-D-1-thiogalactopyranoside (IPTG) to drive high-level protein production via the lac operator-regulated T7 RNA polymerase.^[62]^[63] This approach enables scalable expression, often yielding milligrams of purified protein per liter of culture. An early demonstration of bacterial plasmid subcloning involved transferring antibiotic resistance genes between plasmids, as shown in foundational experiments where restriction endonuclease-generated fragments from separate plasmids—one carrying kanamycin resistance and another tetracycline resistance—were joined in vitro to form functional recombinant molecules capable of conferring dual resistance upon transformation into E. coli.^[7] This technique highlighted the potential for constructing novel plasmids with combined traits. For handling larger DNA fragments, variations employ bacterial artificial chromosomes (BACs), which are low-copy F-factor-based vectors that stably propagate inserts exceeding 100 kb, up to 300 kb, without rearrangements, facilitating subcloning of complex genomic regions for functional studies.^[64]^[65]

In Eukaryotic Expression Systems

Subcloning into eukaryotic expression systems enables the production of recombinant proteins that require post-translational modifications, such as glycosylation, which are often absent in bacterial hosts. These systems utilize specialized vectors designed for propagation in both bacterial and eukaryotic cells, facilitating the transfer of inserts from prokaryotic plasmids to eukaryotic hosts like yeast, insect, or mammalian cells. Key adaptations include promoters responsive to eukaryotic transcription factors, selection markers compatible with eukaryotic metabolism, and elements ensuring proper mRNA processing, such as polyadenylation signals.^[66] In yeast systems, shuttle vectors like pYES2 are commonly employed for subcloning into Saccharomyces cerevisiae. These vectors contain a bacterial origin of replication for initial amplification in E. coli, alongside yeast-specific elements including the GAL1 promoter for inducible expression and the URA3 auxotrophic marker for selection in uracil-deficient strains. The process involves subcloning the gene of interest into the multiple cloning site of pYES2, followed by transformation into yeast cells, where galactose induction activates transcription; this system has been foundational for efficient DNA manipulation in yeast since its development in the late 1980s.^[67]^[68] For mammalian expression, vectors such as pcDNA3.1 are widely used to subclone cDNAs under the control of the cytomegalovirus (CMV) immediate-early promoter, which drives high-level transcription in a broad range of cell lines. Subcloning requires consideration of eukaryotic mRNA processing, including the incorporation of introns for enhanced splicing efficiency in some constructs and the bovine growth hormone (BGH) polyA signal to ensure proper 3' end formation and mRNA stability. These features support transient or stable expression in cells like HEK293, enabling the study of proteins in a native-like cellular environment.^[69]^[66] In insect cell systems, subcloning often utilizes baculovirus vectors like pFastBac for expression in Sf9 or High Five cells. The gene of interest is subcloned into pFastBac, which is then transformed into DH10Bac E. coli cells containing a bacmid; site-specific transposition generates a recombinant bacmid, which is subsequently transfected into insect cells to produce virus particles for protein expression. This recombination-based approach leverages the polyhedrin promoter for high-yield production, particularly suited for secreted or membrane proteins requiring complex glycosylation.^[70]^[66] A critical aspect of subcloning for eukaryotic systems is codon optimization, which adjusts the gene sequence to match the host's tRNA usage bias, thereby enhancing translation efficiency and protein yield. For instance, optimizing for yeast or mammalian codon preferences can increase expression levels by several fold compared to native sequences, as rare codons may stall ribosomes in heterologous hosts. This step is typically performed prior to subcloning and is essential for therapeutic protein production.^[71]^[72]

Advantages and Challenges

Benefits Over Direct Cloning

