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...them. An easy way to do this is gel purification. In gel purification, you use a voltage difference across...backbone. Sample results indicative of successful and unsuccessful ligations are indicated below. A successful...grow overnight cultures for DNA purification. The simplest purification you can do is a miniprep, but if...digests. Of course there’s much more detail and verification required for the process to work well, so let...backbone. Because you lose some DNA during the gel purification step, it is important to digest plenty of starting...prior to the ligation step or prior to the gel purification step, depending on the phosphatase you choose...   2. Isolate Your Insert and Vector by Gel Purification     Now that you’ve cut your insert and vector...

...you.  Starting from plasmids requires amplification, verification, and lentiviral production steps before...the same proportion after amplification as they were prior to amplification. And as anyone who has worked...process for using pooled lentiviral libraries. A) Amplification, validation, and lentiviral generation of a ...pooled library is transformed into E. coli for amplification. Transformed E. coli are allowed to grow on ...into HEK cells allows production of lentivirus. Purification of this lentivirus results in the pooled library...Figure 31.5.2 from McDade et al., 2016.   Amplification When you request a DNA pooled library from Addgene...might receive a similarly-sized aliquot from an amplification done by Addgene.) This small aliquot is not ...

...are used across species: replication, selection, and expression. Replication It’s usually not enough to...chromosome has a single origin of replication (ori), where DNA replication begins, so a bacterial plasmid...Eukaryotes are a bit more complicated. Yeast vectors may contain an autonomously replicating sequence (ARS), a...fast-growing populations of cells, the vector needs to replicate alongside its host, or it will be lost from the...compatible ori that will be recognized by its host’s replication machinery. A shuttle vector designed for unrelated...experiment. Yeast shuttle vectors have these replication sequences for their yeast targets as well as ...episomal vectors is to include viral oris to drive amplification, which helps increase cellular uptake, but this...

...activity of CcdB. Applications of ccdB in plasmid cloning Perhaps the most widely used application of CcdB is...selection markers. Restriction modification systems Because restriction modification systems consist of two enzymes...used as biological tools for a wide range of applications in molecular biology or in vivo studies. Let...types of plasmid addiction systems and their applications. The discovery of toxin-antitoxin systems Toxin-antitoxin...CcdA (antitoxin) where CcdB inferes with DNA replication by binding the GyrA subunit of DNA gyrase and...construct. Other toxin-antitoxin systems and their applications MazE/MazF Aside from CcdB/CcdA, there are many...counterselectable marker to create unmarked genetic modifications in the yeast Pichia pastoris. By combining both...

...two types of replicate controls: technical and biological. In general, technical replicates can be thought... employ transfection, negative, positive, and replicate controls.  Transfection controls: empty vector... Plasmid B (as internal control) This result indicates that the transfection was not successful due to...the interrogation of the independent variable. Replicate controls: technical and biological Reliable results...derived from one source. Conversely, biological replicates ARE independent and can be thought of as "reproducibility...reproducibility controls". Biological replicates are what makes up your sample size (aka your n value)"... provide more in depth information. Technical replicates An example of a technical control is the transfection...

...Student at the University of Manitoba. Location, Location, Location! Failure to Plan (for Storage) Is Planning...Viral Vector Blog Posts from Addgene 1. Location, location, location! What do buying real estate and using...for a house and choosing an AAV are… location, location, location! Just like this common real estate mantra...important factors related to location. Location (1): What tissue? Location (2): Where in the tissue/which...which cell type? Location (3): Traveling from the original location - Axonal Transport in the CNS What...particular experiment! Traveling from the Original Location - Axonal Transport It has been demonstrated that...previous literature using AAVs for DREADD delivery indicates ~7-21 days are required for the onset of gene ...

... It generally stays put, which makes it easy to locate in a genome. But there is a type of mobile DNA,... hyperactive and likes to jump around from one location in the genome to another. This jumping is what...most transposable elements (TEs) results in the duplication of this target site sequence at the site of insertion...This is similar to how retroviruses, like HIV, replicate. Class I TEs do not encode a transposase enzyme...enzyme.  Class I TEs are considered replicative since every time they jump they make a copy of themselves...retroviruses both in their structure and mechanism of replication. They contain two genes: gag and pol. The pol...they move. Most Class II transposons have a non-replicative “cut and paste” mechanism of transposition: they...

