We narrowed to 498 results for: plasmid dna

...stability of modified Ti plasmids during plant infection, as well as plasmid yield during preparation ...selectable marker. Left and right T-DNA borders specify the region of DNA that will be transferred to the ...GreenGate Plasmids Interview: Nicola Patron on Plant Synthetic Biology, MoClo, and More Plasmids 101: Origin...Agrobacterium carries a “tumor-inducing” or Ti plasmid, which allows it to transfer genetic material into...in two species: Agrobacterium and E. coli. Like plasmids used in other systems, binary vectors are cloned...It’s a lot of information to fit into a single plasmid, so most first-generation binary vectors are quite...pKM24KH.To reduce vector size, they shortened the T-DNA borders to 25 bases each. By switching the E. coli...

...comprise a DNA binding domain and an endonuclease domain. What’s distinctive is that the DNA-binding domain... to target a particular DNA sequence? Musunuru: The kit includes 832 plasmids containing prefabricated...effector nuclease (TALEN) kit consisting of 834 plasmids. The researchers showed they could use their TALEN...and can be programmed to bind to essentially any DNA sequence desired. This technology allows you to create...prefabricated pieces that allow you to build a DNA-binding domain to recognize any desired 15 base pair sequence ...the genome in rapid fashion. The two remaining plasmids in the kit have the rest of the protein in place...fluorescent proteins used to sort the cells after the plasmids have been introduced by transfection or electroporation...

...repair DNA. The DNA ends are chewed back to reveal homology, allowing the strands to anneal. DNA synthesis...PITCh plasmid to release the cassette, and an insertion-locus-specific gRNA cleaves genomic DNA. These...Guide Pages Find CRISPR Plasmids for Your Experiments Deposit Your New Plasmid Tools with Us  ...Integration into Target Chromosomes). Using their PITCh plasmids, GFP knock-in cell lines can be created in about...Introduction There are three primary methods for repairing DNA after a double-stranded break. HDR copies the sequence... knock-ins, some labs have used NHEJ for whole plasmid integration; however, since NHEJ is error-prone...additional nucleotides flanking the insertion. If the DNA ends anneal incorrectly, MMEJ may also introduce,...

...disrupting it with an piece of DNA designed in the lab. Specially constructed plasmids can be used to replace ...gene. Here, we'll describe the techniques and the plasmids used to inactivate specific genes in mammalian...mind when choosing a knockout strategy! Knockout plasmids Homologous recombination is a mechanism to accurately...exchanged between two similar or identical molecules of DNA. Gene targeting takes advantage of this natural process...randomly integrated all or large portions of the plasmid. Deliver your construct to your target cells. After...Cre-mediated recombination.   Knockout/Knock-in plasmids Gene targeting methods also make it possible to... and insert GFP into the genome, we’d create a plasmid similar to the one shown below, where the sequence...

...samples at Addgene - DNA sent from depositors, bacterial glycerol stocks, prepped DNA ready for our quality...bacteria with the plasmid can grow. As the bacteria divide, they replicate and retain the plasmid. This allows... Inside Addgene Posts! Learn all about Plasmids in our Plasmids 101 series! ...Every plasmid sample enters Addgene the same way. A package is delivered by a mail courier and then the...dishes, but close to 80% of samples are received as DNA in a microcentrifuge tube. Once a sample enters Addgene...about Developing Lab Management Software    The plasmid's journey begins First, each package is opened and... to hundreds of samples, with an average of 10 plasmids per deposit. Each week an average of 16 deposits...

...Wenning Qin. Single-stranded DNA repair templates Short single-stranded DNA templates have been shown to...editing. How to use Addgene plasmids for Easi-CRISPR You can use Addgene plasmids to create a repair template...of Addgene plasmid options for templates - see the example at right using blue flame plasmid pmScarlet_...desired insert (e.g., mScarlet).   Plasmid ID Plasmid Name Tags 69090 pMJ915 MBP (N ...out our CRISPR Guide Find Plasmids for Cas9 Purification Find CRISPR Plasmids for Mammalian Expression ...pmScarlet_C1! After creating the T7-DNA template, you'd use ivTRT to create the ssDNA construct as described in ...pre-CRISPR was very arduous. First, you’d construct a plasmid with your desired changes, long homology arms and...