Subcloning provides significant efficiency gains by allowing researchers to transfer a verified DNA insert from an initial cloning vector to an optimized destination vector, such as those designed for enhanced stability, higher copy number, or improved expression levels, without requiring re-amplification or re-extraction from the original genomic or PCR source material.^[1] This approach minimizes the introduction of polymerase errors that can occur during repeated PCR amplification and leverages pre-existing, sequence-verified constructs to streamline downstream applications.^[2] The technique offers substantial flexibility, enabling easy host switching—such as from bacterial strains sensitive to methylation (e.g., using dam⁻/dcm⁻ hosts like JM110) to those optimized for mammalian expression—and the addition of regulatory elements like promoters or tags without disrupting the insert integrity.^[1] By first purifying the insert via gel isolation or PCR cleanup, subcloning reduces background noise in cloning libraries, as it eliminates contaminating vector DNA or non-specific fragments that plague direct cloning attempts from complex mixtures.^[73] In terms of cost and time savings, subcloning reuses confirmed inserts, avoiding the labor-intensive and expensive steps of repeated genomic DNA extractions or PCR optimizations, while compatible restriction ends typically yield high success rates, with blunt-end ligations achieving over 90% insert-containing transformants when using optimized buffers.^[73] These efficiencies are particularly evident in streamlined protocols, such as rapid 5–15 minute ligations, which can complete the entire process in under an hour.^[1] Furthermore, subcloning facilitates modular cloning strategies by allowing inserts to be excised and integrated into type IIS restriction enzyme-based systems like Golden Gate assembly, where hierarchical constructs can be built iteratively using standardized parts and fusion sites for seamless, one-pot multi-fragment assemblies.^[74] This integration supports scalable synthetic biology applications, such as constructing genetic circuits or multi-gene pathways, by treating subcloned products as reusable modules compatible across vector standards like MoClo or GoldenBraid.^[75]

Common Limitations and Troubleshooting

Subcloning procedures can encounter several limitations that impact efficiency and reliability. One primary challenge is the low ligation efficiency associated with blunt-end ligation, which is typically 10-fold less efficient than cohesive-end ligation due to the lack of complementary overhangs guiding the reaction.^[76] Another limitation arises from insert instability, particularly when cloning genes that produce toxic proteins to the host cell, leading to deletions, rearrangements, or failed propagation as the host selects against harmful sequences.^[77] Host restrictions further complicate subcloning; for instance, standard E. coli dam⁺ strains methylate DNA at GATC sites, rendering certain restriction enzymes inactive and necessitating the use of dam⁻ strains, which may introduce other propagation issues like reduced plasmid stability.^[78] Troubleshooting these issues requires targeted adjustments to the workflow. For poor transformation efficiency, often resulting in few or no colonies, employing freshly prepared competent cells is essential, as repeated freeze-thaw cycles can significantly diminish competency.^[79] If no recombinant clones are obtained despite successful ligation—as confirmed by control reactions—increasing the insert-to-vector molar ratio to 3:1 or higher can favor productive joins, or switching to recombinase-based systems like In-Fusion cloning can bypass ligation altogether for seamless assembly.^[79] Contamination, such as nuclease activity degrading DNA, can be mitigated through rigorous sterile techniques, including working in a dedicated clean area and treating reagents with DNase to eliminate extraneous nucleic acids.^[80] When issues persist, alternatives like PCR-free methods (e.g., Gibson assembly) or commercial kits such as TOPO cloning offer faster workflows by reducing reliance on restriction-ligation steps and minimizing error-prone handling.^[81] Additionally, for inserts generated via PCR, using high-fidelity polymerases is critical to minimize mutations, as standard Taq polymerase has an error rate of approximately 1 error per 10,000 bases (10⁻⁴ per bp), while high-fidelity polymerases achieve rates as low as 10⁻⁷ per bp.^[82] As of 2025, emerging techniques such as CRISPR-assisted cloning and optimized commercial kits continue to address these limitations by improving precision and reducing error rates in complex assemblies.^[83]

References

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Molecular Cloning Guide
### Summary of Subcloning
[2]
Common Cloning Applications and Strategies - US
Subcloning refers to moving one fragment of a plasmid into another plasmid that can serve as a vector. There are a variety of reasons why it is necessary to ...