...editors catalyze purine-to-purine or pyrimidine-to-pyrimidine base changes. Solid red arrows indicate a conversion...conversion directly catalyzed by the base editor. Dotted red arrows indicate the change introduced to ... point modifications. CRISPR base editing persists through multiple cell divisions, indicating that this...target modification in primary T cells, making them a promising tool for cell therapy applications. Dual...Base editing publication highlights In the table below, you'll find a list of publications we've highlighted...Early CRISPR applications were often limited by the low editing efficiency of homology-directed repair...following base editing and DNA repair. Black arrows indicate natural cellular processes. BER = base excision...

...Each round of amplification should result in a 10-100-fold increase in virus. Purification (2 days) - Purification... Purification is required if rAdV is to be used in vivo. The standard method for purification of rAdV ...vectors (AdV) are attractive vectors for research applications and gene therapy: they can be produced at high...AdVs is what makes them ideal candidates for applications in oncolysis and vaccination!) In the 65 years...Adenovirus-mediated gene delivery: Potential applications for gene and cell-based therapies in the new...genes E1 and E3. Without these genes, AdVs cannot replicate on their own but can be produced in E1-containing...The ever popular pAdEasy system belongs to this category. 3rd Gen AdV (Gutless or high capacity AdV) are...

...lab while the publication page contains all the plasmids deposited from the same publication. Next up, we...number given to every plasmid in our catalog - if you know the catalog number of the plasmid you are searching... Addgene’s plasmids is an indication of popularity. A yellow flame indicates that a plasmid has been ordered...through the depositing lab page, then onto the publication page, and finally on down to the individual plasmid...deposit process and these can be found in this location as well. These maps make it easy for scientists...Great! Now, if I want to use this plasmid in a publication, how do I know who to acknowledge? Depositing...plasmids that are available through Addgene. Publication: If the plasmid has been published, the paper...

... be run in duplicate or triplicate. The closeness of the data points generated by replicate values provides... the standard dilution series in duplicate or triplicate. Replicates allows you to calculate the curve... deviation of each replicate measurement divided by the mean of all the replicates multiplied by 100. ...regularly, and mix samples very well.  Use duplicates or triplicates to increase the accuracy of your experiment... critical for a number of popular scientific applications, and the quality of a standard curve can make...diluted standard as a function of concentration on a scatter plot. For the BCA example, the concentration of...correlation between the actual values and the predicate values and measures how well the data points fit...

...present.  Purification reagent contaminants The reagents used during nucleic acid purification can leave...Selecting Your Plasmid Purification Kit Resources on Addgene.org DNA Quantification Protocol Recovering... and are ready to move on to your downstream application — but wait! Do you know how much plasmid DNA ...(Figure 1B). The A260/230 ratio can be a good indicator of protein contamination, but a number of other...researchers traditionally use the A260/280 ratio as an indicator of protein contamination. However, this ratio ...230 ratio of a sample. Ethanol carry-over from purification protocols is also a common concern, and while... guanidine thiocyanate (used in many plasmid purification kits), which can dramatically reduce the A260...

...of its biggest limitations is that sequence modifications can only be made at restriction enzyme cut sites...homologous recombination. It allows for direct modification of DNA within E. coli and is independent of ...engineering.  It can be used to make an assortment of modifications: insertion and deletion of selectable and non-selectable...expressing the lambda red enzymes. These enzymes then catalyze the homologous recombination of the substrate ...however, only Beta is required when generating a modification with an ssDNA substrate.  Gam: Gam prevents ...regions flanking the target site).  The best applications for dsDNA inserts include: large insertions ...nucleotides long with the desired alteration(s) located in the center of the sequence. Since lambda red...

...your specific application. Consider also that there may be variations within an application. Take immunohistochemistry...website highlights a variation of your application, a publication successfully used it in a similar way...choosing an appropriate antibody first look at the application-specific data provided on the manufacturer’s ... a linear antigen tend to work very well for applications that denature a protein to its primary (linear...the most similar to yours. Take a look at the publications cited on the manufacturer’s website, which may...plan to. To secondary or not to secondary?  The application will also determine whether you should use an...antibody. If you are trying to visualize the precise location of a protein in a tissue section then a directly-conjugated...