...This post is part of our ongoing Plasmids 101 series. Plasmids 101 will provide you with an overview ...of the Plasmids 101 posts here. Now that we have covered antibiotic selection here at Plasmids 101, we...α-complementation plasmid. This way you can quickly and easily identify colonies that not only have your plasmid (antibiotic...rescued by genes supplied on the transformed plasmid. Such plasmids may contain genes that allow for the use... able to select for colonies that contain your plasmid is a great start when cloning, but how about being...being able to choose those that contain plasmid with an insert? Blue-white selection is a widely used ...far, so good, but how does this help us screen plasmids? Blue-white screening in the lab Scientists discovered...

...effects when compared to DNA transfection of gRNA and Cas9 expression plasmids. These results are in line...infiltrate cells. Options for CRISPR delivery include plasmid transfection, RNP electroporation, and viral transduction...Nanoblades because they think of these particles as tiny DNA cutting ninjas that deliver CRISPR to multiple types... Gag in place of SpCas9. gRNA A gRNA targeting a DNA sequence of interest is expressed in 293T cells and...types they tested. Interested in using Nanoblades? Plasmids are available from Addgene. Genome editing primary...generally having lower off-target edits compared to DNA transfection.  Homology directed repair (HDR) with...-based HDR allows for the precise insertion of a DNA sequence ranging from a single nucleotide change ...

...without sickle cell anemia, two DNA fragments are observed because the DNA has the site where MstII cuts... cell anemia the enzyme does not cut the DNA so only one DNA fragment is observed. Today Southern blotting...detects and quantifies a gene or DNA sequence of interest by recording DNA abundance throughout the amplification...mapping informs on DNA sequence through the use of restriction enzymes that cut DNA at specific sites ...specific fragments of a DNA sequence of interest to create a physical map of the DNA. Starting in the 1970s...innovation is nanopore-based DNA sequencing which reads the nucleotides of a DNA strand as it slips through...technologies nanopore-based DNA sequencing machines are relatively small meaning that DNA sequencing could move...

..., DIY DNA ladders. You can find additional hot plasmids in our newsletter or on our hot plasmids webpage...Improved CRISPR Base Editors Hot Plasmid 4: pPSU Plasmids for generating DNA molecular weight markers.  Listen...webpage.   Hot plasmids covered in this segment Hot Plasmid 1: Photocleaveable PhoCl protein for controlling...In the third episode of our Hot Plasmids podcast series, you'll learn about optogenetics tools for controlling.... Listen to Our Segement on PhoCl Segment  Hot Plasmid 2: Ouabain selection for increased CRISPR editing...Listen to the Segement on Ouabain Selection  Hot Plasmid 3: CRISPR base editors with enhanced range and ...Listen to the Segement on the pPSU Plasmids Special thanks to our sound engineer/producer, Eddy Page!...

...created DNA ladders (aka DNA molecular weight markers) that can be used to measure the size of DNA fragments...highlight a subset of the new plasmids in the repository through our hot plasmids articles. These brief articles...articles provide a synopsis of a plasmid or group of plasmids' functions and applications. We hope that... you to find and use the plasmids you need. You can find all the hot plasmids from 2017 below. With over...over 50,000 plasmids, we can't write posts for every great plasmid that comes into the repository, but...write about your plasmids in a future blog post. No time to read? Listen to our hot plasmids segment on the...editing for precise genome modification. Plasmid ID Plasmid Name Cas9 Variant Speacial Features 85169...

...subset of the new plasmids and viral preps in the repository through our hot plasmids articles. These articles...recent plasmid deposits and we hope they'll make it easier for you to find and use the plasmids you need... CRISPR plasmids are always being added to the repository. To find all of the CRISPR plasmids available...known or suspected to be involved in DNA damage response and DNA repair.  A new CRISPR pooled library ...only required three components: a master mix, the DNA of interest, and cell extract.    Graphical...They allow single-nucleotide modifications to edit DNA without requiring a double-stranded break. The Xiao...Xiao Wang Lab has recently deposited a set of plasmids that helps identify base edited cell populations...