[3]
Subcloning - an overview | ScienceDirect Topics
### Summary of Subcloning
[4]
High-Throughput Cloning and Expression Library Creation ... - PMC
Once the entry clone with the desired quality is obtained, the insert may be subcloned to many expression vectors.
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Gene Cloning & Subcloning | Custom DNA Cloning Services
Rating 4.9 (1,044) Subcloning is another basic procedure in molecular biology for transferring DNA inserts from one vector to another to study the gene sequence of interest.Overview · Service Bundles · Custom PCR Cloning ServiceMissing: definition | Show results with:definition
[6]
Recombinant DNA - The Cell - NCBI Bookshelf - NIH
Recombinant DNA technology, which provided scientists with the ability to isolate, sequence, and manipulate individual genes derived from any type of cell.
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Construction of Biologically Functional Bacterial Plasmids In Vitro
Abstract. The construction of new plasmid DNA species by in vitro joining of restriction endonuclease-generated fragments of separate plasmids is described.
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https://doi.org/10.1073/pnas.70.11.3240
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Molecular Cloning Technology - Past, Present and Future | NEB
### Historical Milestones in Molecular Cloning and Subcloning
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History of insulin - PMC - NIH
Jul 16, 2012 · In 1978, the first recombinant DNA human insulin was prepared by David Goeddel and his colleagues (of Genentech) by utilizing and combining the ...
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Transformation of yeast - PubMed
A stable leu2- yeast strain has been transformed to LEU2+ by using a chimeric ColE1 plasmid carrying the yeast leu2 gene.Missing: shuttle vector
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https://www.bioprocessonline.com/doc/gateway-cloning-technologya-universal-cloning-0001
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GATEWAY Cloning Technology—A Universal Cloning System
Dec 10, 1999 · The first round of GATEWAY Cloning Technology product releases is due in December of '99, with more vectors and systems to come. For more ...
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https://blog.addgene.org/plasmids-101-shuttle-vectors
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Plasmids 101: Shuttle Vectors - Addgene Blog
May 20, 2025 · This post describes the design of shuttle vectors, which are designed for replication, selection, and expression in more than one host ...
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The art of vector engineering: towards the construction of next ...
We provide a detailed view following the evolution of vectors built throughout the years destined to study microorganisms and their peculiarities.
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Plasmid Cloning by Restriction Enzyme Digest (with Protocols)
Subcloning by restriction digest is a commonly used lab technique. For the purposes of this tutorial we will discuss how to move a cDNA from one plasmid to ...
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Type II Restriction Enzymes: What You Need to Know | NEB | NEB
### Summary of Type II Restriction Enzymes
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Type II restriction endonucleases—a historical perspective and more
Here we discuss 'Type II' REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it.
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T4 DNA Ligase | NEB
### Summary of T4 DNA Ligase from https://www.neb.com/en-us/products/m0202-t4-dna-ligase
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DNA Ligation | NEB
### Summary of DNA Ligation (Directional Cloning Principles)
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Dephosphorylation | NEB
- **Purpose**: Dephosphorylation prevents vector re-circularization in cloning by removing 5´ phosphate groups using alkaline phosphatase (e.g., Quick CIP).
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Blunting | NEB
### Summary of Blunting in Subcloning Context
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https://www.thermofisher.com/us/en/home/brands/thermo-scientific/molecular-biology/molecular-biology-learning-center/molecular-biology-resource-library/spotlight-articles/optimize-dna-ligase.html
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Optimize Your DNA Ligation with 7 Must-Have Tips
This is typically done by using T4 DNA ligase. T4 DNA ligase is an enzyme that helps create the formation of a phosphodiester bond between the 3'-hydroxyl end ...
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Molecular cloning using polymerase chain reaction, an educational ...