...recombinase catalyzes the site specific recombination event between two loxP sites, which can be located either...maintained).  Translocation: If the sites are on separate DNA molecules, a translocation event is generated...important plasmid elements – promoters, origins of replication, protein tags, and antibiotic resistance markers...creating (excuse the pun) specific, targeted DNA modifications in transgenic animals, embryonic stem cells,...proteins or co-factors, thus allowing for broad applications in a variety of experiments. LoxP (locus of ...and the canonical loxP sequence is ATAACTTCGTATA-GCATACAT-TATACGAAGTTAT. The loxP sequence does not occur...Therefore, inserting loxP sites at deliberate locations in a DNA sequence allows for very specific manipulations...

... your own research! Classification Structure Principles of CRISPR classification While CRISPR systems...Shakespeare for the first time. The discovery and application of CRISPR-Cas9 kicked off over a decade of frenzied...properties. This led to a need to develop a classification system for the array of CRISPR technologies...technologies. Learning the general principles of this classification system will help you gain a deeper appreciation...now seem neatly organized into their respective categories, arriving at a consensus was not as straightforward...multi-pronged analysis to sort effectively. The current classification system relies on a combination of sequence ...a similar function. After analysis, CRISPR classifications were placed into a fairly simple hierarchy:...

...which provides the AAV replication (rep) and capsid (cap) genes. AAV replication uses the host’s polymerase...this AAV purification video! It didn’t exist when I did my first iodixanol gradient purification, but I ...In this post, I’ll share some AAV production, purification, and titration tips, while also summarizing ...adenovirus genes which help mediate AAV viral replication; and 3) the transfer plasmid which encodes a ... that aids in the homologous recombination of duplicated regions like the ITRs. Restriction digest screening...consider performing PEG precipitation. Instead of sonicating the cell pellet, I lyse the cells with this AAV... with benzonase immediately before iodixanol purification. This approach gives me a bit of flexibility...

.... It sounds complicated but has a pretty low learning curve! Restraint: scruffing Location: throat Gauge... Restraint: mechanical restraint or anesthesia Location: tail vein or retro-orbitally Gauge: 27–30 Volume...practice to ensure the proper injection site has been located and to avoid potential off-target pokes to nearby...nearby organs. Restraint: scruffing Location: peritoneal cavity Gauge: 25–27 Volume: < 2–3 ml Skill required...getting a vaccine. Restraint: mechanical restraint Location: thigh Gauge: 25–27 Volume: < 0.02–0.05 ml Skill...Restraint: back scruffing or mechanical restraint Location: back or hind legs Gauge: 25–27 Volume: < 2–3 ...area must be shaved first. Restraint: anesthesia Location: between skin layers Gauge: 26 Volume: < 0.05 ...

...(stay tuned for our affinity purification tag blog!).   Applications of epitope tags   The...success rates across all applications. You can find FLAG antibodies on Addgene’s catalog including a mouse monoclonal...protein purification is not ideal with Myc, as low pH conditions are required during the purification, which...experienced. Finding an antibody that works for your application, specifically detects your protein, is species...and have been widely used across species and applications. In this blog, we will review the most common...that are bound by antibodies for the purpose of purification or detection of the tagged protein. These peptides...not exist, or they don’t exist for a specific application, or they exist but are unreliable for a variety...

...not cut within your insert Are in the desired location in your recipient plasmid (usually in the Multiple...amplify and design primers that will bind to and replicate it. The following image shows the ends of the ...Forward Primer will use the sequence 5'-ATGTGGCATATCTCGAAGTAC-3' for the region that binds the ORF and...primer, making our Forward Primer 5'-GAATTCATGTGGCATATCTCGAAGTAC-3'. Many restriction enzymes do not cut...final Forward Primer sequence of 5'-TAAGCAGAATTCATGTGGCATATCTCGAAGTAC-3'. For the Reverse Primer, the design...need to use the reverse complement to get PCR amplification. We can start similarly, taking the final 18...of the ORF, including the stop codon (5'-TGGCATATCTCGAAGTACTGA-3'), then adding NotI (GCGGCCGC) and then...