...once in the plasmid backbone and another enzyme that cuts within the insert. If the plasmid contains the...or absence of DNA using lysed bacterial colonies, without the need to prep your plasmid. In this case,... PCR product if the plasmid contains the insert and no PCR product if the plasmid does not contain the...precise order of nucleotides within a DNA molecule, in this case a plasmid. Sequencing is one of the surest...resources on the Addgene blog Get all the plasmid basics in our Plasmids 101 series Find more molecular biology...If you’re cloning a plasmid, you’ll need a way to find the needle in the haystack: the one perfect clone...clone that contains the plasmid you’re looking for out of the many cells that don’t. One way to begin ...

...scientists share plasmids across the globe, we’re working on ways to send plasmids as DNA as opposed to ...rate! Automating DNA purification We're developing ways to prep large quantities of DNA because some countries...more efficient. Here, I’ll discuss transformation, DNA purification, and filling vials with agar. I’ll also... transformation. With our ever growing rate of plasmid deposits (over 100 deposits per month!), manual...Biomek. The FXP id also able to do high throughput DNA preps and other molecular work if we need it to. ... shipments, we’ve needed to find a way to purify DNA from many bacterial samples at the same time as opposed...Qiagen BIOROBOT Universal Platform and it suits our plasmid prepping needs perfectly. Working with Qiagen, ...

... Read other Plasmids 101 blog posts New to plasmids? Read our article on What is a Plasmid? Download the...cloning different types of DNA, such as cDNA, PCR fragments, or genomic DNA. Also remember that commercially... the Plasmids 101 eBook Resources on Addgene.org0 Check out protocols for plasmid cloning Find vector... methods are more amenable to combining multiple DNA fragments than others. In today’s post, we will focus...technique, you first perform a round of PCR to generate DNA fragments with 15-40 bp of homology at their ends...combined with an exonuclease, a polymerase, and a DNA ligase to carry out a pooled set of ligations in ...enzymes, optimize reagent concentration, or purify DNA fragments from gels. If you’re relatively new to ...

...genome. The genome itself is a linear double-stranded DNA of ~36kb, with inverted terminal repeats (ITR) present...fiber, penton and hexon proteins. The viral genome DNA is further protected by histone-like proteins forming...regions and can accommodate up to 8.2 kb of transgene DNA. The second generation vectors are deficient in E1...down into 5 key steps: Construction of the rAdV plasmid (~1 week): The AdEasyTM system is the most popular...adenoviral vector constructs. It consists of 2 plasmids: a shuttle vector (in which the transgene of interest...how to generate the final recombinant adenoviral plasmid construct, please see Addgene’s Adenoviral Guide...2.*Pro-Tip*: once the correct recombinant pAdV plasmid is identified, re-transform into a bacterial strain...

...toolbox. Natural plasmids, also called environmental plasmids, are all around us! A plasmid is a small piece...colicin-producing plasmids have been referred to as “Col plasmids” or “Col factors.” Virulence plasmids: microbial...Old Solution but a New Problem Plasmids 101: What is a Plasmid? Plasmids 101: Transformation, Transduction...F. (2023). Plasmid classifications. Plasmid, 126, 102684. https://doi.org/10.1016/j.plasmid.2023.102684...when we think of plasmids, both Archaea and Eukaryota can also harbor these circular DNA passengers. Most...., 2001) Beneficial traits of natural plasmids Natural plasmids often convey a variety of functions that...functions of natural plasmids. Created with BioRender.com. Resistance (R) plasmids: microbial defense...

...and was able to integrate DNA payloads of up to 15 kb. Find evoCAST plasmids here! The new horizons of...proteins integrate a payload sequence into genomic DNA downstream from the Cas target. Conveniently, the... (Tns) to integrate large sequences into genomic DNA downstream of gRNA-specified sites. Created with ...moved a gene required for phage propagation to a plasmid that lacked a promoter — only CAST integration ...20 mutations in TnsB, the subunit that catalyzes DNA insertion, along with both evolved and engineered...Transposon-encoded CRISPR-Cas systems direct RNA-guided DNA integration. Nature, 571(7764), 219–225. https://... Engineering Using CRISPR-Transposons Degrading DNA with Cascade-Cas3 Typing CRISPR Systems Prime Editing...

