Stew Peters meets with Dr. Aryanna Love to discuss the cloning techniques used by the PCR Tests using Luciferase and the Hydras for Chimera DNA changes for the Triple Helix Transformation..
Articles mentioned below..
We herein report the fabrication of core-crosslinked, fluorescent, and surface-functionalized worm-like block copolymer micelles as drug delivery vehicles. The polyether-based diblock terpolymer [allyl-poly(ethylene oxide)-block-poly(2-ethylhexyl glycidyl ether-co-furfuryl glycidyl ether)] was synthesized via anionic ring opening polymerization, and self-assembly in water as a selective solvent led to the formation of long filomicelles. Subsequent cross-linking was realized using hydrophobic bismaleimides as well as a designed fluorescent cross-linker for thermally induced Diels-Alder reactions with the furfuryl units incorporated in the hydrophobic block of the diblock terpolymer. As a fluorescent cross-linker, we synthesized and incorporated a cyanine 5-based bismaleimide in the cross-linking process, which can be used for fluorescence tracking of the particles. Furthermore, we covalently attached glucose to the allyl end groups present on the surface of the micelles to investigate active glucose-mediated transport into suitable cell lines. First studies in 2D as well as 3D cell culture models suggest a glucose-dependent uptake of the particles into cells despite their unusually large size compared to other nanoparticle systems used in drug delivery.
Background: Over the last decades, molecular cloning has transformed biological sciences. Having profoundly impacted various areas such as basic science, clinical, pharmaceutical, and environmental fields, the use of recombinant DNA has successfully started to enter the field of cellular engineering. Here, the polymerase chain reaction (PCR) represents one of the most essential tools. Due to the emergence of novel and efficient PCR reagents, cloning kits, and software, there is a need for a concise and comprehensive protocol that explains all steps of PCR cloning starting from the primer design, performing PCR, sequencing PCR products, analysis of the sequencing data, and finally the assessment of gene expression. It is the aim of this methodology paper to provide a comprehensive protocol with a viable example for applying PCR in gene cloning.
Results: Exemplarily the sequence of the tdTomato fluorescent gene was amplified with PCR primers wherein proper restriction enzyme sites were embedded. Practical criteria for the selection of restriction enzymes and the design of PCR primers are explained. Efficient cloning of PCR products into a plasmid for sequencing and free web-based software for the consecutive analysis of sequencing data is introduced. Finally, confirmation of successful cloning is explained using a fluorescent gene of interest and murine target cells.
Conclusions: Using a practical example, comprehensive PCR-based protocol with important tips was introduced. This methodology paper can serve as a roadmap for researchers who want to quickly exploit the power of PCR-cloning but have their main focus on functional in vitro and in vivo aspects of cellular engineering.
PCR based cloning is incredibly versatile and allows for nearly any piece of DNA to be placed into a backbone vector of choice with minimal limitations.
In its simplest form, PCR based cloning is about making a copy of a piece of DNA and at the same time adding restriction sites to the ends of that piece of DNA so that it can be easily cloned into a plasmid of interest.
For this example, we will describe how to copy a cDNA from one vector into a new vector that is better suited for analyzing the gene’s function. The process is shown graphically in the following cartoon, in which we are adding EcoRI and NotI sites to Your Gene of Interest (YGOI) for ligation into a recipient plasmid.
PCR cloning differs from traditional cloning in that the DNA fragment of interest, and even the vector, can be amplified by the Polymerase Chain Reaction (PCR) and ligated together, without the use of restriction enzymes. PCR cloning is a rapid method for cloning genes, and is often used for projects that require higher throughput than traditional cloning methods can accommodate. It allows for the cloning of DNA fragments that are not available in large amounts.
Typically, a PCR reaction is performed to amplify the sequence of interest, and then it is joined to the vector via a blunt or single-base overhang ligation prior to transformation. Early PCR cloning often used Taq DNA Polymerase to amplify the gene. This results in a PCR product with a single template-independent base addition of an adenine (A) residue to the 3′ end of the PCR product, through the normal action of the polymerase. These “A-tailed” products are then ligated to a complementary T-tailed vector using T4 DNA ligase, followed by transformation.
High-fidelity DNA polymerases are also now routinely used to amplify sequences with the PCR product containing no 3′ extensions. The blunt-end fragments are joined to a plasmid vector through a typical ligation reaction or by the action of an “activated” vector that contains a covalently attached enzyme, typically Topoisomerse I, which facilitates the vector:insert joining. Some PCR cloning systems contain engineered “suicide” vectors that include a toxic gene into which the PCR product must be successfully ligated to allow propagation of the strain that takes up the recombinant molecule during transformation.
A typical drawback common to many PCR cloning methods is a dedicated vector that must be used. These vectors are typically sold by suppliers, like NEB, in a ready-to-use linearized format and can add significant expense to the total cost of cloning. Also, the use of specific vectors restricts the researcher’s choice of antibiotic resistance, promoter identity, fusion partners, and other regulatory elements.
High efficiency, with dedicated vectors
Amenable to high throughput
Limited vector choices
Lack of sequence control at junction
Multi-fragment cloning is not straight forward
Directional cloning is difficult
Evolutionary studies necessary to dissect diverse biological processes have been limited by the lack of reverse genetic approaches in most organisms with sequenced genomes. We established a broadly applicable strategy using zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) for targeted disruption of endogenous genes and cis-acting regulatory elements in diverged nematode species.
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