Jan 19, 2015 · An OD 260/280 ratio of >1.8 and an OD 260/230 ratio of 2 to 2.2 is considered to be pure for DNA samples [16]. The OD 260/280 and 260/230 ratios ...Missing: quantification A260/ A280
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https://pmc.ncbi.nlm.nih.gov/articles/PMC4846332/
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Agarose Gel Electrophoresis for the Separation of DNA Fragments
Apr 20, 2012 · Agarose gel electrophoresis is the most effective way of separating DNA fragments of varying sizes ranging from 100 bp to 25 kb.
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Protocol - How to Purify DNA from an Agarose Gel - Addgene
Gel purification allows you to isolate and purify DNA fragments based on size. The procedure starts with standard agarose gel electrophoresis.
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[PDF] Novagen • pET System Manual • 11th Edition
The pET vectors were originally constructed by Studier and ... other vector elements is included with each pET vector and expression system to allow.
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[PDF] Techniques in Molecular Biology Cloning - Sandiego
How to add RE sites. You may need to add restriction enzyme sites. DNA and Linkers/Adaptors. •. Bothe are short oligonucleotides, custom synthesized that ...
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[PDF] Easy Subcloning - Feinberg Labs
Blunting 3' overhangs: Add 1 μl 2 mM all four dNTPs to your 20 μl restriction digest. Add 0.5-1 μl T4 DNA polymerase, and incubate at 37° for 5 min. T4 ...
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Agarose gel electrophoresis - Bioinformatics
Agarose gel electrophoresis is employed to check the progression of a restriction enzyme digestion, to quickly determine the yield and purity of a DNA isolation ...
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Preparation, Purification, and Quantitation of DNA & RNA
These include: wearing gloves throughout experiments to prevent contamination from RNases found on most human hands, changing gloves after touching skin ...
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https://www.neb.com/en-us/protocols/0001/01/01/dna-ligation-with-t4-dna-ligase-m0202
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Protocol - How to Ligate Plasmid DNA - Addgene
This reaction, called ligation, is performed by the T4 DNA ligase enzyme. The DNA ligase catalyzes the formation of covalent phosphodiester linkages, which ...
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[PDF] T4 DNA Ligase Protocol - Promega Corporation
Typical ligation reactions use 100–200ng of vector DNA. 1. Assemble the following reaction in a sterile microcentrifuge tube: vector DNA. 100ng insert DNA. 17ng.
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Successful Ligation and Cloning of Your Insert - Promega Connections
Oct 23, 2013 · Test various vector:insert DNA ratios to determine the optimal ratio for a particular vector and insert. In most cases, a 1:1 or 1:3 molar ratio ...
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[PDF] Rapid ligation protocol for plasmid cloning of DNA fragments
Standard protocols for DNA ligations are carried out for 1 to 24 h depending on the temperature and type of DNA ends. For routine subcloning, these.
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https://www.sciencedirect.com/science/article/pii/B9780124186873000276
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Transformation of E. coli Via Electroporation - ScienceDirect.com
The main advantages of electroporation over heat-shock transformation are the higher efficiency in the uptake of plasmid DNA and a faster, less involved ...
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High efficiency transformation of E. coli by high voltage electroporation
E. coli can be transformed to extremely high efficiencies by subjecting a mixture of cells and DNA to brief but intense electrical fields of exponential decay ...Missing: heat shock
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Revisiting the Mechanisms Involved in Calcium Chloride Induced ...
Nov 7, 2017 · It was reported by Sjöström et al. (1972) that the optimum concentration of calcium chloride for the uptake of DNA by S. aureus is 0.1 M CaCl2.
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Calcium chloride made E. coli competent for uptake of extraneous ...
In the standard method of transformation of Escherichia coli with extraneous DNA, cells are made competent for DNA uptake by incubating in ice-cold 100 mM CaCl ...