...blog Addgene's Tips for Plasmid Quality Control Plasmids 101: In-house NGS Plasmid Quality Control Now at...tools that rely on DNA amplification and manipulation to produce and edit plasmids. These are prone to...sequencing all incoming plasmids. If you are interested in requesting one of these plasmids, you can request ...data for each of their plasmids, from descriptions of key components of the plasmids to partial, full, or...to ensure all plasmids pass our high-quality standards and contain the expected plasmid features.  ...Once Addgene receives deposited plasmids, they undergo complete plasmid sequencing using an in-house Illumina...will compare the NGS results to the plasmid information, other plasmids in the deposit, NCBI sequence and...

... frequent DNA repair mechanism in general. On average, it accounts for less than 10% of DNA repair, with...though exogenous DNA can be used as well. Below are some considerations for designing donor DNA for successful...homology-directed repair pathway, designing the best donor DNA, and avoiding common mishaps in this class of genome...knock-out. The goal of a knock-out is to disrupt DNA translation by generating a frameshift mutation. ...knock-ins. Knock-in mutations typically require an exact DNA sequence to be incorporated at a precise genomic ...which is done through the design and use of a donor DNA molecule. Your donor molecule will need to have homology...This homology will guide the cell to use the donor DNA as a template for repair, which will result in the...

... is complementary to the DNA target. The 20-nt guide region binds to the DNA sequence immediately downstream... Genome Engineering Guide Plant Plasmids and Resources CRISPR Plasmids and Resources ... types, it has a limited capacity to carry large DNA cargos. As a result, the search for smaller, compact...single RuvC-like domain. In simple terms, Cas9 cuts DNA using two "scissors" (one for each strand), while...PAM (protospacer adjacent motif) near the target DNA, TnpBs also need a short sequence motif called a ...reRNA) or omega RNA (ωRNA) guide the TnpB to its DNA target, much like the single guide RNA (sgRNA) used...downstream of the TAM. This RNA-DNA hybrid formation recruits TnpB to the site and activates its nuclease...

...Chromatin is a complex of DNA and histone proteins that compacts cellular DNA into chromosomes and reduces...reduces the risk of dangerous DNA damage. If the way DNA is wrapped around histones changes, then gene expression...methyl- groups to the DNA, which mostly occurs at CpG islands (regions of the DNA with a high frequency...gene expression that do not involve any changes to DNA sequence (Epigenetics literally means ‘on top of ...This is how most cells in the body contain the same DNA but have very different structure and function, and...change as well. The more frequently and tightly bound DNA is to histones, the more compacted it becomes. This...associated with reduced life-span, but no changes in the DNA sequence could be found. Angelman syndrome and Prader–Willi...

...the transfer plasmid, a plasmid encoding rep and serotype-specific cap genes, and a plasmid encoding adenoviral...transfer plasmid Addgene uses a rigorous barcode matching system that follows the sample from the DNA tube.... coli. In addition, plasmids are typically prepared using endotoxin-free plasmid purification kits.   ...confirmation of transfer plasmids used in Addgene’s viral production. Barcoding allows our DNA and virus to be ...of the viral genome and the absence of unexpected DNA contaminants. The data is also used to determine ...contamination is minimized by using an endotoxin-free plasmid purification protocol. To minimize the immunogenic...lentiviral vector, incubated for 72 hours, and genomic DNA is extracted. Primers and probes targeting integrated...

...Mobile-CRISPRi ICE element forms a conjugative plasmid-like DNA circle and is transferred to recipient bacteria...Browse our CRISPR interference plasmids Find bacterial CRISPR plasmids Read our CRISPR guide ... into the genome and is propagated during normal DNA replication and cell division. Mobile-CRISPRi does...transposon system. This system has two parts: a plasmid expressing the Tn7 transposition genes (tnsA, tnsB... tnsB, tnsC, tnsD, and tnsE), and a plasmid that contains the Mobile CRISPRi cassette flanked by left ...copy of the RP4 transfer machinery mobilize these plasmids for transfer to recipient cells during a tri-parental...due to site selection by TnsD, a sequence-specific DNA binding protein. Selection removes donor bacteria...

...reflection of the large size of the plasmid or silencing of the plasmid by DNA methylation. Another downside...into cells as a donor plasmid containing the transposon, along with a helper plasmid that expresses the ...reprogramming factors. Non-replicating Plasmids: Generating iPSCs with plasmid-based expression requires serial... generating iPSCs by plasmid transfection where 2 of 11 clones tested had plasmid integration. Another...the dose of plasmid the cells receive over the whole reprogramming period and the plasmid will get diluted...larger plasmids have lower rates of transfection. Minicircles: Minicircles are like mini-plasmids. They...periods of time than traditional plasmids due to lower activation of DNA-silencing mechanisms. While minicircles...

... consists of a Ti plasmid, into which the GOI is inserted, and a Ti "helper" plasmid, which contains Vir...necessary for T-DNA processing and insertion into the plant genome. B) The Ti plasmid and helper are transformed... to plant cells. The region of the Ti plasmid between the T-DNA borders (yellow) are recognized by the...for creating plant expression plasmids, including plant CRISPR plasmids from the Yiping Qi lab and the...plant-specific modifications to commonly used CRISPR plasmids are necessary to use the CRISPR system in plant...et al., 2013). Addgene carries Cas9-containing plasmids for knockout, activation and repression of target...expression of both Cas9 and the gRNA off of the same plasmid. Delivering CRISPR components to plant cells Once...

...CRISPR plasmids available at Addgene. We will still periodically focus on specific CRISPR plasmid tools...scaffold and a domain needed for DNA unwinding. They’ve deposited plasmids for active and inactive CasX for...CRISPR guide Find CRISPR plasmids by function Find recently deposited plasmids ...Jennifer Doudna’s lab discovered a new Cas protein, CasX, from metagenomic analysis of microbial DNA from ...In this system, Cas9 generates a double-stranded DNA break at the genomic loci of interest and on either...vector sequence. Homology arms that flank the donor plasmid cargo are complementary to either side of the double-stranded...expression. Read the paper in Nature Find the CasX plasmids Drug inducible transcriptional activation and...

...complementary DNA (cDNA), and then use PCR and molecular cloning to insert the cDNA into the desired plasmid backbone...experiments in planarians with their recent plasmid deposit. These plasmids enable two main types of experiments... cloned into plasmids to investigate for each of these planarian species. These plasmids all have a PR-T4...dsRNA. Students can produce DNA templates via PCR off of the same plasmid and use these to create riboprobes...off of linearized DNA templates which they can easily generate off of a circular plasmid via PCR. Typically...Resources at Addgene.org Find plasmids from the Sánchez lab Find plasmids for other developmental models...of specific gene expression. The 49 deposited plasmids enable students to study gene expression and functions...

...to the genomic DNA of interest  Figure 1. When ABEs are in action they bind DNA so that the TadA...Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 551:464–471 . https://doi....TadA domain can edit the short single-stranded DNA stretch that is accessible. Image from Gaudelli et al...in 40 new ABE8 variants. When comparing on-target DNA editing efficiency in a human cell line for these...ABE8.x-m/d constructs demonstrated a 2.1x on-target DNA-editing efficiency in a human cell line while reducing...pyogenes Cas9 requires the target site in the genomic DNA to contain a specific protospacer adjacent motif ...followed by 2 guanines). This limits the use of ABEs as DNA sites that do not contain a suitable PAM cannot be...

...of the DNA. Finally, in 1953, Franklin along with James Watson and Francis Crick resolved the DNA double...letters of the DNA get translated into the twenty amino acids. Once scientists established that DNA encoded ...dinosaurs by extracting the DNA from fossilized amber and supplementing it with the DNA of present-day frogs ...enzymes generated by fusing a zinc finger DNA-binding domain to a DNA-cleavage domain (FokI). Zinc finger nucleases...designed in 2005. The DNA-binding domain can be engineered to target specific DNA sequences while FokI ...TALENs) were engineered. TALENs follow a DNA-binding and DNA-cleaving strategy similar to the ZFNs, but...mutations, delete short stretches of DNA and even insert new DNA at the target genomic loci.  A last ...