[45]
https://www.addgene.org/protocols/bacterial-transformation/
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Protocol - Bacterial Transformation - Addgene
Nov 13, 2017 · Add 250-1,000 μl LB or SOC media (without antibiotic) to the bacteria and grow in 37°C shaking incubator for 45 min. Pro-Tip This outgrowth step ...Missing: post | Show results with:post<|control11|><|separator|>
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https://www.bioline.com/mwdownloads/download/link/id/2690/pi_50234_soc_v2.pdf
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[PDF] SOC Medium - Bioline
SOC Medium is a rich medium used primarily to aid recovery of bacterial competent cells following transformation. Use of SOC medium improves the molecular ...Missing: post | Show results with:post
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Protocols Inoculating a Liquid Bacterial Culture - Addgene
Some protocols require bacteria to be in the log phase of growth. Check the instructions for your specific protocol and conduct an OD600 to measure the density ...
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Bacterial cultivation media and antibiotics - QIAGEN
Transferring bacteria directly from glycerol stocks, agar stabs, or liquid cultures is not recommended in microbiology as it can result in plasmid loss.
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An Optimized Transformation Protocol for Escherichia coli BW3KD ...
Nov 1, 2022 · Then, 1% culture was transferred to 50 mL fresh LB medium and cultured at 37°C until an OD600 of 0.5 to prepare competent cells for the TSS ...<|separator|>
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Improved M13 phage cloning vectors and host strains: nucleotide ...
Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mpl8 and pUC19 vectors. Author links open overlay panel. Celeste Yanisch- ...
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A rapid alkaline extraction procedure for screening recombinant ...
H.C. Birnboim, J. Doly, A rapid alkaline extraction procedure for screening recombinant plasmid DNA, Nucleic Acids Research, Volume 7, Issue 6, 24 November 1979 ...Missing: miniprep | Show results with:miniprep
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11 Reasons Why Your Plasmid Yield is Low & Easy Fixes
Jan 21, 2025 · ... culture for high copy number plasmids, double the volumes for low copy plasmids. Grow the culture until OD600 is around 3, then pellet the ...
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Engineering Escherichia coli to increase plasmid DNA production in ...
Engineering Escherichia coli to increase plasmid DNA production in high cell-density cultivations in batch mode - PMC.Missing: scaling 37C
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https://www.sigmaaldrich.com/US/en/technical-documents/technical-article/genomics/cloning-and-expression/blue-white-screening
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https://www.thermofisher.com/us/en/home/references/protocols/cloning/transformation-protocol/cloning-transformation.html
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Cloning & Transformation | Thermo Fisher Scientific - US
After amplification with a proofreading polymerase, place samples on ice ... 5-50 ug/ml, 35 ug/ml, 10 ug/ml. Hygromycin, 20-200 ug/ml, 50 ug/ml, 50-200 ug/ml.
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Comparing Cloning Efficiency of the pGEM-T ... - Promega Corporation
The TOPO TA Cloning system worked well for inserts less than 1kb, but showed a striking decrease in performance with larger insert sizes (1–3kb).
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Overview of Protein Expression Systems | Thermo Fisher Scientific
The origin of the target protein—Bacterial proteins are better expressed in bacterial systems, while mammalian proteins are better expressed in mammalian ...
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How are recombinant proteins expressed using bacterial vectors?
Advantages · High yield of protein production. · Low cost and simple culture conditions. · Rapid growth and easy genetic manipulation.<|separator|>
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pET Bacterial Recombinant Protein Expression Vector - VectorBuilder
The pET vector system is a powerful and widely used system for expressing recombinant proteins in E. coli. The gene of interest is cloned into the pET vector ...
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https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/309/466/pb3745en-ms.pdf
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Bacterial Artificial Chromosome Mutagenesis Using Recombineering
Bacterial artificial chromosomes, or BACs, are fertility- (F-) factor-based plasmid vectors that replicate stably in low copy number [2, 3]. Because of their ...
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An easy and versatile 2-step protocol for targeted modification and ...
Mar 20, 2012 · Bacterial artificial chromosomes (BACs) are low copy plasmids based on the F-plasmid of E. coli. They can carry up to 300 kb of foreign DNA. The ...
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A concise guide to choosing suitable gene expression systems ... - NIH
This overview guides both novices and experienced researchers facing challenging targets to select the most appropriate gene expression system for producing ...
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A System of Shuttle Vectors and Yeast Host Strains Designed ... - NIH
A series of yeast shuttle vectors and host strains has been created to allow more efficient manipulation of DNA in Saccharomyces cerevisiae.
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pYES2 Yeast Expression Vector 20 μg | Buy Online | Invitrogen
6–10 day deliveryThe pYES2 vector kit includes 20 μg of expression vector, a TOP10F´ E. coli stab, and an INVSc1 yeast stab. Store the vector at -20°C.
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[PDF] Mammalian Expression Vector User Manual (Version K)
Nov 10, 2010 · The control plasmid, pcDNA™3.1/CAT, is included for use as a positive control for transfection and expression in the cell line of choice.
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[PDF] Bac-to-Bac Baculovirus Expression System 10359 Rev A.0
Aug 13, 2015 · Transform the pFastBac™ construct into MAX Efficiency® DH10Bac™ competent E. coli to generate a recombinant bacmid. 3. Transfect the recombinant ...
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A critical analysis of codon optimization in human therapeutics - PMC
Codon-optimization describes gene engineering approaches that use synonymous codon changes to increase protein production.Optimizing Codon Usage For... · The Genetic Code, Trnas, And... · Figure 2. Trna-Mrna Base...
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Codon optimization with deep learning to enhance protein expression
Oct 19, 2020 · In gene synthesis, codon optimization involves recombination based on different criteria without changing the sequence of the amino acid and can ...
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[PDF] Subcloning Notebook Guide, BR152
Subcloning is a basic procedure in molecular biology required to move inserts from one vector to another to gain the desired functionality to study your ...Missing: definition | Show results with:definition
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A User's Guide to Golden Gate Cloning Methods and Standards - NIH
Nov 2, 2022 · We provide a beginner-friendly guide to Golden Gate assembly, compare the different available standards, and detail the specific features and quirks of ...Introduction · The Golden Gate Core Method · Fusion Site Design
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A User's Guide to Golden Gate Cloning Methods and Standards
Nov 2, 2022 · Summary : In this study, we have adopted Golden Gate modular cloning strategy to develop a robust and versatile DNA assembly platform for the ...Figure 1 · Figure 3 · Figure 5
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Blockerette-Ligated Capture T7-Amplified RT-PCR, a New Method ...
In addition, this method depends on blunt-end ligation, which is 10-fold less efficient than cohesive-end ligation. Because the terminal sequence of DNA may ...
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Remarkable stability of an instability-prone lentiviral vector plasmid ...
Jul 27, 2012 · Plasmid instability can be influenced by a number of factors including the expression of toxic gene products, metabolic burden of plasmid ...
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https://www.neb.com/en-us/tools-and-resources/selection-charts/dam-dcm-and-cpg-methylation
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https://www.neb.com/en-us/tools-and-resources/troubleshooting-guides/troubleshooting-guide-for-cloning
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https://www.sigmaaldrich.com/US/en/technical-documents/technical-article/genomics/cloning-and-expression/troubleshooting-for-molecular-cloning
[81]
Protocols for Cloning Without Restriction Enzymes or Ligases
Jun 8, 2025 · Methods like TOPO, SLIC, and Gibson will give you seamless clones without requiring restriction enzymes or, sometimes, even ligase.
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Efficient strategy for introducing large and multiple changes in ...
Jan 29, 2018 · It requires a high-fidelity DNA polymerase that minimizes unwanted mutations, such as KOD hot start DNA polymerase, Pfu DNA polymerase, or ...